Cleanup: drop tracked *.bak build droppings; ignore /reeval/ and *.bak

26 build-time backup files/dirs (nushell dockerfile .bak dirs, dubbo/scikit
Dockerfile and test_config .bak) had been committed by accident; none are
read by any pipeline. reeval/ is the temporary re-evaluation campaign area
and never dataset content.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Kv8v4m6ePchrw4dxfYarSk

.gitignore

@@ -2,3 +2,9 @@
 **/self_grade/
 **/self_grade_flakycheck/
 **/self_grade_v091rc1/
+
+# Temporary re-evaluation campaign area (never dataset content)
+/reeval/
+
+# Build-time backup droppings
+*.bak

apache_dubbo_dubbo-3.3.3_dubbo-3.3.6/dockerfiles/base/test_config.json.bak

@@ -1,7 +0,0 @@
-[
-  {
-    "name": "default",
-    "test_cmd": "mvn test verify -T 8 -Dsurefire.forkCount=8 -Dsurefire.parallel=classes -Dmaven.test.failure.ignore=true -B -Pjacoco,jdk15ge-simple,'!jdk15ge-add-open',skip-spotless -DtrimStackTrace=false -Dcheckstyle.skip=true -Drat.skip=true -DskipIntegrationTests=false -DembeddedZookeeperPath=/testbed/.tmp/zookeeper -Dsurefire.forkedProcessTimeoutInSeconds=300 2>&1 | tee /output/{output_file}",
-    "description": "Maven test and verify execution with Jacoco coverage and integration tests"
-  }
-]

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G01_48bca0a.bak/Dockerfile

@@ -1,43 +0,0 @@
-# Build on pre-configured base image
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-# Also increase file descriptor limits to avoid "too many open files" error
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo 'ulimit -n 65536' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nulimit -n 65536\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Configure git for commits
-RUN git config --global user.email "test@example.com" && \
-    git config --global user.name "Test"
-
-# Remove the original /testbed from base image and copy local testbed
-# NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Checkout to END state and fix version mismatch
-# The milestone states have root Cargo.toml requiring 0.106.1 but crates are at 0.106.0
-# [ENV-PATCH] Fix version requirements to match crate versions
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-end && \
-    sed -i 's/version = "0.106.1"/version = "0.106.0"/g' Cargo.toml && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version requirements to 0.106.0" && \
-    git tag -f milestone-milestone_G01_48bca0a-end HEAD
-
-# Apply same fix to START state and remove custom_completion field references
-# [ENV-PATCH] The custom_completion field was added in the milestone commits but
-# START state doesn't have it in PositionalArg and Flag structs
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && \
-    sed -i 's/version = "0.106.1"/version = "0.106.0"/g' Cargo.toml && \
-    sed -i '/custom_completion: None,/d' crates/nu-protocol/tests/test_signature.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version requirements and remove custom_completion from test_signature.rs" && \
-    git tag -f milestone-milestone_G01_48bca0a-start HEAD
-
-# Set default state to START
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G01_48bca0a.bak/env_setup_prompt.md

@@ -1,935 +0,0 @@
-You are an expert in Rust software environment configuration. Your task is to configure
-a Docker container so that a given Rust repository can successfully run its test suite
-across TWO different git states (START and END tags).
-
-## RUST TEST FRAMEWORK
-
-| Language | Framework | Test Collect Command | Report Format | **Output File Extension** |
-|----------|-----------|----------------------|---------------|---------------------------|
-| Rust | cargo | `cargo test --no-run` | Console log | **`.log`** |
-
-### Output File Format Reference
-
-When generating `test_config.json`, use the `.log` extension for `{output_file}`:
-
-| Framework | Recommended Extension | Example `{output_file}` |
-|-----------|----------------------|-------------------------|
-| cargo | `.log` | `start_default.log` |
-
-**IMPORTANT**: The test runner (`run_milestone_tests.py`) will automatically use the cargo log parser based on the `--test-framework cargo` argument.
-
-## GOAL
-Configure the environment to:
-1. Make test compilation succeed for BOTH states (START and END)
-2. Run tests successfully with the test runner script
-3. Ensure no tests are skipped due to resolvable environment issues
-4. Ensure commit-related tests (tests modified by milestone commits) are collected AND run (not skipped)
-5. Generate a skip analysis report documenting remaining skips
-
-Generate a complete, buildable Dockerfile that supports dual-state testing.
-
-**IMPORTANT**: You are building on top of a pre-configured BASE IMAGE that already has:
-- Correct Rust toolchain version (rustc, cargo, rustup)
-- All system dependencies installed (OpenSSL, pkg-config, etc.)
-- Cargo dependencies cached (via `cargo fetch`)
-- Environment paths configured (CARGO_HOME, RUSTUP_HOME, PATH)
-- Repository cloned to /testbed
-
-**IMPORTANT**: The local testbed (/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed) already contains pre-created milestone tags:
-- `milestone-milestone_G01_48bca0a-start` (START state tag)
-- `milestone-milestone_G01_48bca0a-end` (END state tag)
-- **DO NOT create these tags in Dockerfile** - they are already included when you `COPY . /testbed/`
-- Simply use `git checkout milestone-milestone_G01_48bca0a-start` or `git checkout milestone-milestone_G01_48bca0a-end` to switch states
-
-Your task is to handle **git state management and compatibility patches** only.
-
----
-
-## ⚠️ DOCKERFILE VERIFICATION CHECKLIST (CRITICAL)
-
-Before finalizing your Dockerfile, verify ALL of the following constraints:
-
-- [ ] **No Source Code Modification**: Dockerfile must not modify source code logic
-- [ ] **No Test Logic Modification**: Dockerfile must not modify test code logic
-- [ ] **No File Deletion**: Dockerfile must not delete test files or any other files
-- [ ] **No Git Checkout to Fix Errors**: Cannot use `git checkout` to revert a file to a previous state to resolve compilation errors
-
-- [ ] **Compilation Error Handling**: If compilation problems occur, follow the minimal fix principle below
-
-### Minimal Fix Principle (Compilation Errors)
-
-```
-  Compilation Error Found
-      │
-      ├─ Locate the exact error position (file:line)
-      │
-      ├─ Error Type Classification:
-      │
-      ├─ Missing type/trait/function/module
-      │   └─→ Use #[cfg(feature = "...")] to conditionally compile
-      │   └─→ Or comment out the ENTIRE function/test containing the error
-      │
-      ├─ Trait implementation mismatch
-      │   └─→ Comment out the ENTIRE impl block or function
-      │
-      ├─ Lifetime/borrow checker errors
-      │   └─→ Comment out the ENTIRE function containing the error
-      │
-      └─ Feature flag issues
-          └─→ Fix via Cargo.toml features or environment variables (NOT code changes)
-```
-
-**Core Principles:**
-1. **NEVER skip/exclude entire crates or modules** - only comment out specific functions/tests
-2. **Comment out ENTIRE functions (not single lines)** - maintain code logic integrity
-3. **Preserve ALL tests that can compile normally** - maximize test coverage
-4. **Feature flag issues → fix via Cargo.toml or ENV** - not by modifying code
-
-**Specific Rules for Rust:**
-- For `Cargo.toml`: Can modify `[features]` section or comment out individual dependency lines
-- For test code: Comment out the **entire test function** (including `#[test]` attribute), not individual lines
-- For helper functions used by tests: Comment out the **entire function** if it causes compilation errors
-- **NEVER comment out an entire file** just because one function has compilation errors
-- **NEVER exclude an entire crate/module** just because one function has compilation errors
-
----
-
-### Inputs
-
-Milestone ID: milestone_G01_48bca0a
-Milestone Commits: ["71baeff", "aeb5178", "48bca0a"] (list of commit SHAs included in this milestone)
-Commit Changed Tests Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/commit_level/patched_tests (directory containing per-commit test changes)
-Start Tag: milestone-milestone_G01_48bca0a-start (earlier git state - may have missing features)
-End Tag: milestone-milestone_G01_48bca0a-end (later git state - has all features)
-Repository Path: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed (source repository on host, used as build context)
-Source Directories: ["src/", "crates/"] (directories containing source code)
-Test Directory: test (directory containing tests, default: "tests/")
-Base Image: nushell_nushell_0.106.0_0.108.0/base:latest (pre-configured image with all dependencies)
-Base Image Dockerfile: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/base/dockerfiles/Dockerfile (Dockerfile used to build the base image)
-Test Runner Script: harness.test_runner.run_milestone_tests (script to run milestone tests)
-Test Results Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results (where test results are saved)
-Work Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 (harness workspace directory for this run)
-
-### Expected Outputs
-
-1. **Dockerfile**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G01_48bca0a/Dockerfile
-   - Build successfully on top of nushell_nushell_0.106.0_0.108.0/base:latest
-   - Support both START state (milestone-milestone_G01_48bca0a-start) and END state (milestone-milestone_G01_48bca0a-end)
-   - Configure environment for both states; if conflicts exist, prioritize END state
-   - Default to START state when container starts
-
-2. **Test Config**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G01_48bca0a/test_config.json
-   - Configure test runner to run tests as comprehensively as possible
-   - Include all test modes the repository supports (unit tests, integration tests, doc tests)
-   - Goal: maximize test coverage and collect complete test results
-
-3. **Skip Analysis Report**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G01_48bca0a/attempt_1/skip_analysis.md
-   - Analysis of all skipped/ignored tests based on test results
-   - Classification by skip reason (resolvable vs acceptable)
-   - Confirmation that no environment-related skips remain
-
----
-
-## RUST TEST COMMANDS
-
-### Cargo Test Commands
-
-```bash
-# Compile tests without running (test collection)
-cargo test --no-run
-
-# Compile tests for all targets (lib, bins, tests, examples, benches)
-cargo test --no-run --all-targets
-
-# Run all tests
-cargo test
-
-# Run tests with specific options
-cargo test --no-fail-fast -- --test-threads={workers}
-
-# Run tests with verbose output
-cargo test -- --nocapture
-
-# Run only unit tests (in src/)
-cargo test --lib
-
-# Run only integration tests (in tests/)
-cargo test --test '*'
-
-# Run tests for a specific package in a workspace
-cargo test -p package_name
-
-# Run tests for all packages in a workspace
-cargo test --workspace
-
-# Run tests with all features enabled
-cargo test --all-features
-
-# Run tests with specific features
-cargo test --features "feature1 feature2"
-
-# Run tests without default features
-cargo test --no-default-features
-
-# Run doc tests only
-cargo test --doc
-
-# List all tests without running
-cargo test -- --list
-
-# Run ignored tests
-cargo test -- --ignored
-
-# Run both normal and ignored tests
-cargo test -- --include-ignored
-```
-
-### Test Output Format
-
-Cargo test output follows this format:
-```
-running X tests
-test module::test_name ... ok
-test module::another_test ... FAILED
-test module::ignored_test ... ignored
-test module::skipped_test ... ignored, reason: "requires feature X"
-
-test result: FAILED. X passed; Y failed; Z ignored; 0 measured; 0 filtered out
-```
-
----
-
-## CRITICAL WORKFLOW (FOLLOW THIS ORDER)
-
-⚠️ **You MUST follow this exact workflow sequence:**
-
-```
-PHASE 0: Analyze Rust Project Structure
-    └── Check Cargo.toml → Identify workspace/crates → Determine features → List test targets
-
-PHASE 1: Write Initial Dockerfile & Test END State
-    └── Build minimal image → Test compilation for END state → Verify success
-
-PHASE 2: Test START State & Apply Minimal Patches (if needed)
-    └── Test START compilation → Apply patches if needed → Verify both states pass
-
-PHASE 2.5: Generate test_config.json
-    └── Create test configuration file required by test runner
-
-PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-    └── Run {test_runner_script} → Analyze ignored tests → Identify environment issues
-
-PHASE 4: Fix Environment Issues (iterate until resolved)
-    └── Update Dockerfile → Re-run tests → Verify issues are resolved
-
-PHASE 4.5: Validate Commit-Related Tests
-    └── Verify tests modified by milestone commits are collected AND not ignored
-
-PHASE 5: Finalize & Generate Skip Analysis
-    └── Set default state to START → Create skip_analysis.md → Clean up
-```
-
----
-
-### PHASE 0: Analyze Rust Project Structure
-**Understand the Rust project before proceeding**
-
-1. **Check project type (single crate vs workspace):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat Cargo.toml | head -30"
-   ```
-
-   **Single crate indicators:**
-   ```toml
-   [package]
-   name = "my_crate"
-   version = "0.1.0"
-   ```
-
-   **Workspace indicators:**
-   ```toml
-   [workspace]
-   members = [
-       "crate1",
-       "crate2",
-   ]
-   ```
-
-2. **List all crates in workspace (if applicable):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cargo metadata --no-deps --format-version 1 | jq '.packages[].name'"
-   ```
-
-3. **Check available features:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-   ```
-
-4. **Identify test targets:**
-
-   ```bash
-   # Check for integration tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la tests/ 2>/dev/null"
-
-   # Check for unit tests in src/
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '#\[test\]' src/ | head -20"
-
-   # Check for doc tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '```rust' src/ | head -10"
-
-   # Check for benchmark tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la benches/ 2>/dev/null"
-   ```
-
-5. **Check Rust toolchain requirements:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat rust-toolchain.toml rust-toolchain 2>/dev/null"
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "rustc --version && cargo --version"
-   ```
-
-6. **Record your analysis:**
-
-   ```
-   PROJECT TYPE: <single_crate|workspace>
-   WORKSPACE MEMBERS: <list of crate names if workspace>
-   AVAILABLE FEATURES: <list of features>
-   TEST TARGETS: <lib|tests|examples|benches|doc>
-   RUST TOOLCHAIN: <stable|nightly|specific version>
-   ```
-
-⚠️ **DO NOT PROCEED to Phase 1 until you understand the project structure!**
-
-### IMPORTANT: Building on Base Image
-
-Since you are building on top of `nushell_nushell_0.106.0_0.108.0/base:latest`, you do NOT need to:
-- Install Rust toolchain
-- Install system dependencies
-- Run `cargo fetch` or `cargo build`
-- Configure environment paths
-
-Your Dockerfile only needs to:
-1. Checkout to the correct git states
-2. Apply minimal patches if START state has compilation issues
-
-**Temp image name**: `test-milestone-milestone_G01_48bca0a-temp` (unique for this milestone)
-
-**CRITICAL RULES:**
-- ❌ **NEVER modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository
-- ✅ **Use a working copy for exploration** (create with `cp -r` if needed)
-- ✅ **Build using**: `docker build -t test-milestone-milestone_G01_48bca0a-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-- ✅ **Clean up test images when done**: `docker rmi test-milestone-milestone_G01_48bca0a-temp`
-
----
-
-### PHASE 1: Write Initial Dockerfile & Test END State
-**Start with a minimal Dockerfile based on the base image**
-
-1. **Write the initial Dockerfile:**
-
-   ```dockerfile
-   # Build on pre-configured base image
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Set umask to ensure files created in container are world-writable
-   # This prevents permission issues when test results are written to mounted volumes
-   RUN echo 'umask 000' >> /etc/bash.bashrc && \
-       echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-       chmod +x /entrypoint.sh
-   ENTRYPOINT ["/entrypoint.sh"]
-   CMD ["bash"]
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Checkout to END state (all features available)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-end
-   ```
-
-2. **Build and test END state compilation:**
-
-   ```bash
-   docker build -t test-milestone-milestone_G01_48bca0a-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-   ```
-
-   Then test compilation:
-
-   ```bash
-   # For single crate
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && cargo test --no-run"
-
-   # For workspace
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && cargo test --workspace --no-run"
-
-   # With all features
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && cargo test --all-features --no-run"
-   ```
-
-3. **SUCCESS CRITERIA for END state:**
-   - Exit code 0
-   - Output shows "Compiling" and "Finished" messages
-   - NO compilation errors
-   - Test binaries are generated
-
-   ⚠️ **DO NOT PROCEED to Phase 2 until END state compiles!**
-
----
-
-### PHASE 2: Test START State & Apply Minimal Patches (if needed)
-**Handle the earlier codebase state which may lack features**
-
-1. **Test START state compilation:**
-
-   ```bash
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && cargo test --no-run"
-   ```
-
-2. **Handle results:**
-
-   **Case A: Compilation succeeds immediately**
-   ✅ Both states work! Proceed to PHASE 2.5.
-
-   **Case B: Compilation fails**
-   Apply Rust-specific minimal patches. See "RUST-SPECIFIC PATCHING" section.
-
-   ⚠️ **RUST COMPILATION**: Like Java, Rust requires ALL code to compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-3. **VALIDATION - Both states MUST compile:**
-   ```bash
-   docker build -t test-milestone-milestone_G01_48bca0a-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-   # Test END state
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && git checkout milestone-milestone_G01_48bca0a-end && cargo test --no-run"
-
-   # Test START state
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && cargo test --no-run"
-   ```
-
----
-
-### PHASE 2.5: Generate test_config.json
-**Create test configuration file required by test runner**
-
-The test_config.json defines how the test runner should execute tests.
-
-**Format:**
-```json
-[
-  {
-    "name": "config_name",
-    "test_states": ["start", "end"],
-    "test_cmd": "test command with placeholders",
-    "description": "What this configuration tests"
-  }
-]
-```
-
-**Available placeholders:** `{workers}`, `{timeout}`, `{output_file}`
-
-**Basic Example (Single Crate):**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests"
-  }
-]
-```
-
-**Workspace Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --workspace --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests"
-  }
-]
-```
-
-**With Features Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --all-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests with all features"
-  },
-  {
-    "name": "no_default_features",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-default-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Tests without default features"
-  }
-]
-```
-
-**Multiple Test Targets Example:**
-```json
-[
-  {
-    "name": "unit",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --lib --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Unit tests only"
-  },
-  {
-    "name": "integration",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --test '*' --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Integration tests only"
-  },
-  {
-    "name": "doc",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --doc --no-fail-fast 2>&1 | tee /output/{output_file}",
-    "description": "Doc tests only"
-  }
-]
-```
-
-**Guidelines:**
-1. **Always include "default" configuration** that runs all tests
-2. **Discover special test modes:**
-
-   ```bash
-   # Check for feature flags
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-
-   # Check for test-specific features
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && grep -E 'test-|testing' Cargo.toml"
-
-   # Check for conditional compilation in tests
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && grep -r '#\[cfg(test)\]' src/ | head -10"
-
-   # Check for ignored tests that might need special flags
-   docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && grep -r '#\[ignore\]' . | head -20"
-   ```
-
----
-
-### PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-**Run full tests and identify environment-related issues**
-
-1. **Run tests using the test runner script:**
-
-   ```bash
-   python -m harness.test_runner.run_milestone_tests \
-     --milestone-id milestone_G01_48bca0a \
-     --image-name test-milestone-milestone_G01_48bca0a-temp \
-     --output-dir /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results \
-     --language rust \
-     --test-framework cargo \
-     --max-retries 1
-   ```
-
-2. **Analyze test results:**
-
-   After tests complete, examine the output log for ignored tests:
-
-   ```bash
-   # Find ignored tests
-   grep "ignored" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G01_48bca0a/attempt_1/end_default.log
-
-   # Find failed tests
-   grep "FAILED" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G01_48bca0a/attempt_1/end_default.log
-   ```
-
-3. **Classification of Rust test skip/ignore reasons:**
-
-   | Pattern | Classification | Action |
-   |---------|----------------|--------|
-   | `#[ignore]` without reason | Review | Check if intentional |
-   | `#[ignore = "requires X"]` | Depends | Check if X is environment-related |
-   | `#[ignore = "flaky"]` | Acceptable | Intentionally ignored |
-   | `#[ignore = "slow"]` | Acceptable | Run with `--include-ignored` if needed |
-   | `#[cfg(feature = "X")]` not enabled | Resolvable | Enable feature in test_config.json |
-   | Missing system library | Resolvable | Install in Dockerfile |
-   | Network-dependent test | Acceptable | Requires external resources |
-
-4. **Common Rust environment issues:**
-
-   | Error Pattern | Cause | Solution |
-   |---------------|-------|----------|
-   | `error: could not find native static library` | Missing C library | `RUN apt-get install libXXX-dev` |
-   | `error: linking with cc failed` | Missing linker deps | Install build-essential |
-   | `RUSTFLAGS` related | Build flags issue | Set `ENV RUSTFLAGS="..."` |
-   | `openssl` errors | Missing OpenSSL | Install `libssl-dev` |
-   | `pkg-config` errors | Missing pkg-config | Install `pkg-config` |
-
-5. **If resolvable environment issues found → Proceed to PHASE 4**
-   **If no resolvable issues → Proceed to PHASE 4.5**
-
----
-
-### PHASE 4: Fix Environment Issues
-**Resolve environment-related issues by updating Dockerfile**
-
-**Common fixes for Rust projects:**
-
-```dockerfile
-# Install missing system libraries
-RUN apt-get update && apt-get install -y \
-    libssl-dev \
-    pkg-config \
-    libclang-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-# Set environment variables
-ENV RUST_BACKTRACE=1
-ENV CARGO_NET_GIT_FETCH_WITH_CLI=true
-
-# Enable specific features by default
-ENV CARGO_FEATURE_FLAGS="--all-features"
-
-# Fix OpenSSL issues
-ENV OPENSSL_DIR=/usr
-ENV OPENSSL_LIB_DIR=/usr/lib/x86_64-linux-gnu
-ENV OPENSSL_INCLUDE_DIR=/usr/include
-
-# Fetch dependencies again after changes
-RUN cd /testbed && cargo fetch
-```
-
-**Iteration loop:**
-
-1. Update Dockerfile with fix
-2. Rebuild: `docker build -t test-milestone-milestone_G01_48bca0a-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-3. Re-run tests with test runner script
-4. Check if issue is resolved by comparing results
-5. Repeat until no resolvable issues remain
-
----
-
-### PHASE 4.5: Validate Commit-Related Tests
-**Ensure tests modified by milestone commits are collected AND not ignored**
-
-1. **Run the collect_milestone_patched_tests.py script:**
-
-   ```bash
-   python -m harness.prepare_images.collect_milestone_patched_tests \
-     /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 \
-     --repo /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed \
-     --milestone milestone_G01_48bca0a
-   ```
-
-   This script:
-   - Extracts symbol changes (added/modified/deleted tests) from each commit
-   - Aggregates patched tests at the milestone level
-   - Matches patched test IDs to actual test results (nodeids)
-   - Generates a report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_G01_48bca0a.json`
-
-2. **Check the output JSON file:**
-
-   The output format is:
-   ```json
-   {
-     "milestone_id": "milestone_G01_48bca0a",
-     "commits": ["abc1234", "def5678"],
-     "test_ids": {
-       "added": [...],      // Tests added by commits
-       "modified": [...],   // Tests modified by commits
-       "deleted": [...],    // Tests deleted by commits
-       "effective": [...]   // Effective tests = (added ∪ modified) - deleted
-     },
-     "collected": {
-       "patched_in_results": [...],      // ✅ Patched tests found in test results
-       "patched_not_in_results": [],     // ⚠️ MUST BE EMPTY!
-       "test_id_to_nodeid": {...},       // Mapping from test_id to nodeid
-       "status": {
-         "start": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []},
-         "end": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []}
-       },
-       "transitions": {
-         "fixed": [],        // start failed/error -> end passed
-         "broken": [],       // start passed -> end failed/error
-         "still_passing": [],
-         "still_failing": [],
-         "other": []
-       }
-     },
-     "summary": {...}
-   }
-   ```
-
-3. **⚠️ CRITICAL VALIDATION: `collected.patched_not_in_results` MUST be empty!**
-
-   This field lists patched tests that were NOT found in test results. If not empty, it means:
-   - Some patched tests failed to compile (possibly commented out incorrectly)
-   - Some patched tests were excluded from test collection
-   - The test_id to nodeid matching failed
-
-   **How to verify:**
-   ```bash
-   # Check if patched_not_in_results is empty
-   cat /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_G01_48bca0a.json | jq '.collected.patched_not_in_results'
-   # Expected output: []
-   ```
-
-4. **If `patched_not_in_results` is NOT empty:**
-   - Identify which tests are missing from results
-   - Check if those tests were incorrectly commented out or excluded
-   - Return to PHASE 4 to fix environment issues
-   - Re-run tests and re-validate until `patched_not_in_results` is empty
-
-5. **Also verify no commit-related tests are ignored:**
-   - Check `collected.status.end.skipped` - patched tests should not be ignored
-   - If ignored due to environment issues, return to PHASE 4 to fix
-
----
-
-### PHASE 5: Finalize Dockerfile & Generate Skip Analysis
-**Set default state to START, create skip analysis report, and clean up**
-
-1. **Ensure Dockerfile sets default state to START:**
-
-   ```dockerfile
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Environment fixes (if any)
-   # RUN apt-get update && apt-get install -y ...
-   # ENV RUST_BACKTRACE=1
-
-   # Checkout to END state (for any patching if needed)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-end
-
-   # [If patches needed, add them here]
-
-   # Set default git state to START
-   RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start
-   ```
-
-2. **Final validation**
-
-3. **Generate skip analysis report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G01_48bca0a/attempt_1/skip_analysis.md`**
-
-4. **Clean up:**
-   ```bash
-   docker rmi test-milestone-milestone_G01_48bca0a-temp
-   ```
-
----
-
-## RUST-SPECIFIC PATCHING
-
-### How to Apply Patches in Dockerfile
-
-⚠️ **Apply patches using patch files or sed commands in the Dockerfile. DO NOT modify /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed!**
-
-⚠️ **CRITICAL**: After applying patches, you MUST commit the changes and move the tag to preserve patches across git checkouts. Without this step, patches will be lost when switching between START and END states!
-
-⚠️ **NEVER DELETE FILES**: When applying patches, you must NEVER delete any files (e.g., using `rm`, `git rm`, or similar commands). Only modify file contents. Deleting files can break test discovery and cause unexpected issues.
-
-### Rust Compilation Error Handling
-
-**CRITICAL**: Rust is a compiled language. Unlike Python/JavaScript, ALL code must compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-**Goal**: Comment out the minimal amount of code that causes compilation errors, so that the maximum number of tests can compile and run.
-
-### Patching Strategies for Rust
-
-#### Strategy 1: Use `#[cfg]` Attributes (Preferred)
-
-The best way to handle compilation errors in Rust is to use conditional compilation:
-
-```rust
-// Original code that fails in START state:
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();  // This doesn't exist in START state
-    assert!(result.is_ok());
-}
-
-// Patched version using cfg:
-#[cfg(feature = "new_feature")]
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();
-    assert!(result.is_ok());
-}
-```
-
-**Dockerfile example:**
-```dockerfile
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && \
-    # Add cfg attribute before test function
-    sed -i 's/#\[test\]\nfn test_new_feature/#[cfg(feature = "env_patch")]\n#[test]\nfn test_new_feature/' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add cfg guard for test_new_feature" && \
-    git tag -f milestone-milestone_G01_48bca0a-start HEAD
-```
-
-#### Strategy 2: Comment Out Test Functions
-
-When a test function uses APIs that don't exist in START state:
-
-```dockerfile
-# Comment out a specific test function (from line 45 to line 55)
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && \
-    sed -i '45,55 s/^/\/\/ [ENV-PATCH] /' src/tests.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_new_feature for START state" && \
-    git tag -f milestone-milestone_G01_48bca0a-start HEAD
-```
-
-**Better approach using markers:**
-```dockerfile
-# Find and comment out specific test
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && \
-    # Add /* before #[test] and */ after the closing brace
-    sed -i '/#\[test\]/,/^}$/{
-        /fn test_problematic/,/^}$/ {
-            s/^/\/\/ [ENV-PATCH] /
-        }
-    }' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_problematic" && \
-    git tag -f milestone-milestone_G01_48bca0a-start HEAD
-```
-
-#### Strategy 3: Comment Out Entire Module (Last Resort)
-
-Only when module-level code causes compilation errors:
-
-```dockerfile
-# Comment out entire test module
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && \
-    sed -i '/^mod tests {/,/^}/ s/^/\/\/ [ENV-PATCH] /' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests module" && \
-    git tag -f milestone-milestone_G01_48bca0a-start HEAD
-```
-
-#### Strategy 4: Modify Cargo.toml Features
-
-If the issue is feature-related:
-
-```dockerfile
-# Add a feature flag for conditional compilation
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && \
-    sed -i '/\[features\]/a env_patch = []' Cargo.toml && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add env_patch feature flag" && \
-    git tag -f milestone-milestone_G01_48bca0a-start HEAD
-```
-
-### Common Rust Compilation Error Patterns
-
-| Error Pattern | Cause | Solution |
-|---------------|-------|----------|
-| `cannot find function X in this scope` | Function doesn't exist in START | Comment out test using it |
-| `cannot find type X in this scope` | Type doesn't exist in START | Comment out test using it |
-| `trait X is not implemented for Y` | Trait impl missing in START | Comment out test using it |
-| `mismatched types` | API signature changed | Comment out test using it |
-| `unresolved import X::Y` | Module/item doesn't exist | Comment out import and tests |
-| `no method named X found` | Method doesn't exist in START | Comment out test using it |
-| `struct X has no field Y` | Field doesn't exist in START | Comment out test using it |
-| `lifetime mismatch` | Lifetime requirements changed | Comment out test using it |
-
-### Example: Full Patching Workflow
-
-```dockerfile
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Checkout to START state and apply patches
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start && \
-    # Patch 1: Comment out test that uses new API (lines 120-135)
-    sed -i '120,135 s/^/\/\/ [ENV-PATCH] /' src/api/tests.rs && \
-    # Patch 2: Comment out test that uses new struct field (lines 45-52)
-    sed -i '45,52 s/^/\/\/ [ENV-PATCH] /' tests/integration_test.rs && \
-    # Commit patches and move tag
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests using APIs not in START state" && \
-    git tag -f milestone-milestone_G01_48bca0a-start HEAD
-
-# Verify END state still compiles
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-end && cargo test --no-run
-
-# Set default to START
-RUN cd /testbed && git checkout milestone-milestone_G01_48bca0a-start
-```
-
-### Verify Patches Persist
-
-```bash
-docker build -t test-milestone-milestone_G01_48bca0a-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-# Test START state (verify patches applied)
-docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && cargo test --no-run"
-
-# Test END state (verify patches persist after checkout)
-docker run --rm test-milestone-milestone_G01_48bca0a-temp bash -c "cd /testbed && git checkout milestone-milestone_G01_48bca0a-end && cargo test --no-run"
-```
-
----
-
-## FINAL CHECKLIST
-
-### Before Completing Your Work
-Ensure you have:
-- [ ] **PHASE 0 completed**: Analyzed Rust project structure (single crate vs workspace, features, test targets)
-- [ ] Dockerfile based on `FROM nushell_nushell_0.106.0_0.108.0/base:latest`
-- [ ] **Testbed replaced**: `RUN rm -rf /testbed` + `COPY . /testbed/` included in Dockerfile
-- [ ] Both START and END states compile successfully (`cargo test --no-run`)
-- [ ] Minimal patches only (if needed)
-- [ ] No artificial skips
-- [ ] **Patches committed and tags moved** (if patches applied):
-  - [ ] Used `git add -A && git commit` after applying patches
-  - [ ] Used `git tag -f <TAG> HEAD` to move tag to patched commit
-  - [ ] Verified patches persist across `git checkout` (test switching between states)
-- [ ] **Full tests run** using test runner script with `--language rust --test-framework cargo`
-- [ ] **No resolvable environment-related issues** remaining
-- [ ] **Commit-related tests validated** using `collect_milestone_patched_tests.py`:
-  - [ ] Ran: `python -m harness.prepare_images.collect_milestone_patched_tests /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 --milestone milestone_G01_48bca0a`
-  - [ ] **`collected.patched_not_in_results` is EMPTY** (all patched tests found in results)
-  - [ ] No patched tests in `collected.status.end.skipped` (no environment-related ignores)
-- [ ] **test_config.json** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G01_48bca0a/test_config.json` with correct cargo test command
-- [ ] **Skip analysis report** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G01_48bca0a/attempt_1/skip_analysis.md`
-- [ ] Default state is START
-- [ ] Cleaned up: `docker rmi test-milestone-milestone_G01_48bca0a-temp`
-
----
-
-## COMMON PITFALLS TO AVOID
-
-❌ **Apply patches without committing and moving tags** - patches will be lost on `git checkout`!
-❌ **Forget to verify patches persist** - always test switching between START and END states after patching
-❌ **Modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository, use Dockerfile commands instead
-❌ **Skip PHASE 0** - understanding Rust project structure is essential
-❌ **Proceed to next phase before current phase compiles** - validate each phase before moving on
-❌ **Comment out entire files/crates** - only comment out specific functions/tests
-❌ **Forget workspace flag** - use `cargo test --workspace` for workspace projects
-❌ **Ignore feature flags** - check if tests require specific features to be enabled
-
-✅ **Always commit patches and move tags** (`git add -A && git commit && git tag -f <TAG> HEAD`)
-✅ **Test both states after applying patches** to ensure patches persist across checkout
-✅ **Document patched code** in Dockerfile comments (which functions, why)
-✅ **Use `[ENV-PATCH]` prefix** in commit messages and comments for tracking
-✅ **Use conditional compilation** (`#[cfg]`) when possible instead of commenting out
-✅ **Check all feature combinations** if the project uses feature flags

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G01_48bca0a.bak/test_config.json

@@ -1,12 +0,0 @@
-[
-  {
-    "name": "default",
-    "test_states": [
-      "start",
-      "end"
-    ],
-    "test_cmd": "cargo test --workspace --profile ci --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests excluding plugin crates using CI profile",
-    "framework": "cargo"
-  }
-]

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G02_da9615f.bak/Dockerfile

@@ -1,64 +0,0 @@
-# Build on pre-configured base image
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Remove the original /testbed from base image and copy local testbed
-# NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Make sure git considers this a safe directory and configure git user
-RUN git config --global --add safe.directory /testbed && \
-    git config --global user.email "env-patch@localhost" && \
-    git config --global user.name "ENV-PATCH"
-
-# Copy fix scripts to /tmp before git operations (so they won't be affected by checkouts)
-RUN cp /testbed/fix_reedline_api.py /tmp/fix_reedline_api.py && \
-    cp /testbed/fix_custom_completion.py /tmp/fix_custom_completion.py
-
-# Checkout to END state (all features available)
-# Tags already exist in testbed - just checkout, don't create tags
-RUN cd /testbed && git checkout -f milestone-milestone_G02_da9615f-end
-
-# [ENV-PATCH] Fix version mismatch and API compatibility issues:
-# 1. Cargo.toml requires 0.106.2 but crates have 0.106.0 - downgrade requirements
-# 2. PipelineData::value() method doesn't exist - replace with PipelineData::Value enum variant
-# 3. Fix Rust let chains syntax (unstable feature) in nu-parser/src/parser.rs - rewrite to nested if-let
-RUN cd /testbed && \
-    sed -i 's/version = "0.106.2"/version = "0.106.0"/g' Cargo.toml && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    sed -i '1249,1255c\            if let SyntaxShape::Keyword(ref keyword, ..) = positional.shape {\n                if keyword == b"catch" {\n                    if let [nu_protocol::CompileError::NotInALoop { .. }] =\n                        \&working_set.compile_errors[compile_error_count..]\n                    {\n                        working_set.compile_errors.truncate(compile_error_count);\n                    }\n                }\n            }' crates/nu-parser/src/parser.rs && \
-    python3 /tmp/fix_custom_completion.py && \
-    python3 /tmp/fix_reedline_api.py && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version mismatch and API compatibility" && \
-    git tag -f milestone-milestone_G02_da9615f-end HEAD
-
-# Checkout to START state and apply the same fixes
-RUN cd /testbed && git checkout -f milestone-milestone_G02_da9615f-start && \
-    sed -i 's/version = "0.106.2"/version = "0.106.0"/g' Cargo.toml && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    sed -i '1249,1255c\            if let SyntaxShape::Keyword(ref keyword, ..) = positional.shape {\n                if keyword == b"catch" {\n                    if let [nu_protocol::CompileError::NotInALoop { .. }] =\n                        \&working_set.compile_errors[compile_error_count..]\n                    {\n                        working_set.compile_errors.truncate(compile_error_count);\n                    }\n                }\n            }' crates/nu-parser/src/parser.rs && \
-    python3 /tmp/fix_custom_completion.py && \
-    python3 /tmp/fix_reedline_api.py && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version mismatch and API compatibility" && \
-    git tag -f milestone-milestone_G02_da9615f-start HEAD
-
-# Checkout back to END state for building tests
-RUN cd /testbed && git checkout -f milestone-milestone_G02_da9615f-end
-
-# Build tests for END state (reuse cached artifacts from base image where possible)
-RUN cd /testbed && cargo test --no-run --profile ci --workspace --exclude 'nu_plugin_*' -j 4
-
-# Set default git state to START
-RUN cd /testbed && git checkout -f milestone-milestone_G02_da9615f-start

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G02_da9615f.bak/env_patch_script/fix_reedline_api.py

@@ -1,95 +0,0 @@
-#!/usr/bin/env python3
-"""
-Fix reedline API compatibility issues by removing TraversalDirection and with_immediately_accept usage.
-This script properly handles the multi-line code blocks that sed struggles with.
-"""
-
-import re
-import sys
-from pathlib import Path
-
-def fix_reedline_config(file_path):
-    """Remove TraversalDirection import and tab_traversal match expression."""
-    with open(file_path, 'r') as f:
-        content = f.read()
-
-    # Remove TraversalDirection from imports
-    content = re.sub(
-        r',\s*TraversalDirection\s*,',
-        ',',
-        content
-    )
-    content = re.sub(
-        r'TraversalDirection\s*,',
-        '',
-        content
-    )
-
-    # Remove the entire tab_traversal match block (lines 292-306)
-    # Pattern: from "columnar_menu = match extract_value("tab_traversal"..."
-    # to the matching closing brace with Err(_) => columnar_menu,
-    pattern = r'''columnar_menu\s*=\s*match\s+extract_value\("tab_traversal",.*?\{\s*
-\s*Ok\(tab_traversal\)\s*=>\s*match\s+tab_traversal\.coerce_str\(\)\?\.as_ref\(\)\s*\{.*?
-\s*\},\s*
-\s*Err\(_\)\s*=>\s*columnar_menu,\s*
-\s*\};'''
-
-    content = re.sub(pattern, '', content, flags=re.DOTALL)
-
-    with open(file_path, 'w') as f:
-        f.write(content)
-
-    return True
-
-def fix_repl(file_path):
-    """Remove with_immediately_accept method calls."""
-    with open(file_path, 'r') as f:
-        lines = f.readlines()
-
-    new_lines = []
-    i = 0
-
-    while i < len(lines):
-        line = lines[i]
-
-        # Check if this line contains .with_immediately_accept
-        if '.with_immediately_accept(' in line:
-            # Check if the previous non-empty line needs a semicolon
-            if new_lines:
-                # Find the last non-empty, non-comment line
-                for j in range(len(new_lines) - 1, -1, -1):
-                    prev_line = new_lines[j].rstrip()
-                    if prev_line and not prev_line.strip().startswith('//'):
-                        # If it ends with ) but not with ; or }, add a semicolon
-                        if prev_line.endswith(')') and not prev_line.endswith(';') and not prev_line.endswith('}'):
-                            new_lines[j] = prev_line + ';\n'
-                        break
-            i += 1
-            continue
-
-        new_lines.append(line)
-        i += 1
-
-    with open(file_path, 'w') as f:
-        f.writelines(new_lines)
-
-    return True
-
-if __name__ == '__main__':
-    testbed_path = Path('/testbed')
-
-    print("Fixing reedline API compatibility...")
-
-    # Fix reedline_config.rs
-    reedline_config = testbed_path / 'crates/nu-cli/src/reedline_config.rs'
-    if reedline_config.exists():
-        fix_reedline_config(reedline_config)
-        print(f"✓ Fixed {reedline_config}")
-
-    # Fix repl.rs
-    repl_file = testbed_path / 'crates/nu-cli/src/repl.rs'
-    if repl_file.exists():
-        fix_repl(repl_file)
-        print(f"✓ Fixed {repl_file}")
-
-    print("Done!")

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G02_da9615f.bak/env_setup_prompt.md

@@ -1,935 +0,0 @@
-You are an expert in Rust software environment configuration. Your task is to configure
-a Docker container so that a given Rust repository can successfully run its test suite
-across TWO different git states (START and END tags).
-
-## RUST TEST FRAMEWORK
-
-| Language | Framework | Test Collect Command | Report Format | **Output File Extension** |
-|----------|-----------|----------------------|---------------|---------------------------|
-| Rust | cargo | `cargo test --no-run` | Console log | **`.log`** |
-
-### Output File Format Reference
-
-When generating `test_config.json`, use the `.log` extension for `{output_file}`:
-
-| Framework | Recommended Extension | Example `{output_file}` |
-|-----------|----------------------|-------------------------|
-| cargo | `.log` | `start_default.log` |
-
-**IMPORTANT**: The test runner (`run_milestone_tests.py`) will automatically use the cargo log parser based on the `--test-framework cargo` argument.
-
-## GOAL
-Configure the environment to:
-1. Make test compilation succeed for BOTH states (START and END)
-2. Run tests successfully with the test runner script
-3. Ensure no tests are skipped due to resolvable environment issues
-4. Ensure commit-related tests (tests modified by milestone commits) are collected AND run (not skipped)
-5. Generate a skip analysis report documenting remaining skips
-
-Generate a complete, buildable Dockerfile that supports dual-state testing.
-
-**IMPORTANT**: You are building on top of a pre-configured BASE IMAGE that already has:
-- Correct Rust toolchain version (rustc, cargo, rustup)
-- All system dependencies installed (OpenSSL, pkg-config, etc.)
-- Cargo dependencies cached (via `cargo fetch`)
-- Environment paths configured (CARGO_HOME, RUSTUP_HOME, PATH)
-- Repository cloned to /testbed
-
-**IMPORTANT**: The local testbed (/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed) already contains pre-created milestone tags:
-- `milestone-milestone_G02_da9615f-start` (START state tag)
-- `milestone-milestone_G02_da9615f-end` (END state tag)
-- **DO NOT create these tags in Dockerfile** - they are already included when you `COPY . /testbed/`
-- Simply use `git checkout milestone-milestone_G02_da9615f-start` or `git checkout milestone-milestone_G02_da9615f-end` to switch states
-
-Your task is to handle **git state management and compatibility patches** only.
-
----
-
-## ⚠️ DOCKERFILE VERIFICATION CHECKLIST (CRITICAL)
-
-Before finalizing your Dockerfile, verify ALL of the following constraints:
-
-- [ ] **No Source Code Modification**: Dockerfile must not modify source code logic
-- [ ] **No Test Logic Modification**: Dockerfile must not modify test code logic
-- [ ] **No File Deletion**: Dockerfile must not delete test files or any other files
-- [ ] **No Git Checkout to Fix Errors**: Cannot use `git checkout` to revert a file to a previous state to resolve compilation errors
-
-- [ ] **Compilation Error Handling**: If compilation problems occur, follow the minimal fix principle below
-
-### Minimal Fix Principle (Compilation Errors)
-
-```
-  Compilation Error Found
-      │
-      ├─ Locate the exact error position (file:line)
-      │
-      ├─ Error Type Classification:
-      │
-      ├─ Missing type/trait/function/module
-      │   └─→ Use #[cfg(feature = "...")] to conditionally compile
-      │   └─→ Or comment out the ENTIRE function/test containing the error
-      │
-      ├─ Trait implementation mismatch
-      │   └─→ Comment out the ENTIRE impl block or function
-      │
-      ├─ Lifetime/borrow checker errors
-      │   └─→ Comment out the ENTIRE function containing the error
-      │
-      └─ Feature flag issues
-          └─→ Fix via Cargo.toml features or environment variables (NOT code changes)
-```
-
-**Core Principles:**
-1. **NEVER skip/exclude entire crates or modules** - only comment out specific functions/tests
-2. **Comment out ENTIRE functions (not single lines)** - maintain code logic integrity
-3. **Preserve ALL tests that can compile normally** - maximize test coverage
-4. **Feature flag issues → fix via Cargo.toml or ENV** - not by modifying code
-
-**Specific Rules for Rust:**
-- For `Cargo.toml`: Can modify `[features]` section or comment out individual dependency lines
-- For test code: Comment out the **entire test function** (including `#[test]` attribute), not individual lines
-- For helper functions used by tests: Comment out the **entire function** if it causes compilation errors
-- **NEVER comment out an entire file** just because one function has compilation errors
-- **NEVER exclude an entire crate/module** just because one function has compilation errors
-
----
-
-### Inputs
-
-Milestone ID: milestone_G02_da9615f
-Milestone Commits: ["da9615f"] (list of commit SHAs included in this milestone)
-Commit Changed Tests Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/commit_level/patched_tests (directory containing per-commit test changes)
-Start Tag: milestone-milestone_G02_da9615f-start (earlier git state - may have missing features)
-End Tag: milestone-milestone_G02_da9615f-end (later git state - has all features)
-Repository Path: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed (source repository on host, used as build context)
-Source Directories: ["src/", "crates/"] (directories containing source code)
-Test Directory: test (directory containing tests, default: "tests/")
-Base Image: nushell_nushell_0.106.0_0.108.0/base:latest (pre-configured image with all dependencies)
-Base Image Dockerfile: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/base/dockerfiles/Dockerfile (Dockerfile used to build the base image)
-Test Runner Script: harness.test_runner.run_milestone_tests (script to run milestone tests)
-Test Results Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results (where test results are saved)
-Work Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 (harness workspace directory for this run)
-
-### Expected Outputs
-
-1. **Dockerfile**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G02_da9615f/Dockerfile
-   - Build successfully on top of nushell_nushell_0.106.0_0.108.0/base:latest
-   - Support both START state (milestone-milestone_G02_da9615f-start) and END state (milestone-milestone_G02_da9615f-end)
-   - Configure environment for both states; if conflicts exist, prioritize END state
-   - Default to START state when container starts
-
-2. **Test Config**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G02_da9615f/test_config.json
-   - Configure test runner to run tests as comprehensively as possible
-   - Include all test modes the repository supports (unit tests, integration tests, doc tests)
-   - Goal: maximize test coverage and collect complete test results
-
-3. **Skip Analysis Report**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G02_da9615f/attempt_1/skip_analysis.md
-   - Analysis of all skipped/ignored tests based on test results
-   - Classification by skip reason (resolvable vs acceptable)
-   - Confirmation that no environment-related skips remain
-
----
-
-## RUST TEST COMMANDS
-
-### Cargo Test Commands
-
-```bash
-# Compile tests without running (test collection)
-cargo test --no-run
-
-# Compile tests for all targets (lib, bins, tests, examples, benches)
-cargo test --no-run --all-targets
-
-# Run all tests
-cargo test
-
-# Run tests with specific options
-cargo test --no-fail-fast -- --test-threads={workers}
-
-# Run tests with verbose output
-cargo test -- --nocapture
-
-# Run only unit tests (in src/)
-cargo test --lib
-
-# Run only integration tests (in tests/)
-cargo test --test '*'
-
-# Run tests for a specific package in a workspace
-cargo test -p package_name
-
-# Run tests for all packages in a workspace
-cargo test --workspace
-
-# Run tests with all features enabled
-cargo test --all-features
-
-# Run tests with specific features
-cargo test --features "feature1 feature2"
-
-# Run tests without default features
-cargo test --no-default-features
-
-# Run doc tests only
-cargo test --doc
-
-# List all tests without running
-cargo test -- --list
-
-# Run ignored tests
-cargo test -- --ignored
-
-# Run both normal and ignored tests
-cargo test -- --include-ignored
-```
-
-### Test Output Format
-
-Cargo test output follows this format:
-```
-running X tests
-test module::test_name ... ok
-test module::another_test ... FAILED
-test module::ignored_test ... ignored
-test module::skipped_test ... ignored, reason: "requires feature X"
-
-test result: FAILED. X passed; Y failed; Z ignored; 0 measured; 0 filtered out
-```
-
----
-
-## CRITICAL WORKFLOW (FOLLOW THIS ORDER)
-
-⚠️ **You MUST follow this exact workflow sequence:**
-
-```
-PHASE 0: Analyze Rust Project Structure
-    └── Check Cargo.toml → Identify workspace/crates → Determine features → List test targets
-
-PHASE 1: Write Initial Dockerfile & Test END State
-    └── Build minimal image → Test compilation for END state → Verify success
-
-PHASE 2: Test START State & Apply Minimal Patches (if needed)
-    └── Test START compilation → Apply patches if needed → Verify both states pass
-
-PHASE 2.5: Generate test_config.json
-    └── Create test configuration file required by test runner
-
-PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-    └── Run {test_runner_script} → Analyze ignored tests → Identify environment issues
-
-PHASE 4: Fix Environment Issues (iterate until resolved)
-    └── Update Dockerfile → Re-run tests → Verify issues are resolved
-
-PHASE 4.5: Validate Commit-Related Tests
-    └���─ Verify tests modified by milestone commits are collected AND not ignored
-
-PHASE 5: Finalize & Generate Skip Analysis
-    └── Set default state to START → Create skip_analysis.md → Clean up
-```
-
----
-
-### PHASE 0: Analyze Rust Project Structure
-**Understand the Rust project before proceeding**
-
-1. **Check project type (single crate vs workspace):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat Cargo.toml | head -30"
-   ```
-
-   **Single crate indicators:**
-   ```toml
-   [package]
-   name = "my_crate"
-   version = "0.1.0"
-   ```
-
-   **Workspace indicators:**
-   ```toml
-   [workspace]
-   members = [
-       "crate1",
-       "crate2",
-   ]
-   ```
-
-2. **List all crates in workspace (if applicable):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cargo metadata --no-deps --format-version 1 | jq '.packages[].name'"
-   ```
-
-3. **Check available features:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-   ```
-
-4. **Identify test targets:**
-
-   ```bash
-   # Check for integration tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la tests/ 2>/dev/null"
-
-   # Check for unit tests in src/
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '#\[test\]' src/ | head -20"
-
-   # Check for doc tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '```rust' src/ | head -10"
-
-   # Check for benchmark tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la benches/ 2>/dev/null"
-   ```
-
-5. **Check Rust toolchain requirements:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat rust-toolchain.toml rust-toolchain 2>/dev/null"
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "rustc --version && cargo --version"
-   ```
-
-6. **Record your analysis:**
-
-   ```
-   PROJECT TYPE: <single_crate|workspace>
-   WORKSPACE MEMBERS: <list of crate names if workspace>
-   AVAILABLE FEATURES: <list of features>
-   TEST TARGETS: <lib|tests|examples|benches|doc>
-   RUST TOOLCHAIN: <stable|nightly|specific version>
-   ```
-
-⚠️ **DO NOT PROCEED to Phase 1 until you understand the project structure!**
-
-### IMPORTANT: Building on Base Image
-
-Since you are building on top of `nushell_nushell_0.106.0_0.108.0/base:latest`, you do NOT need to:
-- Install Rust toolchain
-- Install system dependencies
-- Run `cargo fetch` or `cargo build`
-- Configure environment paths
-
-Your Dockerfile only needs to:
-1. Checkout to the correct git states
-2. Apply minimal patches if START state has compilation issues
-
-**Temp image name**: `test-milestone-milestone_G02_da9615f-temp` (unique for this milestone)
-
-**CRITICAL RULES:**
-- ❌ **NEVER modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository
-- ✅ **Use a working copy for exploration** (create with `cp -r` if needed)
-- ✅ **Build using**: `docker build -t test-milestone-milestone_G02_da9615f-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-- ✅ **Clean up test images when done**: `docker rmi test-milestone-milestone_G02_da9615f-temp`
-
----
-
-### PHASE 1: Write Initial Dockerfile & Test END State
-**Start with a minimal Dockerfile based on the base image**
-
-1. **Write the initial Dockerfile:**
-
-   ```dockerfile
-   # Build on pre-configured base image
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Set umask to ensure files created in container are world-writable
-   # This prevents permission issues when test results are written to mounted volumes
-   RUN echo 'umask 000' >> /etc/bash.bashrc && \
-       echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-       chmod +x /entrypoint.sh
-   ENTRYPOINT ["/entrypoint.sh"]
-   CMD ["bash"]
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Checkout to END state (all features available)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-end
-   ```
-
-2. **Build and test END state compilation:**
-
-   ```bash
-   docker build -t test-milestone-milestone_G02_da9615f-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-   ```
-
-   Then test compilation:
-
-   ```bash
-   # For single crate
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && cargo test --no-run"
-
-   # For workspace
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && cargo test --workspace --no-run"
-
-   # With all features
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && cargo test --all-features --no-run"
-   ```
-
-3. **SUCCESS CRITERIA for END state:**
-   - Exit code 0
-   - Output shows "Compiling" and "Finished" messages
-   - NO compilation errors
-   - Test binaries are generated
-
-   ⚠️ **DO NOT PROCEED to Phase 2 until END state compiles!**
-
----
-
-### PHASE 2: Test START State & Apply Minimal Patches (if needed)
-**Handle the earlier codebase state which may lack features**
-
-1. **Test START state compilation:**
-
-   ```bash
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && git checkout milestone-milestone_G02_da9615f-start && cargo test --no-run"
-   ```
-
-2. **Handle results:**
-
-   **Case A: Compilation succeeds immediately**
-   ✅ Both states work! Proceed to PHASE 2.5.
-
-   **Case B: Compilation fails**
-   Apply Rust-specific minimal patches. See "RUST-SPECIFIC PATCHING" section.
-
-   ⚠️ **RUST COMPILATION**: Like Java, Rust requires ALL code to compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-3. **VALIDATION - Both states MUST compile:**
-   ```bash
-   docker build -t test-milestone-milestone_G02_da9615f-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-   # Test END state
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && git checkout milestone-milestone_G02_da9615f-end && cargo test --no-run"
-
-   # Test START state
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && git checkout milestone-milestone_G02_da9615f-start && cargo test --no-run"
-   ```
-
----
-
-### PHASE 2.5: Generate test_config.json
-**Create test configuration file required by test runner**
-
-The test_config.json defines how the test runner should execute tests.
-
-**Format:**
-```json
-[
-  {
-    "name": "config_name",
-    "test_states": ["start", "end"],
-    "test_cmd": "test command with placeholders",
-    "description": "What this configuration tests"
-  }
-]
-```
-
-**Available placeholders:** `{workers}`, `{timeout}`, `{output_file}`
-
-**Basic Example (Single Crate):**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests"
-  }
-]
-```
-
-**Workspace Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --workspace --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests"
-  }
-]
-```
-
-**With Features Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --all-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests with all features"
-  },
-  {
-    "name": "no_default_features",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-default-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Tests without default features"
-  }
-]
-```
-
-**Multiple Test Targets Example:**
-```json
-[
-  {
-    "name": "unit",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --lib --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Unit tests only"
-  },
-  {
-    "name": "integration",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --test '*' --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Integration tests only"
-  },
-  {
-    "name": "doc",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --doc --no-fail-fast 2>&1 | tee /output/{output_file}",
-    "description": "Doc tests only"
-  }
-]
-```
-
-**Guidelines:**
-1. **Always include "default" configuration** that runs all tests
-2. **Discover special test modes:**
-
-   ```bash
-   # Check for feature flags
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-
-   # Check for test-specific features
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && grep -E 'test-|testing' Cargo.toml"
-
-   # Check for conditional compilation in tests
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && grep -r '#\[cfg(test)\]' src/ | head -10"
-
-   # Check for ignored tests that might need special flags
-   docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && grep -r '#\[ignore\]' . | head -20"
-   ```
-
----
-
-### PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-**Run full tests and identify environment-related issues**
-
-1. **Run tests using the test runner script:**
-
-   ```bash
-   python -m harness.test_runner.run_milestone_tests \
-     --milestone-id milestone_G02_da9615f \
-     --image-name test-milestone-milestone_G02_da9615f-temp \
-     --output-dir /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results \
-     --language rust \
-     --test-framework cargo \
-     --max-retries 1
-   ```
-
-2. **Analyze test results:**
-
-   After tests complete, examine the output log for ignored tests:
-
-   ```bash
-   # Find ignored tests
-   grep "ignored" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G02_da9615f/attempt_1/end_default.log
-
-   # Find failed tests
-   grep "FAILED" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G02_da9615f/attempt_1/end_default.log
-   ```
-
-3. **Classification of Rust test skip/ignore reasons:**
-
-   | Pattern | Classification | Action |
-   |---------|----------------|--------|
-   | `#[ignore]` without reason | Review | Check if intentional |
-   | `#[ignore = "requires X"]` | Depends | Check if X is environment-related |
-   | `#[ignore = "flaky"]` | Acceptable | Intentionally ignored |
-   | `#[ignore = "slow"]` | Acceptable | Run with `--include-ignored` if needed |
-   | `#[cfg(feature = "X")]` not enabled | Resolvable | Enable feature in test_config.json |
-   | Missing system library | Resolvable | Install in Dockerfile |
-   | Network-dependent test | Acceptable | Requires external resources |
-
-4. **Common Rust environment issues:**
-
-   | Error Pattern | Cause | Solution |
-   |---------------|-------|----------|
-   | `error: could not find native static library` | Missing C library | `RUN apt-get install libXXX-dev` |
-   | `error: linking with cc failed` | Missing linker deps | Install build-essential |
-   | `RUSTFLAGS` related | Build flags issue | Set `ENV RUSTFLAGS="..."` |
-   | `openssl` errors | Missing OpenSSL | Install `libssl-dev` |
-   | `pkg-config` errors | Missing pkg-config | Install `pkg-config` |
-
-5. **If resolvable environment issues found → Proceed to PHASE 4**
-   **If no resolvable issues → Proceed to PHASE 4.5**
-
----
-
-### PHASE 4: Fix Environment Issues
-**Resolve environment-related issues by updating Dockerfile**
-
-**Common fixes for Rust projects:**
-
-```dockerfile
-# Install missing system libraries
-RUN apt-get update && apt-get install -y \
-    libssl-dev \
-    pkg-config \
-    libclang-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-# Set environment variables
-ENV RUST_BACKTRACE=1
-ENV CARGO_NET_GIT_FETCH_WITH_CLI=true
-
-# Enable specific features by default
-ENV CARGO_FEATURE_FLAGS="--all-features"
-
-# Fix OpenSSL issues
-ENV OPENSSL_DIR=/usr
-ENV OPENSSL_LIB_DIR=/usr/lib/x86_64-linux-gnu
-ENV OPENSSL_INCLUDE_DIR=/usr/include
-
-# Fetch dependencies again after changes
-RUN cd /testbed && cargo fetch
-```
-
-**Iteration loop:**
-
-1. Update Dockerfile with fix
-2. Rebuild: `docker build -t test-milestone-milestone_G02_da9615f-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-3. Re-run tests with test runner script
-4. Check if issue is resolved by comparing results
-5. Repeat until no resolvable issues remain
-
----
-
-### PHASE 4.5: Validate Commit-Related Tests
-**Ensure tests modified by milestone commits are collected AND not ignored**
-
-1. **Run the collect_milestone_patched_tests.py script:**
-
-   ```bash
-   python -m harness.prepare_images.collect_milestone_patched_tests \
-     /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 \
-     --repo /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed \
-     --milestone milestone_G02_da9615f
-   ```
-
-   This script:
-   - Extracts symbol changes (added/modified/deleted tests) from each commit
-   - Aggregates patched tests at the milestone level
-   - Matches patched test IDs to actual test results (nodeids)
-   - Generates a report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_G02_da9615f.json`
-
-2. **Check the output JSON file:**
-
-   The output format is:
-   ```json
-   {
-     "milestone_id": "milestone_G02_da9615f",
-     "commits": ["abc1234", "def5678"],
-     "test_ids": {
-       "added": [...],      // Tests added by commits
-       "modified": [...],   // Tests modified by commits
-       "deleted": [...],    // Tests deleted by commits
-       "effective": [...]   // Effective tests = (added ∪ modified) - deleted
-     },
-     "collected": {
-       "patched_in_results": [...],      // ✅ Patched tests found in test results
-       "patched_not_in_results": [],     // ⚠️ MUST BE EMPTY!
-       "test_id_to_nodeid": {...},       // Mapping from test_id to nodeid
-       "status": {
-         "start": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []},
-         "end": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []}
-       },
-       "transitions": {
-         "fixed": [],        // start failed/error -> end passed
-         "broken": [],       // start passed -> end failed/error
-         "still_passing": [],
-         "still_failing": [],
-         "other": []
-       }
-     },
-     "summary": {...}
-   }
-   ```
-
-3. **⚠️ CRITICAL VALIDATION: `collected.patched_not_in_results` MUST be empty!**
-
-   This field lists patched tests that were NOT found in test results. If not empty, it means:
-   - Some patched tests failed to compile (possibly commented out incorrectly)
-   - Some patched tests were excluded from test collection
-   - The test_id to nodeid matching failed
-
-   **How to verify:**
-   ```bash
-   # Check if patched_not_in_results is empty
-   cat /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_G02_da9615f.json | jq '.collected.patched_not_in_results'
-   # Expected output: []
-   ```
-
-4. **If `patched_not_in_results` is NOT empty:**
-   - Identify which tests are missing from results
-   - Check if those tests were incorrectly commented out or excluded
-   - Return to PHASE 4 to fix environment issues
-   - Re-run tests and re-validate until `patched_not_in_results` is empty
-
-5. **Also verify no commit-related tests are ignored:**
-   - Check `collected.status.end.skipped` - patched tests should not be ignored
-   - If ignored due to environment issues, return to PHASE 4 to fix
-
----
-
-### PHASE 5: Finalize Dockerfile & Generate Skip Analysis
-**Set default state to START, create skip analysis report, and clean up**
-
-1. **Ensure Dockerfile sets default state to START:**
-
-   ```dockerfile
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Environment fixes (if any)
-   # RUN apt-get update && apt-get install -y ...
-   # ENV RUST_BACKTRACE=1
-
-   # Checkout to END state (for any patching if needed)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-end
-
-   # [If patches needed, add them here]
-
-   # Set default git state to START
-   RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-start
-   ```
-
-2. **Final validation**
-
-3. **Generate skip analysis report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G02_da9615f/attempt_1/skip_analysis.md`**
-
-4. **Clean up:**
-   ```bash
-   docker rmi test-milestone-milestone_G02_da9615f-temp
-   ```
-
----
-
-## RUST-SPECIFIC PATCHING
-
-### How to Apply Patches in Dockerfile
-
-⚠️ **Apply patches using patch files or sed commands in the Dockerfile. DO NOT modify /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed!**
-
-⚠️ **CRITICAL**: After applying patches, you MUST commit the changes and move the tag to preserve patches across git checkouts. Without this step, patches will be lost when switching between START and END states!
-
-⚠️ **NEVER DELETE FILES**: When applying patches, you must NEVER delete any files (e.g., using `rm`, `git rm`, or similar commands). Only modify file contents. Deleting files can break test discovery and cause unexpected issues.
-
-### Rust Compilation Error Handling
-
-**CRITICAL**: Rust is a compiled language. Unlike Python/JavaScript, ALL code must compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-**Goal**: Comment out the minimal amount of code that causes compilation errors, so that the maximum number of tests can compile and run.
-
-### Patching Strategies for Rust
-
-#### Strategy 1: Use `#[cfg]` Attributes (Preferred)
-
-The best way to handle compilation errors in Rust is to use conditional compilation:
-
-```rust
-// Original code that fails in START state:
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();  // This doesn't exist in START state
-    assert!(result.is_ok());
-}
-
-// Patched version using cfg:
-#[cfg(feature = "new_feature")]
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();
-    assert!(result.is_ok());
-}
-```
-
-**Dockerfile example:**
-```dockerfile
-RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-start && \
-    # Add cfg attribute before test function
-    sed -i 's/#\[test\]\nfn test_new_feature/#[cfg(feature = "env_patch")]\n#[test]\nfn test_new_feature/' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add cfg guard for test_new_feature" && \
-    git tag -f milestone-milestone_G02_da9615f-start HEAD
-```
-
-#### Strategy 2: Comment Out Test Functions
-
-When a test function uses APIs that don't exist in START state:
-
-```dockerfile
-# Comment out a specific test function (from line 45 to line 55)
-RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-start && \
-    sed -i '45,55 s/^/\/\/ [ENV-PATCH] /' src/tests.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_new_feature for START state" && \
-    git tag -f milestone-milestone_G02_da9615f-start HEAD
-```
-
-**Better approach using markers:**
-```dockerfile
-# Find and comment out specific test
-RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-start && \
-    # Add /* before #[test] and */ after the closing brace
-    sed -i '/#\[test\]/,/^}$/{
-        /fn test_problematic/,/^}$/ {
-            s/^/\/\/ [ENV-PATCH] /
-        }
-    }' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_problematic" && \
-    git tag -f milestone-milestone_G02_da9615f-start HEAD
-```
-
-#### Strategy 3: Comment Out Entire Module (Last Resort)
-
-Only when module-level code causes compilation errors:
-
-```dockerfile
-# Comment out entire test module
-RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-start && \
-    sed -i '/^mod tests {/,/^}/ s/^/\/\/ [ENV-PATCH] /' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests module" && \
-    git tag -f milestone-milestone_G02_da9615f-start HEAD
-```
-
-#### Strategy 4: Modify Cargo.toml Features
-
-If the issue is feature-related:
-
-```dockerfile
-# Add a feature flag for conditional compilation
-RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-start && \
-    sed -i '/\[features\]/a env_patch = []' Cargo.toml && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add env_patch feature flag" && \
-    git tag -f milestone-milestone_G02_da9615f-start HEAD
-```
-
-### Common Rust Compilation Error Patterns
-
-| Error Pattern | Cause | Solution |
-|---------------|-------|----------|
-| `cannot find function X in this scope` | Function doesn't exist in START | Comment out test using it |
-| `cannot find type X in this scope` | Type doesn't exist in START | Comment out test using it |
-| `trait X is not implemented for Y` | Trait impl missing in START | Comment out test using it |
-| `mismatched types` | API signature changed | Comment out test using it |
-| `unresolved import X::Y` | Module/item doesn't exist | Comment out import and tests |
-| `no method named X found` | Method doesn't exist in START | Comment out test using it |
-| `struct X has no field Y` | Field doesn't exist in START | Comment out test using it |
-| `lifetime mismatch` | Lifetime requirements changed | Comment out test using it |
-
-### Example: Full Patching Workflow
-
-```dockerfile
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Checkout to START state and apply patches
-RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-start && \
-    # Patch 1: Comment out test that uses new API (lines 120-135)
-    sed -i '120,135 s/^/\/\/ [ENV-PATCH] /' src/api/tests.rs && \
-    # Patch 2: Comment out test that uses new struct field (lines 45-52)
-    sed -i '45,52 s/^/\/\/ [ENV-PATCH] /' tests/integration_test.rs && \
-    # Commit patches and move tag
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests using APIs not in START state" && \
-    git tag -f milestone-milestone_G02_da9615f-start HEAD
-
-# Verify END state still compiles
-RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-end && cargo test --no-run
-
-# Set default to START
-RUN cd /testbed && git checkout milestone-milestone_G02_da9615f-start
-```
-
-### Verify Patches Persist
-
-```bash
-docker build -t test-milestone-milestone_G02_da9615f-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-# Test START state (verify patches applied)
-docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && cargo test --no-run"
-
-# Test END state (verify patches persist after checkout)
-docker run --rm test-milestone-milestone_G02_da9615f-temp bash -c "cd /testbed && git checkout milestone-milestone_G02_da9615f-end && cargo test --no-run"
-```
-
----
-
-## FINAL CHECKLIST
-
-### Before Completing Your Work
-Ensure you have:
-- [ ] **PHASE 0 completed**: Analyzed Rust project structure (single crate vs workspace, features, test targets)
-- [ ] Dockerfile based on `FROM nushell_nushell_0.106.0_0.108.0/base:latest`
-- [ ] **Testbed replaced**: `RUN rm -rf /testbed` + `COPY . /testbed/` included in Dockerfile
-- [ ] Both START and END states compile successfully (`cargo test --no-run`)
-- [ ] Minimal patches only (if needed)
-- [ ] No artificial skips
-- [ ] **Patches committed and tags moved** (if patches applied):
-  - [ ] Used `git add -A && git commit` after applying patches
-  - [ ] Used `git tag -f <TAG> HEAD` to move tag to patched commit
-  - [ ] Verified patches persist across `git checkout` (test switching between states)
-- [ ] **Full tests run** using test runner script with `--language rust --test-framework cargo`
-- [ ] **No resolvable environment-related issues** remaining
-- [ ] **Commit-related tests validated** using `collect_milestone_patched_tests.py`:
-  - [ ] Ran: `python -m harness.prepare_images.collect_milestone_patched_tests /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 --milestone milestone_G02_da9615f`
-  - [ ] **`collected.patched_not_in_results` is EMPTY** (all patched tests found in results)
-  - [ ] No patched tests in `collected.status.end.skipped` (no environment-related ignores)
-- [ ] **test_config.json** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G02_da9615f/test_config.json` with correct cargo test command
-- [ ] **Skip analysis report** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G02_da9615f/attempt_1/skip_analysis.md`
-- [ ] Default state is START
-- [ ] Cleaned up: `docker rmi test-milestone-milestone_G02_da9615f-temp`
-
----
-
-## COMMON PITFALLS TO AVOID
-
-❌ **Apply patches without committing and moving tags** - patches will be lost on `git checkout`!
-❌ **Forget to verify patches persist** - always test switching between START and END states after patching
-❌ **Modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository, use Dockerfile commands instead
-❌ **Skip PHASE 0** - understanding Rust project structure is essential
-❌ **Proceed to next phase before current phase compiles** - validate each phase before moving on
-❌ **Comment out entire files/crates** - only comment out specific functions/tests
-❌ **Forget workspace flag** - use `cargo test --workspace` for workspace projects
-❌ **Ignore feature flags** - check if tests require specific features to be enabled
-
-✅ **Always commit patches and move tags** (`git add -A && git commit && git tag -f <TAG> HEAD`)
-✅ **Test both states after applying patches** to ensure patches persist across checkout
-✅ **Document patched code** in Dockerfile comments (which functions, why)
-✅ **Use `[ENV-PATCH]` prefix** in commit messages and comments for tracking
-✅ **Use conditional compilation** (`#[cfg]`) when possible instead of commenting out
-✅ **Check all feature combinations** if the project uses feature flags

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G02_da9615f.bak/test_config.json

@@ -1,12 +0,0 @@
-[
-  {
-    "name": "default",
-    "test_states": [
-      "start",
-      "end"
-    ],
-    "test_cmd": "cd /testbed && cargo test --profile ci --workspace --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests excluding plugins",
-    "framework": "cargo"
-  }
-]

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G05_be6e868.bak/Dockerfile

@@ -1,108 +0,0 @@
-# Build on pre-configured base image which has working compilation (version 0.106.0)
-# The base image already has all crates compiled successfully
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Git configuration for patching
-RUN git config --global --add safe.directory /testbed && \
-    git config --global user.email "docker@build.local" && \
-    git config --global user.name "Docker Build"
-
-# The base image has a working /testbed with compiled code
-# We only need to apply the nu-lsp source changes from the milestone
-# This avoids recompiling other crates that may have breaking changes
-
-# Copy nu-lsp source files and Cargo.toml from milestone testbed (currently at START state)
-COPY crates/nu-lsp/src/ /tmp/nu-lsp-start-src/
-COPY crates/nu-lsp/Cargo.toml /tmp/nu-lsp-start-cargo.toml
-# Copy fix script
-COPY fix_reedline_api.py /tmp/fix_reedline_api.py
-
-# Fix version numbers in START state Cargo.toml to match base image (0.106.0)
-# This resolves dependency conflicts where nu-lsp may require nu-cli = "^0.106.1" but base only has 0.106.0
-RUN sed -i 's/"0\.10[67]\.[0-9]*"/"0.106.0"/g' /tmp/nu-lsp-start-cargo.toml
-
-# Create START state: apply milestone START nu-lsp code on top of base
-RUN cd /testbed && \
-    # Create a branch for START state
-    git checkout -b milestone-start-branch && \
-    # Replace nu-lsp/src with START state version from milestone
-    rm -rf crates/nu-lsp/src && \
-    cp -r /tmp/nu-lsp-start-src crates/nu-lsp/src && \
-    # Replace nu-lsp/Cargo.toml to get correct dependencies
-    cp /tmp/nu-lsp-start-cargo.toml crates/nu-lsp/Cargo.toml && \
-    # Fix reedline API compatibility
-    python3 /tmp/fix_reedline_api.py && \
-    # Fix PipelineData::value capitalization in nu-lsp
-    sed -i 's/PipelineData::value/PipelineData::Value/g' crates/nu-lsp/src/lib.rs && \
-    # Commit and tag
-    git add -A && \
-    git commit -m "Apply milestone nu-lsp START state" && \
-    git tag -f milestone-milestone_G05_be6e868-start HEAD
-
-# Now we need to get the END state nu-lsp files
-# The testbed is at START state during COPY, so we need to extract END state differently
-# We'll use git to checkout END in the container from the milestone testbed
-
-# Copy the milestone testbed's .git directory to extract END state files
-COPY .git/ /tmp/milestone-git/
-
-# Extract END state nu-lsp files from milestone git history
-RUN cd /tmp && \
-    mkdir milestone-checkout && \
-    cd milestone-checkout && \
-    git init && \
-    git remote add origin /tmp/milestone-git && \
-    git fetch origin milestone-milestone_G05_be6e868-end && \
-    git checkout FETCH_HEAD -- crates/nu-lsp/src crates/nu-lsp/Cargo.toml && \
-    cp -r crates/nu-lsp/src /tmp/nu-lsp-end-src && \
-    cp crates/nu-lsp/Cargo.toml /tmp/nu-lsp-end-cargo.toml
-
-# Fix version numbers in extracted END state Cargo.toml to match base image (0.106.0)
-# This resolves dependency conflicts where nu-lsp may require nu-cli = "^0.106.1" but base only has 0.106.0
-RUN sed -i 's/"0\.10[67]\.[0-9]*"/"0.106.0"/g' /tmp/nu-lsp-end-cargo.toml
-
-# Create END state: apply milestone END nu-lsp code on top of base
-RUN cd /testbed && \
-    # Create a branch for END state from base
-    git checkout 1b01625e1e && \
-    git checkout -b milestone-end-branch && \
-    # Replace nu-lsp/src with END state version from milestone
-    rm -rf crates/nu-lsp/src && \
-    cp -r /tmp/nu-lsp-end-src crates/nu-lsp/src && \
-    # Replace nu-lsp/Cargo.toml to get correct dependencies
-    cp /tmp/nu-lsp-end-cargo.toml crates/nu-lsp/Cargo.toml && \
-    # Fix reedline API compatibility
-    python3 /tmp/fix_reedline_api.py && \
-    # Fix PipelineData::value capitalization in nu-lsp
-    sed -i 's/PipelineData::value/PipelineData::Value/g' crates/nu-lsp/src/lib.rs && \
-    # Commit and tag
-    git add -A && \
-    git commit -m "Apply milestone nu-lsp END state" && \
-    git tag -f milestone-milestone_G05_be6e868-end HEAD
-
-# Clean up temp files
-RUN rm -rf /tmp/nu-lsp-start-src /tmp/nu-lsp-end-src /tmp/milestone-git /tmp/milestone-checkout \
-    /tmp/nu-lsp-start-cargo.toml /tmp/nu-lsp-end-cargo.toml
-
-# Rebuild nu-lsp for END state to verify compilation
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-end && \
-    cargo build --profile ci -p nu-lsp -j 4
-
-# Build all workspace tests (excluding plugins)
-RUN cd /testbed && cargo test --no-run --profile ci --workspace --exclude nu_plugin_* -j 4
-
-# Verify START state also compiles
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start && \
-    cargo build --profile ci -p nu-lsp -j 4 && \
-    cargo test --no-run --profile ci --workspace --exclude nu_plugin_* -j 4
-
-# Set default git state to START
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G05_be6e868.bak/env_patch_script/fix_reedline_api.py

@@ -1,95 +0,0 @@
-#!/usr/bin/env python3
-"""
-Fix reedline API compatibility issues by removing TraversalDirection and with_immediately_accept usage.
-This script properly handles the multi-line code blocks that sed struggles with.
-"""
-
-import re
-import sys
-from pathlib import Path
-
-def fix_reedline_config(file_path):
-    """Remove TraversalDirection import and tab_traversal match expression."""
-    with open(file_path, 'r') as f:
-        content = f.read()
-
-    # Remove TraversalDirection from imports
-    content = re.sub(
-        r',\s*TraversalDirection\s*,',
-        ',',
-        content
-    )
-    content = re.sub(
-        r'TraversalDirection\s*,',
-        '',
-        content
-    )
-
-    # Remove the entire tab_traversal match block (lines 292-306)
-    # Pattern: from "columnar_menu = match extract_value("tab_traversal"..."
-    # to the matching closing brace with Err(_) => columnar_menu,
-    pattern = r'''columnar_menu\s*=\s*match\s+extract_value\("tab_traversal",.*?\{\s*
-\s*Ok\(tab_traversal\)\s*=>\s*match\s+tab_traversal\.coerce_str\(\)\?\.as_ref\(\)\s*\{.*?
-\s*\},\s*
-\s*Err\(_\)\s*=>\s*columnar_menu,\s*
-\s*\};'''
-
-    content = re.sub(pattern, '', content, flags=re.DOTALL)
-
-    with open(file_path, 'w') as f:
-        f.write(content)
-
-    return True
-
-def fix_repl(file_path):
-    """Remove with_immediately_accept method calls."""
-    with open(file_path, 'r') as f:
-        lines = f.readlines()
-
-    new_lines = []
-    i = 0
-
-    while i < len(lines):
-        line = lines[i]
-
-        # Check if this line contains .with_immediately_accept
-        if '.with_immediately_accept(' in line:
-            # Check if the previous non-empty line needs a semicolon
-            if new_lines:
-                # Find the last non-empty, non-comment line
-                for j in range(len(new_lines) - 1, -1, -1):
-                    prev_line = new_lines[j].rstrip()
-                    if prev_line and not prev_line.strip().startswith('//'):
-                        # If it ends with ) but not with ; or }, add a semicolon
-                        if prev_line.endswith(')') and not prev_line.endswith(';') and not prev_line.endswith('}'):
-                            new_lines[j] = prev_line + ';\n'
-                        break
-            i += 1
-            continue
-
-        new_lines.append(line)
-        i += 1
-
-    with open(file_path, 'w') as f:
-        f.writelines(new_lines)
-
-    return True
-
-if __name__ == '__main__':
-    testbed_path = Path('/testbed')
-
-    print("Fixing reedline API compatibility...")
-
-    # Fix reedline_config.rs
-    reedline_config = testbed_path / 'crates/nu-cli/src/reedline_config.rs'
-    if reedline_config.exists():
-        fix_reedline_config(reedline_config)
-        print(f"✓ Fixed {reedline_config}")
-
-    # Fix repl.rs
-    repl_file = testbed_path / 'crates/nu-cli/src/repl.rs'
-    if repl_file.exists():
-        fix_repl(repl_file)
-        print(f"✓ Fixed {repl_file}")
-
-    print("Done!")

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G05_be6e868.bak/env_setup_prompt.md

@@ -1,935 +0,0 @@
-You are an expert in Rust software environment configuration. Your task is to configure
-a Docker container so that a given Rust repository can successfully run its test suite
-across TWO different git states (START and END tags).
-
-## RUST TEST FRAMEWORK
-
-| Language | Framework | Test Collect Command | Report Format | **Output File Extension** |
-|----------|-----------|----------------------|---------------|---------------------------|
-| Rust | cargo | `cargo test --no-run` | Console log | **`.log`** |
-
-### Output File Format Reference
-
-When generating `test_config.json`, use the `.log` extension for `{output_file}`:
-
-| Framework | Recommended Extension | Example `{output_file}` |
-|-----------|----------------------|-------------------------|
-| cargo | `.log` | `start_default.log` |
-
-**IMPORTANT**: The test runner (`run_milestone_tests.py`) will automatically use the cargo log parser based on the `--test-framework cargo` argument.
-
-## GOAL
-Configure the environment to:
-1. Make test compilation succeed for BOTH states (START and END)
-2. Run tests successfully with the test runner script
-3. Ensure no tests are skipped due to resolvable environment issues
-4. Ensure commit-related tests (tests modified by milestone commits) are collected AND run (not skipped)
-5. Generate a skip analysis report documenting remaining skips
-
-Generate a complete, buildable Dockerfile that supports dual-state testing.
-
-**IMPORTANT**: You are building on top of a pre-configured BASE IMAGE that already has:
-- Correct Rust toolchain version (rustc, cargo, rustup)
-- All system dependencies installed (OpenSSL, pkg-config, etc.)
-- Cargo dependencies cached (via `cargo fetch`)
-- Environment paths configured (CARGO_HOME, RUSTUP_HOME, PATH)
-- Repository cloned to /testbed
-
-**IMPORTANT**: The local testbed (/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed) already contains pre-created milestone tags:
-- `milestone-milestone_G05_be6e868-start` (START state tag)
-- `milestone-milestone_G05_be6e868-end` (END state tag)
-- **DO NOT create these tags in Dockerfile** - they are already included when you `COPY . /testbed/`
-- Simply use `git checkout milestone-milestone_G05_be6e868-start` or `git checkout milestone-milestone_G05_be6e868-end` to switch states
-
-Your task is to handle **git state management and compatibility patches** only.
-
----
-
-## ⚠️ DOCKERFILE VERIFICATION CHECKLIST (CRITICAL)
-
-Before finalizing your Dockerfile, verify ALL of the following constraints:
-
-- [ ] **No Source Code Modification**: Dockerfile must not modify source code logic
-- [ ] **No Test Logic Modification**: Dockerfile must not modify test code logic
-- [ ] **No File Deletion**: Dockerfile must not delete test files or any other files
-- [ ] **No Git Checkout to Fix Errors**: Cannot use `git checkout` to revert a file to a previous state to resolve compilation errors
-
-- [ ] **Compilation Error Handling**: If compilation problems occur, follow the minimal fix principle below
-
-### Minimal Fix Principle (Compilation Errors)
-
-```
-  Compilation Error Found
-      │
-      ├─ Locate the exact error position (file:line)
-      │
-      ├─ Error Type Classification:
-      │
-      ├─ Missing type/trait/function/module
-      │   └─→ Use #[cfg(feature = "...")] to conditionally compile
-      │   └─→ Or comment out the ENTIRE function/test containing the error
-      │
-      ├─ Trait implementation mismatch
-      │   └─→ Comment out the ENTIRE impl block or function
-      │
-      ├─ Lifetime/borrow checker errors
-      │   └─→ Comment out the ENTIRE function containing the error
-      │
-      └─ Feature flag issues
-          └─→ Fix via Cargo.toml features or environment variables (NOT code changes)
-```
-
-**Core Principles:**
-1. **NEVER skip/exclude entire crates or modules** - only comment out specific functions/tests
-2. **Comment out ENTIRE functions (not single lines)** - maintain code logic integrity
-3. **Preserve ALL tests that can compile normally** - maximize test coverage
-4. **Feature flag issues → fix via Cargo.toml or ENV** - not by modifying code
-
-**Specific Rules for Rust:**
-- For `Cargo.toml`: Can modify `[features]` section or comment out individual dependency lines
-- For test code: Comment out the **entire test function** (including `#[test]` attribute), not individual lines
-- For helper functions used by tests: Comment out the **entire function** if it causes compilation errors
-- **NEVER comment out an entire file** just because one function has compilation errors
-- **NEVER exclude an entire crate/module** just because one function has compilation errors
-
----
-
-### Inputs
-
-Milestone ID: milestone_G05_be6e868
-Milestone Commits: ["5ce9c38", "be6e868", "46be984", "d1a8249", "1f68415"] (list of commit SHAs included in this milestone)
-Commit Changed Tests Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/commit_level/patched_tests (directory containing per-commit test changes)
-Start Tag: milestone-milestone_G05_be6e868-start (earlier git state - may have missing features)
-End Tag: milestone-milestone_G05_be6e868-end (later git state - has all features)
-Repository Path: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed (source repository on host, used as build context)
-Source Directories: ["src/", "crates/"] (directories containing source code)
-Test Directory: test (directory containing tests, default: "tests/")
-Base Image: nushell_nushell_0.106.0_0.108.0/base:latest (pre-configured image with all dependencies)
-Base Image Dockerfile: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/base/dockerfiles/Dockerfile (Dockerfile used to build the base image)
-Test Runner Script: harness.test_runner.run_milestone_tests (script to run milestone tests)
-Test Results Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results (where test results are saved)
-Work Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 (harness workspace directory for this run)
-
-### Expected Outputs
-
-1. **Dockerfile**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G05_be6e868/Dockerfile
-   - Build successfully on top of nushell_nushell_0.106.0_0.108.0/base:latest
-   - Support both START state (milestone-milestone_G05_be6e868-start) and END state (milestone-milestone_G05_be6e868-end)
-   - Configure environment for both states; if conflicts exist, prioritize END state
-   - Default to START state when container starts
-
-2. **Test Config**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G05_be6e868/test_config.json
-   - Configure test runner to run tests as comprehensively as possible
-   - Include all test modes the repository supports (unit tests, integration tests, doc tests)
-   - Goal: maximize test coverage and collect complete test results
-
-3. **Skip Analysis Report**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G05_be6e868/attempt_1/skip_analysis.md
-   - Analysis of all skipped/ignored tests based on test results
-   - Classification by skip reason (resolvable vs acceptable)
-   - Confirmation that no environment-related skips remain
-
----
-
-## RUST TEST COMMANDS
-
-### Cargo Test Commands
-
-```bash
-# Compile tests without running (test collection)
-cargo test --no-run
-
-# Compile tests for all targets (lib, bins, tests, examples, benches)
-cargo test --no-run --all-targets
-
-# Run all tests
-cargo test
-
-# Run tests with specific options
-cargo test --no-fail-fast -- --test-threads={workers}
-
-# Run tests with verbose output
-cargo test -- --nocapture
-
-# Run only unit tests (in src/)
-cargo test --lib
-
-# Run only integration tests (in tests/)
-cargo test --test '*'
-
-# Run tests for a specific package in a workspace
-cargo test -p package_name
-
-# Run tests for all packages in a workspace
-cargo test --workspace
-
-# Run tests with all features enabled
-cargo test --all-features
-
-# Run tests with specific features
-cargo test --features "feature1 feature2"
-
-# Run tests without default features
-cargo test --no-default-features
-
-# Run doc tests only
-cargo test --doc
-
-# List all tests without running
-cargo test -- --list
-
-# Run ignored tests
-cargo test -- --ignored
-
-# Run both normal and ignored tests
-cargo test -- --include-ignored
-```
-
-### Test Output Format
-
-Cargo test output follows this format:
-```
-running X tests
-test module::test_name ... ok
-test module::another_test ... FAILED
-test module::ignored_test ... ignored
-test module::skipped_test ... ignored, reason: "requires feature X"
-
-test result: FAILED. X passed; Y failed; Z ignored; 0 measured; 0 filtered out
-```
-
----
-
-## CRITICAL WORKFLOW (FOLLOW THIS ORDER)
-
-⚠️ **You MUST follow this exact workflow sequence:**
-
-```
-PHASE 0: Analyze Rust Project Structure
-    └── Check Cargo.toml → Identify workspace/crates → Determine features → List test targets
-
-PHASE 1: Write Initial Dockerfile & Test END State
-    └── Build minimal image → Test compilation for END state → Verify success
-
-PHASE 2: Test START State & Apply Minimal Patches (if needed)
-    └── Test START compilation → Apply patches if needed → Verify both states pass
-
-PHASE 2.5: Generate test_config.json
-    └── Create test configuration file required by test runner
-
-PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-    └── Run {test_runner_script} → Analyze ignored tests → Identify environment issues
-
-PHASE 4: Fix Environment Issues (iterate until resolved)
-    └── Update Dockerfile → Re-run tests → Verify issues are resolved
-
-PHASE 4.5: Validate Commit-Related Tests
-    └── Verify tests modified by milestone commits are collected AND not ignored
-
-PHASE 5: Finalize & Generate Skip Analysis
-    └── Set default state to START → Create skip_analysis.md → Clean up
-```
-
----
-
-### PHASE 0: Analyze Rust Project Structure
-**Understand the Rust project before proceeding**
-
-1. **Check project type (single crate vs workspace):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat Cargo.toml | head -30"
-   ```
-
-   **Single crate indicators:**
-   ```toml
-   [package]
-   name = "my_crate"
-   version = "0.1.0"
-   ```
-
-   **Workspace indicators:**
-   ```toml
-   [workspace]
-   members = [
-       "crate1",
-       "crate2",
-   ]
-   ```
-
-2. **List all crates in workspace (if applicable):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cargo metadata --no-deps --format-version 1 | jq '.packages[].name'"
-   ```
-
-3. **Check available features:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-   ```
-
-4. **Identify test targets:**
-
-   ```bash
-   # Check for integration tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la tests/ 2>/dev/null"
-
-   # Check for unit tests in src/
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '#\[test\]' src/ | head -20"
-
-   # Check for doc tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '```rust' src/ | head -10"
-
-   # Check for benchmark tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la benches/ 2>/dev/null"
-   ```
-
-5. **Check Rust toolchain requirements:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat rust-toolchain.toml rust-toolchain 2>/dev/null"
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "rustc --version && cargo --version"
-   ```
-
-6. **Record your analysis:**
-
-   ```
-   PROJECT TYPE: <single_crate|workspace>
-   WORKSPACE MEMBERS: <list of crate names if workspace>
-   AVAILABLE FEATURES: <list of features>
-   TEST TARGETS: <lib|tests|examples|benches|doc>
-   RUST TOOLCHAIN: <stable|nightly|specific version>
-   ```
-
-⚠️ **DO NOT PROCEED to Phase 1 until you understand the project structure!**
-
-### IMPORTANT: Building on Base Image
-
-Since you are building on top of `nushell_nushell_0.106.0_0.108.0/base:latest`, you do NOT need to:
-- Install Rust toolchain
-- Install system dependencies
-- Run `cargo fetch` or `cargo build`
-- Configure environment paths
-
-Your Dockerfile only needs to:
-1. Checkout to the correct git states
-2. Apply minimal patches if START state has compilation issues
-
-**Temp image name**: `test-milestone-milestone_G05_be6e868-temp` (unique for this milestone)
-
-**CRITICAL RULES:**
-- ❌ **NEVER modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository
-- ✅ **Use a working copy for exploration** (create with `cp -r` if needed)
-- ✅ **Build using**: `docker build -t test-milestone-milestone_G05_be6e868-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-- ✅ **Clean up test images when done**: `docker rmi test-milestone-milestone_G05_be6e868-temp`
-
----
-
-### PHASE 1: Write Initial Dockerfile & Test END State
-**Start with a minimal Dockerfile based on the base image**
-
-1. **Write the initial Dockerfile:**
-
-   ```dockerfile
-   # Build on pre-configured base image
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Set umask to ensure files created in container are world-writable
-   # This prevents permission issues when test results are written to mounted volumes
-   RUN echo 'umask 000' >> /etc/bash.bashrc && \
-       echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-       chmod +x /entrypoint.sh
-   ENTRYPOINT ["/entrypoint.sh"]
-   CMD ["bash"]
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Checkout to END state (all features available)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-end
-   ```
-
-2. **Build and test END state compilation:**
-
-   ```bash
-   docker build -t test-milestone-milestone_G05_be6e868-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-   ```
-
-   Then test compilation:
-
-   ```bash
-   # For single crate
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && cargo test --no-run"
-
-   # For workspace
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && cargo test --workspace --no-run"
-
-   # With all features
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && cargo test --all-features --no-run"
-   ```
-
-3. **SUCCESS CRITERIA for END state:**
-   - Exit code 0
-   - Output shows "Compiling" and "Finished" messages
-   - NO compilation errors
-   - Test binaries are generated
-
-   ⚠️ **DO NOT PROCEED to Phase 2 until END state compiles!**
-
----
-
-### PHASE 2: Test START State & Apply Minimal Patches (if needed)
-**Handle the earlier codebase state which may lack features**
-
-1. **Test START state compilation:**
-
-   ```bash
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && git checkout milestone-milestone_G05_be6e868-start && cargo test --no-run"
-   ```
-
-2. **Handle results:**
-
-   **Case A: Compilation succeeds immediately**
-   ✅ Both states work! Proceed to PHASE 2.5.
-
-   **Case B: Compilation fails**
-   Apply Rust-specific minimal patches. See "RUST-SPECIFIC PATCHING" section.
-
-   ⚠️ **RUST COMPILATION**: Like Java, Rust requires ALL code to compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-3. **VALIDATION - Both states MUST compile:**
-   ```bash
-   docker build -t test-milestone-milestone_G05_be6e868-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-   # Test END state
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && git checkout milestone-milestone_G05_be6e868-end && cargo test --no-run"
-
-   # Test START state
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && git checkout milestone-milestone_G05_be6e868-start && cargo test --no-run"
-   ```
-
----
-
-### PHASE 2.5: Generate test_config.json
-**Create test configuration file required by test runner**
-
-The test_config.json defines how the test runner should execute tests.
-
-**Format:**
-```json
-[
-  {
-    "name": "config_name",
-    "test_states": ["start", "end"],
-    "test_cmd": "test command with placeholders",
-    "description": "What this configuration tests"
-  }
-]
-```
-
-**Available placeholders:** `{workers}`, `{timeout}`, `{output_file}`
-
-**Basic Example (Single Crate):**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests"
-  }
-]
-```
-
-**Workspace Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --workspace --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests"
-  }
-]
-```
-
-**With Features Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --all-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests with all features"
-  },
-  {
-    "name": "no_default_features",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-default-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Tests without default features"
-  }
-]
-```
-
-**Multiple Test Targets Example:**
-```json
-[
-  {
-    "name": "unit",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --lib --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Unit tests only"
-  },
-  {
-    "name": "integration",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --test '*' --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Integration tests only"
-  },
-  {
-    "name": "doc",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --doc --no-fail-fast 2>&1 | tee /output/{output_file}",
-    "description": "Doc tests only"
-  }
-]
-```
-
-**Guidelines:**
-1. **Always include "default" configuration** that runs all tests
-2. **Discover special test modes:**
-
-   ```bash
-   # Check for feature flags
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-
-   # Check for test-specific features
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && grep -E 'test-|testing' Cargo.toml"
-
-   # Check for conditional compilation in tests
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && grep -r '#\[cfg(test)\]' src/ | head -10"
-
-   # Check for ignored tests that might need special flags
-   docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && grep -r '#\[ignore\]' . | head -20"
-   ```
-
----
-
-### PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-**Run full tests and identify environment-related issues**
-
-1. **Run tests using the test runner script:**
-
-   ```bash
-   python -m harness.test_runner.run_milestone_tests \
-     --milestone-id milestone_G05_be6e868 \
-     --image-name test-milestone-milestone_G05_be6e868-temp \
-     --output-dir /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results \
-     --language rust \
-     --test-framework cargo \
-     --max-retries 1
-   ```
-
-2. **Analyze test results:**
-
-   After tests complete, examine the output log for ignored tests:
-
-   ```bash
-   # Find ignored tests
-   grep "ignored" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G05_be6e868/attempt_1/end_default.log
-
-   # Find failed tests
-   grep "FAILED" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G05_be6e868/attempt_1/end_default.log
-   ```
-
-3. **Classification of Rust test skip/ignore reasons:**
-
-   | Pattern | Classification | Action |
-   |---------|----------------|--------|
-   | `#[ignore]` without reason | Review | Check if intentional |
-   | `#[ignore = "requires X"]` | Depends | Check if X is environment-related |
-   | `#[ignore = "flaky"]` | Acceptable | Intentionally ignored |
-   | `#[ignore = "slow"]` | Acceptable | Run with `--include-ignored` if needed |
-   | `#[cfg(feature = "X")]` not enabled | Resolvable | Enable feature in test_config.json |
-   | Missing system library | Resolvable | Install in Dockerfile |
-   | Network-dependent test | Acceptable | Requires external resources |
-
-4. **Common Rust environment issues:**
-
-   | Error Pattern | Cause | Solution |
-   |---------------|-------|----------|
-   | `error: could not find native static library` | Missing C library | `RUN apt-get install libXXX-dev` |
-   | `error: linking with cc failed` | Missing linker deps | Install build-essential |
-   | `RUSTFLAGS` related | Build flags issue | Set `ENV RUSTFLAGS="..."` |
-   | `openssl` errors | Missing OpenSSL | Install `libssl-dev` |
-   | `pkg-config` errors | Missing pkg-config | Install `pkg-config` |
-
-5. **If resolvable environment issues found → Proceed to PHASE 4**
-   **If no resolvable issues → Proceed to PHASE 4.5**
-
----
-
-### PHASE 4: Fix Environment Issues
-**Resolve environment-related issues by updating Dockerfile**
-
-**Common fixes for Rust projects:**
-
-```dockerfile
-# Install missing system libraries
-RUN apt-get update && apt-get install -y \
-    libssl-dev \
-    pkg-config \
-    libclang-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-# Set environment variables
-ENV RUST_BACKTRACE=1
-ENV CARGO_NET_GIT_FETCH_WITH_CLI=true
-
-# Enable specific features by default
-ENV CARGO_FEATURE_FLAGS="--all-features"
-
-# Fix OpenSSL issues
-ENV OPENSSL_DIR=/usr
-ENV OPENSSL_LIB_DIR=/usr/lib/x86_64-linux-gnu
-ENV OPENSSL_INCLUDE_DIR=/usr/include
-
-# Fetch dependencies again after changes
-RUN cd /testbed && cargo fetch
-```
-
-**Iteration loop:**
-
-1. Update Dockerfile with fix
-2. Rebuild: `docker build -t test-milestone-milestone_G05_be6e868-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-3. Re-run tests with test runner script
-4. Check if issue is resolved by comparing results
-5. Repeat until no resolvable issues remain
-
----
-
-### PHASE 4.5: Validate Commit-Related Tests
-**Ensure tests modified by milestone commits are collected AND not ignored**
-
-1. **Run the collect_milestone_patched_tests.py script:**
-
-   ```bash
-   python -m harness.prepare_images.collect_milestone_patched_tests \
-     /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 \
-     --repo /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed \
-     --milestone milestone_G05_be6e868
-   ```
-
-   This script:
-   - Extracts symbol changes (added/modified/deleted tests) from each commit
-   - Aggregates patched tests at the milestone level
-   - Matches patched test IDs to actual test results (nodeids)
-   - Generates a report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_G05_be6e868.json`
-
-2. **Check the output JSON file:**
-
-   The output format is:
-   ```json
-   {
-     "milestone_id": "milestone_G05_be6e868",
-     "commits": ["abc1234", "def5678"],
-     "test_ids": {
-       "added": [...],      // Tests added by commits
-       "modified": [...],   // Tests modified by commits
-       "deleted": [...],    // Tests deleted by commits
-       "effective": [...]   // Effective tests = (added ∪ modified) - deleted
-     },
-     "collected": {
-       "patched_in_results": [...],      // ✅ Patched tests found in test results
-       "patched_not_in_results": [],     // ⚠️ MUST BE EMPTY!
-       "test_id_to_nodeid": {...},       // Mapping from test_id to nodeid
-       "status": {
-         "start": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []},
-         "end": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []}
-       },
-       "transitions": {
-         "fixed": [],        // start failed/error -> end passed
-         "broken": [],       // start passed -> end failed/error
-         "still_passing": [],
-         "still_failing": [],
-         "other": []
-       }
-     },
-     "summary": {...}
-   }
-   ```
-
-3. **⚠️ CRITICAL VALIDATION: `collected.patched_not_in_results` MUST be empty!**
-
-   This field lists patched tests that were NOT found in test results. If not empty, it means:
-   - Some patched tests failed to compile (possibly commented out incorrectly)
-   - Some patched tests were excluded from test collection
-   - The test_id to nodeid matching failed
-
-   **How to verify:**
-   ```bash
-   # Check if patched_not_in_results is empty
-   cat /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_G05_be6e868.json | jq '.collected.patched_not_in_results'
-   # Expected output: []
-   ```
-
-4. **If `patched_not_in_results` is NOT empty:**
-   - Identify which tests are missing from results
-   - Check if those tests were incorrectly commented out or excluded
-   - Return to PHASE 4 to fix environment issues
-   - Re-run tests and re-validate until `patched_not_in_results` is empty
-
-5. **Also verify no commit-related tests are ignored:**
-   - Check `collected.status.end.skipped` - patched tests should not be ignored
-   - If ignored due to environment issues, return to PHASE 4 to fix
-
----
-
-### PHASE 5: Finalize Dockerfile & Generate Skip Analysis
-**Set default state to START, create skip analysis report, and clean up**
-
-1. **Ensure Dockerfile sets default state to START:**
-
-   ```dockerfile
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Environment fixes (if any)
-   # RUN apt-get update && apt-get install -y ...
-   # ENV RUST_BACKTRACE=1
-
-   # Checkout to END state (for any patching if needed)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-end
-
-   # [If patches needed, add them here]
-
-   # Set default git state to START
-   RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start
-   ```
-
-2. **Final validation**
-
-3. **Generate skip analysis report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G05_be6e868/attempt_1/skip_analysis.md`**
-
-4. **Clean up:**
-   ```bash
-   docker rmi test-milestone-milestone_G05_be6e868-temp
-   ```
-
----
-
-## RUST-SPECIFIC PATCHING
-
-### How to Apply Patches in Dockerfile
-
-⚠️ **Apply patches using patch files or sed commands in the Dockerfile. DO NOT modify /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed!**
-
-⚠️ **CRITICAL**: After applying patches, you MUST commit the changes and move the tag to preserve patches across git checkouts. Without this step, patches will be lost when switching between START and END states!
-
-⚠️ **NEVER DELETE FILES**: When applying patches, you must NEVER delete any files (e.g., using `rm`, `git rm`, or similar commands). Only modify file contents. Deleting files can break test discovery and cause unexpected issues.
-
-### Rust Compilation Error Handling
-
-**CRITICAL**: Rust is a compiled language. Unlike Python/JavaScript, ALL code must compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-**Goal**: Comment out the minimal amount of code that causes compilation errors, so that the maximum number of tests can compile and run.
-
-### Patching Strategies for Rust
-
-#### Strategy 1: Use `#[cfg]` Attributes (Preferred)
-
-The best way to handle compilation errors in Rust is to use conditional compilation:
-
-```rust
-// Original code that fails in START state:
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();  // This doesn't exist in START state
-    assert!(result.is_ok());
-}
-
-// Patched version using cfg:
-#[cfg(feature = "new_feature")]
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();
-    assert!(result.is_ok());
-}
-```
-
-**Dockerfile example:**
-```dockerfile
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start && \
-    # Add cfg attribute before test function
-    sed -i 's/#\[test\]\nfn test_new_feature/#[cfg(feature = "env_patch")]\n#[test]\nfn test_new_feature/' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add cfg guard for test_new_feature" && \
-    git tag -f milestone-milestone_G05_be6e868-start HEAD
-```
-
-#### Strategy 2: Comment Out Test Functions
-
-When a test function uses APIs that don't exist in START state:
-
-```dockerfile
-# Comment out a specific test function (from line 45 to line 55)
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start && \
-    sed -i '45,55 s/^/\/\/ [ENV-PATCH] /' src/tests.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_new_feature for START state" && \
-    git tag -f milestone-milestone_G05_be6e868-start HEAD
-```
-
-**Better approach using markers:**
-```dockerfile
-# Find and comment out specific test
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start && \
-    # Add /* before #[test] and */ after the closing brace
-    sed -i '/#\[test\]/,/^}$/{
-        /fn test_problematic/,/^}$/ {
-            s/^/\/\/ [ENV-PATCH] /
-        }
-    }' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_problematic" && \
-    git tag -f milestone-milestone_G05_be6e868-start HEAD
-```
-
-#### Strategy 3: Comment Out Entire Module (Last Resort)
-
-Only when module-level code causes compilation errors:
-
-```dockerfile
-# Comment out entire test module
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start && \
-    sed -i '/^mod tests {/,/^}/ s/^/\/\/ [ENV-PATCH] /' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests module" && \
-    git tag -f milestone-milestone_G05_be6e868-start HEAD
-```
-
-#### Strategy 4: Modify Cargo.toml Features
-
-If the issue is feature-related:
-
-```dockerfile
-# Add a feature flag for conditional compilation
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start && \
-    sed -i '/\[features\]/a env_patch = []' Cargo.toml && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add env_patch feature flag" && \
-    git tag -f milestone-milestone_G05_be6e868-start HEAD
-```
-
-### Common Rust Compilation Error Patterns
-
-| Error Pattern | Cause | Solution |
-|---------------|-------|----------|
-| `cannot find function X in this scope` | Function doesn't exist in START | Comment out test using it |
-| `cannot find type X in this scope` | Type doesn't exist in START | Comment out test using it |
-| `trait X is not implemented for Y` | Trait impl missing in START | Comment out test using it |
-| `mismatched types` | API signature changed | Comment out test using it |
-| `unresolved import X::Y` | Module/item doesn't exist | Comment out import and tests |
-| `no method named X found` | Method doesn't exist in START | Comment out test using it |
-| `struct X has no field Y` | Field doesn't exist in START | Comment out test using it |
-| `lifetime mismatch` | Lifetime requirements changed | Comment out test using it |
-
-### Example: Full Patching Workflow
-
-```dockerfile
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Checkout to START state and apply patches
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start && \
-    # Patch 1: Comment out test that uses new API (lines 120-135)
-    sed -i '120,135 s/^/\/\/ [ENV-PATCH] /' src/api/tests.rs && \
-    # Patch 2: Comment out test that uses new struct field (lines 45-52)
-    sed -i '45,52 s/^/\/\/ [ENV-PATCH] /' tests/integration_test.rs && \
-    # Commit patches and move tag
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests using APIs not in START state" && \
-    git tag -f milestone-milestone_G05_be6e868-start HEAD
-
-# Verify END state still compiles
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-end && cargo test --no-run
-
-# Set default to START
-RUN cd /testbed && git checkout milestone-milestone_G05_be6e868-start
-```
-
-### Verify Patches Persist
-
-```bash
-docker build -t test-milestone-milestone_G05_be6e868-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-# Test START state (verify patches applied)
-docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && cargo test --no-run"
-
-# Test END state (verify patches persist after checkout)
-docker run --rm test-milestone-milestone_G05_be6e868-temp bash -c "cd /testbed && git checkout milestone-milestone_G05_be6e868-end && cargo test --no-run"
-```
-
----
-
-## FINAL CHECKLIST
-
-### Before Completing Your Work
-Ensure you have:
-- [ ] **PHASE 0 completed**: Analyzed Rust project structure (single crate vs workspace, features, test targets)
-- [ ] Dockerfile based on `FROM nushell_nushell_0.106.0_0.108.0/base:latest`
-- [ ] **Testbed replaced**: `RUN rm -rf /testbed` + `COPY . /testbed/` included in Dockerfile
-- [ ] Both START and END states compile successfully (`cargo test --no-run`)
-- [ ] Minimal patches only (if needed)
-- [ ] No artificial skips
-- [ ] **Patches committed and tags moved** (if patches applied):
-  - [ ] Used `git add -A && git commit` after applying patches
-  - [ ] Used `git tag -f <TAG> HEAD` to move tag to patched commit
-  - [ ] Verified patches persist across `git checkout` (test switching between states)
-- [ ] **Full tests run** using test runner script with `--language rust --test-framework cargo`
-- [ ] **No resolvable environment-related issues** remaining
-- [ ] **Commit-related tests validated** using `collect_milestone_patched_tests.py`:
-  - [ ] Ran: `python -m harness.prepare_images.collect_milestone_patched_tests /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 --milestone milestone_G05_be6e868`
-  - [ ] **`collected.patched_not_in_results` is EMPTY** (all patched tests found in results)
-  - [ ] No patched tests in `collected.status.end.skipped` (no environment-related ignores)
-- [ ] **test_config.json** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_G05_be6e868/test_config.json` with correct cargo test command
-- [ ] **Skip analysis report** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_G05_be6e868/attempt_1/skip_analysis.md`
-- [ ] Default state is START
-- [ ] Cleaned up: `docker rmi test-milestone-milestone_G05_be6e868-temp`
-
----
-
-## COMMON PITFALLS TO AVOID
-
-❌ **Apply patches without committing and moving tags** - patches will be lost on `git checkout`!
-❌ **Forget to verify patches persist** - always test switching between START and END states after patching
-❌ **Modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository, use Dockerfile commands instead
-❌ **Skip PHASE 0** - understanding Rust project structure is essential
-❌ **Proceed to next phase before current phase compiles** - validate each phase before moving on
-❌ **Comment out entire files/crates** - only comment out specific functions/tests
-❌ **Forget workspace flag** - use `cargo test --workspace` for workspace projects
-❌ **Ignore feature flags** - check if tests require specific features to be enabled
-
-✅ **Always commit patches and move tags** (`git add -A && git commit && git tag -f <TAG> HEAD`)
-✅ **Test both states after applying patches** to ensure patches persist across checkout
-✅ **Document patched code** in Dockerfile comments (which functions, why)
-✅ **Use `[ENV-PATCH]` prefix** in commit messages and comments for tracking
-✅ **Use conditional compilation** (`#[cfg]`) when possible instead of commenting out
-✅ **Check all feature combinations** if the project uses feature flags

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G05_be6e868.bak/skip_analysis.md

@@ -1,81 +0,0 @@
-# Skip Analysis for milestone_G05_be6e868
-
-## Summary
-
-| Category | Count |
-|----------|-------|
-| Total Tests | 62 |
-| Passed | 61 |
-| Failed | 1 |
-| Ignored | 0 |
-
-## Test Results
-
-Both START and END states produce identical test results.
-
-### Failing Tests
-
-#### 1. `hover::hover_tests::hover_on_external_command`
-
-**Location:** `crates/nu-lsp/src/hover.rs:358`
-
-**Failure Message:**
-```
-assertion failed: hover_text.contains("SLEEP")
-```
-
-**Root Cause:** Environment-dependent test
-
-**Analysis:**
-This test verifies that hovering over an external command (like `sleep`) in the LSP shows documentation from the system's man pages. The test specifically checks that the hover text contains "SLEEP" (the man page header for the sleep command).
-
-The test fails because:
-1. The Docker container is a minimal build environment without man pages installed
-2. The `man` command is either not available or man-db package is not installed
-3. Even if `man` is available, the man pages for coreutils (including `sleep`) are not included
-
-**Code Reference:**
-```rust
-#[cfg(not(windows))]
-assert!(hover_text.contains("SLEEP"));
-#[cfg(windows)]
-assert!(hover_text.contains("Start-Sleep"));
-```
-
-**Skip Recommendation:** Yes - this is an acceptable skip
-
-**Justification:**
-- This test is testing OS-level integration (man page availability), not the core LSP functionality
-- The actual hover functionality works correctly; it's the content being hovered over that depends on the environment
-- Installing man pages in the container would add ~100MB+ to the image size for a single test
-- The test passes in development environments where man pages are typically available
-- This test failure is consistent between START and END states, meaning it does not affect milestone validation
-
-## Ignored Tests
-
-None.
-
-## Recommendations
-
-1. **No action required** - The single failing test is environment-dependent and does not indicate any issues with the milestone changes
-2. The test should be considered as "expected to fail" in CI/Docker environments without man pages
-3. All 61 passing tests adequately cover the nu-lsp functionality being tested in this milestone
-
-## Milestone Commits Covered
-
-- `5ce9c38` - Changes to nu-lsp
-- `be6e868` - Changes to nu-lsp
-- `46be984` - Changes to nu-lsp
-- `d1a8249` - Changes to nu-lsp
-- `1f68415` - Changes to nu-lsp
-
-## Test Configuration
-
-```json
-{
-  "name": "default",
-  "test_states": ["start", "end"],
-  "test_cmd": "cargo test --profile ci -p nu-lsp --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-  "description": "All nu-lsp tests"
-}
-```

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_G05_be6e868.bak/test_config.json

@@ -1,12 +0,0 @@
-[
-  {
-    "name": "default",
-    "test_states": [
-      "start",
-      "end"
-    ],
-    "test_cmd": "cargo test --profile ci --workspace --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests excluding plugins",
-    "framework": "cargo"
-  }
-]

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_M08_docs.bak/Dockerfile

@@ -1,105 +0,0 @@
-# Build on pre-configured base image for nushell
-# Base image already has Rust 1.86.0, dependencies, and cargo build cache
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Remove the original /testbed from base image and copy local testbed
-# NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-RUN rm -rf /testbed
-COPY . /testbed/
-COPY --from=patches fix_reedline_api.py /testbed/fix_reedline_api.py
-
-# Ensure git knows this directory is safe and configure git identity for patches
-RUN git config --global --add safe.directory /testbed && \
-    git config --global user.email "env-patch@test.local" && \
-    git config --global user.name "ENV-PATCH"
-
-# Copy fix script to /tmp before git operations (so it won't be affected by checkouts)
-RUN cp /testbed/fix_reedline_api.py /tmp/fix_reedline_api.py
-
-# [ENV-PATCH] Fix multiple environment issues:
-# 1. Version mismatch: root Cargo.toml requires ^0.107.1 but crates have 0.106.x
-#    Solution: Normalize ALL version numbers (0.106.x and 0.107.x) to 0.106.0
-# 2. ureq version mismatch: Cargo.toml has ureq 3.x but code uses ureq 2.x API
-# 3. Rust version: milestone requires 1.87.0 but base image has 1.86.0
-# 4. Test compilation errors due to API/typo issues:
-#    - PipelineData::value -> PipelineData::Value (case typo in 2 files)
-#    - NuOpts experimental field doesn't exist
-#    - completion -> custom_completion field rename
-# We fix by normalizing all crate versions to 0.106.0, downgrading ureq to 2.12, and fixing/commenting broken tests
-
-# Fix END state
-RUN cd /testbed && git checkout -f milestone-milestone_M08_docs-end && \
-    # Normalize ALL nu-* crate versions to 0.106.0 (handles both 0.106.x and 0.107.x)
-    find . -name "Cargo.toml" -exec sed -i 's/"0\.10[67]\.[0-9]*"/"0.106.0"/g' {} \; && \
-    # Also fix version declarations without quotes (version = 0.106.x or ^0.107.x patterns)
-    find . -name "Cargo.toml" -exec sed -i 's/= "\^0\.10[67]\.[0-9]*"/= "0.106.0"/g' {} \; && \
-    # Downgrade ureq from 3.x to 2.x (code was written for 2.x API)
-    sed -i 's/ureq = { version = "=3.0.12"/ureq = { version = "2.12"/g' Cargo.toml && \
-    # Downgrade rust-version to 1.86.0 to match base image toolchain
-    sed -i 's/rust-version = "1.87.0"/rust-version = "1.86.0"/g' Cargo.toml && \
-    # Comment out test with PipelineData::value typo (lines 143-153 in custom_value/mod.rs)
-    sed -i '143,153 s/^/\/\/ [ENV-PATCH] /' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    # Fix PipelineData::value -> PipelineData::Value typo (case fix, not logic change)
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Comment out test with NuOpts experimental field (lines 739-758 in external.rs)
-    sed -i '739,758 s/^/\/\/ [ENV-PATCH] /' tests/shell/pipeline/commands/external.rs && \
-    # Fix completion -> custom_completion field rename (field name change, not logic change)
-    sed -i 's/completion: None,/custom_completion: None,/g' crates/nu-protocol/tests/test_signature.rs && \
-    # [ENV-PATCH] Pin interprocess to 2.2.2 to match base image (newer versions change ListenerNonblockingMode API)
-    sed -i 's/^interprocess = "2\.2\.0"$/interprocess = "=2.2.2"/' Cargo.toml && \
-    # Update Cargo.lock: only update workspace crates (version normalization) and changed deps
-    # DO NOT delete Cargo.lock — fresh resolution pulls crates needing Rust 1.88+ (comfy-table, ar_archive_writer)
-    cargo update --workspace && \
-    # Fix reedline API compatibility
-    python3 /tmp/fix_reedline_api.py && \
-    # Fix let chains syntax in parser.rs (not stable in Rust 1.86)
-    sed -i '1253,1259c\            if let SyntaxShape::Keyword(ref keyword, ..) = positional.shape {\n                if keyword == b"catch" {\n                    if let [nu_protocol::CompileError::NotInALoop { .. }] =\n                        \&working_set.compile_errors[compile_error_count..]\n                    {\n                        working_set.compile_errors.truncate(compile_error_count);\n                    }\n                }\n            }' crates/nu-parser/src/parser.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version mismatches and test compilation errors" && \
-    git tag -f milestone-milestone_M08_docs-end HEAD
-
-# Fix START state
-RUN cd /testbed && git checkout -f milestone-milestone_M08_docs-start && \
-    # Normalize ALL nu-* crate versions to 0.106.0 (handles both 0.106.x and 0.107.x)
-    find . -name "Cargo.toml" -exec sed -i 's/"0\.10[67]\.[0-9]*"/"0.106.0"/g' {} \; && \
-    # Also fix version declarations without quotes (version = 0.106.x or ^0.107.x patterns)
-    find . -name "Cargo.toml" -exec sed -i 's/= "\^0\.10[67]\.[0-9]*"/= "0.106.0"/g' {} \; && \
-    # Downgrade ureq from 3.x to 2.x (code was written for 2.x API)
-    sed -i 's/ureq = { version = "=3.0.12"/ureq = { version = "2.12"/g' Cargo.toml && \
-    # Downgrade rust-version to 1.86.0 to match base image toolchain
-    sed -i 's/rust-version = "1.87.0"/rust-version = "1.86.0"/g' Cargo.toml && \
-    # Comment out test with PipelineData::value typo (lines 143-153 in custom_value/mod.rs)
-    sed -i '143,153 s/^/\/\/ [ENV-PATCH] /' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    # Fix PipelineData::value -> PipelineData::Value typo (case fix, not logic change)
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Comment out test with NuOpts experimental field (lines 739-758 in external.rs)
-    sed -i '739,758 s/^/\/\/ [ENV-PATCH] /' tests/shell/pipeline/commands/external.rs && \
-    # Fix completion -> custom_completion field rename (field name change, not logic change)
-    sed -i 's/completion: None,/custom_completion: None,/g' crates/nu-protocol/tests/test_signature.rs && \
-    # [ENV-PATCH] Pin interprocess to 2.2.2 to match base image (newer versions change ListenerNonblockingMode API)
-    sed -i 's/^interprocess = "2\.2\.0"$/interprocess = "=2.2.2"/' Cargo.toml && \
-    # Update Cargo.lock: only update workspace crates (version normalization) and changed deps
-    # DO NOT delete Cargo.lock — fresh resolution pulls crates needing Rust 1.88+ (comfy-table, ar_archive_writer)
-    cargo update --workspace && \
-    # Fix reedline API compatibility
-    python3 /tmp/fix_reedline_api.py && \
-    # Fix let chains syntax in parser.rs (not stable in Rust 1.86) - same pattern as END state but different line numbers
-    sed -i '1250,1256c\            if let SyntaxShape::Keyword(ref keyword, ..) = positional.shape {\n                if keyword == b"catch" {\n                    if let [nu_protocol::CompileError::NotInALoop { .. }] =\n                        \&working_set.compile_errors[compile_error_count..]\n                    {\n                        working_set.compile_errors.truncate(compile_error_count);\n                    }\n                }\n            }' crates/nu-parser/src/parser.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version mismatches and test compilation errors" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-
-# Verify END state compiles
-RUN cd /testbed && git checkout -f milestone-milestone_M08_docs-end && \
-    cargo test --no-run --profile ci --workspace --exclude nu_plugin_* -j 4
-
-# Set default git state to START
-RUN cd /testbed && git checkout -f milestone-milestone_M08_docs-start

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_M08_docs.bak/Dockerfile.bak

@@ -1,96 +0,0 @@
-# Build on pre-configured base image for nushell
-# Base image already has Rust 1.86.0, dependencies, and cargo build cache
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Remove the original /testbed from base image and copy local testbed
-# NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Ensure git knows this directory is safe and configure git identity for patches
-RUN git config --global --add safe.directory /testbed && \
-    git config --global user.email "env-patch@test.local" && \
-    git config --global user.name "ENV-PATCH"
-
-# Copy fix script to /tmp before git operations (so it won't be affected by checkouts)
-RUN cp /testbed/fix_reedline_api.py /tmp/fix_reedline_api.py
-
-# [ENV-PATCH] Fix multiple environment issues:
-# 1. Version mismatch: root Cargo.toml requires ^0.107.1 but crates have 0.106.x
-#    Solution: Normalize ALL version numbers (0.106.x and 0.107.x) to 0.106.0
-# 2. ureq version mismatch: Cargo.toml has ureq 3.x but code uses ureq 2.x API
-# 3. Rust version: milestone requires 1.87.0 but base image has 1.86.0
-# 4. Test compilation errors due to API/typo issues:
-#    - PipelineData::value -> PipelineData::Value (case typo in 2 files)
-#    - NuOpts experimental field doesn't exist
-#    - completion -> custom_completion field rename
-# We fix by normalizing all crate versions to 0.106.0, downgrading ureq to 2.12, and fixing/commenting broken tests
-
-# Fix END state
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-end && \
-    # Normalize ALL nu-* crate versions to 0.106.0 (handles both 0.106.x and 0.107.x)
-    find . -name "Cargo.toml" -exec sed -i 's/"0\.10[67]\.[0-9]*"/"0.106.0"/g' {} \; && \
-    # Also fix version declarations without quotes (version = 0.106.x or ^0.107.x patterns)
-    find . -name "Cargo.toml" -exec sed -i 's/= "\^0\.10[67]\.[0-9]*"/= "0.106.0"/g' {} \; && \
-    # Downgrade ureq from 3.x to 2.x (code was written for 2.x API)
-    sed -i 's/ureq = { version = "=3.0.12"/ureq = { version = "2.12"/g' Cargo.toml && \
-    # Downgrade rust-version to 1.86.0 to match base image toolchain
-    sed -i 's/rust-version = "1.87.0"/rust-version = "1.86.0"/g' Cargo.toml && \
-    # Comment out test with PipelineData::value typo (lines 143-153 in custom_value/mod.rs)
-    sed -i '143,153 s/^/\/\/ [ENV-PATCH] /' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    # Fix PipelineData::value -> PipelineData::Value typo (case fix, not logic change)
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Comment out test with NuOpts experimental field (lines 739-758 in external.rs)
-    sed -i '739,758 s/^/\/\/ [ENV-PATCH] /' tests/shell/pipeline/commands/external.rs && \
-    # Fix completion -> custom_completion field rename (field name change, not logic change)
-    sed -i 's/completion: None,/custom_completion: None,/g' crates/nu-protocol/tests/test_signature.rs && \
-    # Remove Cargo.lock to regenerate with correct versions
-    rm -f Cargo.lock && \
-    # Fix reedline API compatibility
-    python3 /tmp/fix_reedline_api.py && \
-    # Fix let chains syntax in parser.rs (not stable in Rust 1.86)
-    sed -i '1253,1259c\            if let SyntaxShape::Keyword(ref keyword, ..) = positional.shape {\n                if keyword == b"catch" {\n                    if let [nu_protocol::CompileError::NotInALoop { .. }] =\n                        \&working_set.compile_errors[compile_error_count..]\n                    {\n                        working_set.compile_errors.truncate(compile_error_count);\n                    }\n                }\n            }' crates/nu-parser/src/parser.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version mismatches and test compilation errors" && \
-    git tag -f milestone-milestone_M08_docs-end HEAD
-
-# Fix START state
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start && \
-    # Normalize ALL nu-* crate versions to 0.106.0 (handles both 0.106.x and 0.107.x)
-    find . -name "Cargo.toml" -exec sed -i 's/"0\.10[67]\.[0-9]*"/"0.106.0"/g' {} \; && \
-    # Also fix version declarations without quotes (version = 0.106.x or ^0.107.x patterns)
-    find . -name "Cargo.toml" -exec sed -i 's/= "\^0\.10[67]\.[0-9]*"/= "0.106.0"/g' {} \; && \
-    # Downgrade ureq from 3.x to 2.x (code was written for 2.x API)
-    sed -i 's/ureq = { version = "=3.0.12"/ureq = { version = "2.12"/g' Cargo.toml && \
-    # Downgrade rust-version to 1.86.0 to match base image toolchain
-    sed -i 's/rust-version = "1.87.0"/rust-version = "1.86.0"/g' Cargo.toml && \
-    # Comment out test with PipelineData::value typo (lines 143-153 in custom_value/mod.rs)
-    sed -i '143,153 s/^/\/\/ [ENV-PATCH] /' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    # Fix PipelineData::value -> PipelineData::Value typo (case fix, not logic change)
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Comment out test with NuOpts experimental field (lines 739-758 in external.rs)
-    sed -i '739,758 s/^/\/\/ [ENV-PATCH] /' tests/shell/pipeline/commands/external.rs && \
-    # Fix completion -> custom_completion field rename (field name change, not logic change)
-    sed -i 's/completion: None,/custom_completion: None,/g' crates/nu-protocol/tests/test_signature.rs && \
-    # Remove Cargo.lock to regenerate with correct versions
-    rm -f Cargo.lock && \
-    # Fix reedline API compatibility
-    python3 /tmp/fix_reedline_api.py && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version mismatches and test compilation errors" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-
-# Verify END state compiles
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-end && \
-    cargo test --no-run --profile ci --workspace --exclude nu_plugin_* -j 4
-
-# Set default git state to START
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_M08_docs.bak/env_patch_script/fix_reedline_api.py

@@ -1,95 +0,0 @@
-#!/usr/bin/env python3
-"""
-Fix reedline API compatibility issues by removing TraversalDirection and with_immediately_accept usage.
-This script properly handles the multi-line code blocks that sed struggles with.
-"""
-
-import re
-import sys
-from pathlib import Path
-
-def fix_reedline_config(file_path):
-    """Remove TraversalDirection import and tab_traversal match expression."""
-    with open(file_path, 'r') as f:
-        content = f.read()
-
-    # Remove TraversalDirection from imports
-    content = re.sub(
-        r',\s*TraversalDirection\s*,',
-        ',',
-        content
-    )
-    content = re.sub(
-        r'TraversalDirection\s*,',
-        '',
-        content
-    )
-
-    # Remove the entire tab_traversal match block (lines 292-306)
-    # Pattern: from "columnar_menu = match extract_value("tab_traversal"..."
-    # to the matching closing brace with Err(_) => columnar_menu,
-    pattern = r'''columnar_menu\s*=\s*match\s+extract_value\("tab_traversal",.*?\{\s*
-\s*Ok\(tab_traversal\)\s*=>\s*match\s+tab_traversal\.coerce_str\(\)\?\.as_ref\(\)\s*\{.*?
-\s*\},\s*
-\s*Err\(_\)\s*=>\s*columnar_menu,\s*
-\s*\};'''
-
-    content = re.sub(pattern, '', content, flags=re.DOTALL)
-
-    with open(file_path, 'w') as f:
-        f.write(content)
-
-    return True
-
-def fix_repl(file_path):
-    """Remove with_immediately_accept method calls."""
-    with open(file_path, 'r') as f:
-        lines = f.readlines()
-
-    new_lines = []
-    i = 0
-
-    while i < len(lines):
-        line = lines[i]
-
-        # Check if this line contains .with_immediately_accept
-        if '.with_immediately_accept(' in line:
-            # Check if the previous non-empty line needs a semicolon
-            if new_lines:
-                # Find the last non-empty, non-comment line
-                for j in range(len(new_lines) - 1, -1, -1):
-                    prev_line = new_lines[j].rstrip()
-                    if prev_line and not prev_line.strip().startswith('//'):
-                        # If it ends with ) but not with ; or }, add a semicolon
-                        if prev_line.endswith(')') and not prev_line.endswith(';') and not prev_line.endswith('}'):
-                            new_lines[j] = prev_line + ';\n'
-                        break
-            i += 1
-            continue
-
-        new_lines.append(line)
-        i += 1
-
-    with open(file_path, 'w') as f:
-        f.writelines(new_lines)
-
-    return True
-
-if __name__ == '__main__':
-    testbed_path = Path('/testbed')
-
-    print("Fixing reedline API compatibility...")
-
-    # Fix reedline_config.rs
-    reedline_config = testbed_path / 'crates/nu-cli/src/reedline_config.rs'
-    if reedline_config.exists():
-        fix_reedline_config(reedline_config)
-        print(f"✓ Fixed {reedline_config}")
-
-    # Fix repl.rs
-    repl_file = testbed_path / 'crates/nu-cli/src/repl.rs'
-    if repl_file.exists():
-        fix_repl(repl_file)
-        print(f"✓ Fixed {repl_file}")
-
-    print("Done!")

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_M08_docs.bak/env_setup_prompt.md

@@ -1,935 +0,0 @@
-You are an expert in Rust software environment configuration. Your task is to configure
-a Docker container so that a given Rust repository can successfully run its test suite
-across TWO different git states (START and END tags).
-
-## RUST TEST FRAMEWORK
-
-| Language | Framework | Test Collect Command | Report Format | **Output File Extension** |
-|----------|-----------|----------------------|---------------|---------------------------|
-| Rust | cargo | `cargo test --no-run` | Console log | **`.log`** |
-
-### Output File Format Reference
-
-When generating `test_config.json`, use the `.log` extension for `{output_file}`:
-
-| Framework | Recommended Extension | Example `{output_file}` |
-|-----------|----------------------|-------------------------|
-| cargo | `.log` | `start_default.log` |
-
-**IMPORTANT**: The test runner (`run_milestone_tests.py`) will automatically use the cargo log parser based on the `--test-framework cargo` argument.
-
-## GOAL
-Configure the environment to:
-1. Make test compilation succeed for BOTH states (START and END)
-2. Run tests successfully with the test runner script
-3. Ensure no tests are skipped due to resolvable environment issues
-4. Ensure commit-related tests (tests modified by milestone commits) are collected AND run (not skipped)
-5. Generate a skip analysis report documenting remaining skips
-
-Generate a complete, buildable Dockerfile that supports dual-state testing.
-
-**IMPORTANT**: You are building on top of a pre-configured BASE IMAGE that already has:
-- Correct Rust toolchain version (rustc, cargo, rustup)
-- All system dependencies installed (OpenSSL, pkg-config, etc.)
-- Cargo dependencies cached (via `cargo fetch`)
-- Environment paths configured (CARGO_HOME, RUSTUP_HOME, PATH)
-- Repository cloned to /testbed
-
-**IMPORTANT**: The local testbed (/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed) already contains pre-created milestone tags:
-- `milestone-milestone_M08_docs-start` (START state tag)
-- `milestone-milestone_M08_docs-end` (END state tag)
-- **DO NOT create these tags in Dockerfile** - they are already included when you `COPY . /testbed/`
-- Simply use `git checkout milestone-milestone_M08_docs-start` or `git checkout milestone-milestone_M08_docs-end` to switch states
-
-Your task is to handle **git state management and compatibility patches** only.
-
----
-
-## ⚠️ DOCKERFILE VERIFICATION CHECKLIST (CRITICAL)
-
-Before finalizing your Dockerfile, verify ALL of the following constraints:
-
-- [ ] **No Source Code Modification**: Dockerfile must not modify source code logic
-- [ ] **No Test Logic Modification**: Dockerfile must not modify test code logic
-- [ ] **No File Deletion**: Dockerfile must not delete test files or any other files
-- [ ] **No Git Checkout to Fix Errors**: Cannot use `git checkout` to revert a file to a previous state to resolve compilation errors
-
-- [ ] **Compilation Error Handling**: If compilation problems occur, follow the minimal fix principle below
-
-### Minimal Fix Principle (Compilation Errors)
-
-```
-  Compilation Error Found
-      │
-      ├─ Locate the exact error position (file:line)
-      │
-      ├─ Error Type Classification:
-      │
-      ├─ Missing type/trait/function/module
-      │   └─→ Use #[cfg(feature = "...")] to conditionally compile
-      │   └─→ Or comment out the ENTIRE function/test containing the error
-      │
-      ├─ Trait implementation mismatch
-      │   └─→ Comment out the ENTIRE impl block or function
-      │
-      ├─ Lifetime/borrow checker errors
-      │   └─→ Comment out the ENTIRE function containing the error
-      │
-      └─ Feature flag issues
-          └─→ Fix via Cargo.toml features or environment variables (NOT code changes)
-```
-
-**Core Principles:**
-1. **NEVER skip/exclude entire crates or modules** - only comment out specific functions/tests
-2. **Comment out ENTIRE functions (not single lines)** - maintain code logic integrity
-3. **Preserve ALL tests that can compile normally** - maximize test coverage
-4. **Feature flag issues → fix via Cargo.toml or ENV** - not by modifying code
-
-**Specific Rules for Rust:**
-- For `Cargo.toml`: Can modify `[features]` section or comment out individual dependency lines
-- For test code: Comment out the **entire test function** (including `#[test]` attribute), not individual lines
-- For helper functions used by tests: Comment out the **entire function** if it causes compilation errors
-- **NEVER comment out an entire file** just because one function has compilation errors
-- **NEVER exclude an entire crate/module** just because one function has compilation errors
-
----
-
-### Inputs
-
-Milestone ID: milestone_M08_docs
-Milestone Commits: ["7cc1a86", "7133a04", "da54ed8", "cd1094c", "e115306", "218e70a"] (list of commit SHAs included in this milestone)
-Commit Changed Tests Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/commit_level/patched_tests (directory containing per-commit test changes)
-Start Tag: milestone-milestone_M08_docs-start (earlier git state - may have missing features)
-End Tag: milestone-milestone_M08_docs-end (later git state - has all features)
-Repository Path: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed (source repository on host, used as build context)
-Source Directories: ["src/", "crates/"] (directories containing source code)
-Test Directory: test (directory containing tests, default: "tests/")
-Base Image: nushell_nushell_0.106.0_0.108.0/base:latest (pre-configured image with all dependencies)
-Base Image Dockerfile: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/base/dockerfiles/Dockerfile (Dockerfile used to build the base image)
-Test Runner Script: harness.test_runner.run_milestone_tests (script to run milestone tests)
-Test Results Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results (where test results are saved)
-Work Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 (harness workspace directory for this run)
-
-### Expected Outputs
-
-1. **Dockerfile**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_M08_docs/Dockerfile
-   - Build successfully on top of nushell_nushell_0.106.0_0.108.0/base:latest
-   - Support both START state (milestone-milestone_M08_docs-start) and END state (milestone-milestone_M08_docs-end)
-   - Configure environment for both states; if conflicts exist, prioritize END state
-   - Default to START state when container starts
-
-2. **Test Config**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_M08_docs/test_config.json
-   - Configure test runner to run tests as comprehensively as possible
-   - Include all test modes the repository supports (unit tests, integration tests, doc tests)
-   - Goal: maximize test coverage and collect complete test results
-
-3. **Skip Analysis Report**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_M08_docs/attempt_1/skip_analysis.md
-   - Analysis of all skipped/ignored tests based on test results
-   - Classification by skip reason (resolvable vs acceptable)
-   - Confirmation that no environment-related skips remain
-
----
-
-## RUST TEST COMMANDS
-
-### Cargo Test Commands
-
-```bash
-# Compile tests without running (test collection)
-cargo test --no-run
-
-# Compile tests for all targets (lib, bins, tests, examples, benches)
-cargo test --no-run --all-targets
-
-# Run all tests
-cargo test
-
-# Run tests with specific options
-cargo test --no-fail-fast -- --test-threads={workers}
-
-# Run tests with verbose output
-cargo test -- --nocapture
-
-# Run only unit tests (in src/)
-cargo test --lib
-
-# Run only integration tests (in tests/)
-cargo test --test '*'
-
-# Run tests for a specific package in a workspace
-cargo test -p package_name
-
-# Run tests for all packages in a workspace
-cargo test --workspace
-
-# Run tests with all features enabled
-cargo test --all-features
-
-# Run tests with specific features
-cargo test --features "feature1 feature2"
-
-# Run tests without default features
-cargo test --no-default-features
-
-# Run doc tests only
-cargo test --doc
-
-# List all tests without running
-cargo test -- --list
-
-# Run ignored tests
-cargo test -- --ignored
-
-# Run both normal and ignored tests
-cargo test -- --include-ignored
-```
-
-### Test Output Format
-
-Cargo test output follows this format:
-```
-running X tests
-test module::test_name ... ok
-test module::another_test ... FAILED
-test module::ignored_test ... ignored
-test module::skipped_test ... ignored, reason: "requires feature X"
-
-test result: FAILED. X passed; Y failed; Z ignored; 0 measured; 0 filtered out
-```
-
----
-
-## CRITICAL WORKFLOW (FOLLOW THIS ORDER)
-
-⚠️ **You MUST follow this exact workflow sequence:**
-
-```
-PHASE 0: Analyze Rust Project Structure
-    └── Check Cargo.toml → Identify workspace/crates → Determine features → List test targets
-
-PHASE 1: Write Initial Dockerfile & Test END State
-    └── Build minimal image → Test compilation for END state → Verify success
-
-PHASE 2: Test START State & Apply Minimal Patches (if needed)
-    └── Test START compilation → Apply patches if needed → Verify both states pass
-
-PHASE 2.5: Generate test_config.json
-    └── Create test configuration file required by test runner
-
-PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-    └── Run {test_runner_script} → Analyze ignored tests → Identify environment issues
-
-PHASE 4: Fix Environment Issues (iterate until resolved)
-    └── Update Dockerfile → Re-run tests → Verify issues are resolved
-
-PHASE 4.5: Validate Commit-Related Tests
-    └── Verify tests modified by milestone commits are collected AND not ignored
-
-PHASE 5: Finalize & Generate Skip Analysis
-    └── Set default state to START → Create skip_analysis.md → Clean up
-```
-
----
-
-### PHASE 0: Analyze Rust Project Structure
-**Understand the Rust project before proceeding**
-
-1. **Check project type (single crate vs workspace):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat Cargo.toml | head -30"
-   ```
-
-   **Single crate indicators:**
-   ```toml
-   [package]
-   name = "my_crate"
-   version = "0.1.0"
-   ```
-
-   **Workspace indicators:**
-   ```toml
-   [workspace]
-   members = [
-       "crate1",
-       "crate2",
-   ]
-   ```
-
-2. **List all crates in workspace (if applicable):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cargo metadata --no-deps --format-version 1 | jq '.packages[].name'"
-   ```
-
-3. **Check available features:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-   ```
-
-4. **Identify test targets:**
-
-   ```bash
-   # Check for integration tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la tests/ 2>/dev/null"
-
-   # Check for unit tests in src/
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '#\[test\]' src/ | head -20"
-
-   # Check for doc tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '```rust' src/ | head -10"
-
-   # Check for benchmark tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la benches/ 2>/dev/null"
-   ```
-
-5. **Check Rust toolchain requirements:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat rust-toolchain.toml rust-toolchain 2>/dev/null"
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "rustc --version && cargo --version"
-   ```
-
-6. **Record your analysis:**
-
-   ```
-   PROJECT TYPE: <single_crate|workspace>
-   WORKSPACE MEMBERS: <list of crate names if workspace>
-   AVAILABLE FEATURES: <list of features>
-   TEST TARGETS: <lib|tests|examples|benches|doc>
-   RUST TOOLCHAIN: <stable|nightly|specific version>
-   ```
-
-⚠️ **DO NOT PROCEED to Phase 1 until you understand the project structure!**
-
-### IMPORTANT: Building on Base Image
-
-Since you are building on top of `nushell_nushell_0.106.0_0.108.0/base:latest`, you do NOT need to:
-- Install Rust toolchain
-- Install system dependencies
-- Run `cargo fetch` or `cargo build`
-- Configure environment paths
-
-Your Dockerfile only needs to:
-1. Checkout to the correct git states
-2. Apply minimal patches if START state has compilation issues
-
-**Temp image name**: `test-milestone-milestone_M08_docs-temp` (unique for this milestone)
-
-**CRITICAL RULES:**
-- ❌ **NEVER modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository
-- ✅ **Use a working copy for exploration** (create with `cp -r` if needed)
-- ✅ **Build using**: `docker build -t test-milestone-milestone_M08_docs-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-- ✅ **Clean up test images when done**: `docker rmi test-milestone-milestone_M08_docs-temp`
-
----
-
-### PHASE 1: Write Initial Dockerfile & Test END State
-**Start with a minimal Dockerfile based on the base image**
-
-1. **Write the initial Dockerfile:**
-
-   ```dockerfile
-   # Build on pre-configured base image
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Set umask to ensure files created in container are world-writable
-   # This prevents permission issues when test results are written to mounted volumes
-   RUN echo 'umask 000' >> /etc/bash.bashrc && \
-       echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-       chmod +x /entrypoint.sh
-   ENTRYPOINT ["/entrypoint.sh"]
-   CMD ["bash"]
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Checkout to END state (all features available)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_M08_docs-end
-   ```
-
-2. **Build and test END state compilation:**
-
-   ```bash
-   docker build -t test-milestone-milestone_M08_docs-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-   ```
-
-   Then test compilation:
-
-   ```bash
-   # For single crate
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && cargo test --no-run"
-
-   # For workspace
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && cargo test --workspace --no-run"
-
-   # With all features
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && cargo test --all-features --no-run"
-   ```
-
-3. **SUCCESS CRITERIA for END state:**
-   - Exit code 0
-   - Output shows "Compiling" and "Finished" messages
-   - NO compilation errors
-   - Test binaries are generated
-
-   ⚠️ **DO NOT PROCEED to Phase 2 until END state compiles!**
-
----
-
-### PHASE 2: Test START State & Apply Minimal Patches (if needed)
-**Handle the earlier codebase state which may lack features**
-
-1. **Test START state compilation:**
-
-   ```bash
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && git checkout milestone-milestone_M08_docs-start && cargo test --no-run"
-   ```
-
-2. **Handle results:**
-
-   **Case A: Compilation succeeds immediately**
-   ✅ Both states work! Proceed to PHASE 2.5.
-
-   **Case B: Compilation fails**
-   Apply Rust-specific minimal patches. See "RUST-SPECIFIC PATCHING" section.
-
-   ⚠️ **RUST COMPILATION**: Like Java, Rust requires ALL code to compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-3. **VALIDATION - Both states MUST compile:**
-   ```bash
-   docker build -t test-milestone-milestone_M08_docs-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-   # Test END state
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && git checkout milestone-milestone_M08_docs-end && cargo test --no-run"
-
-   # Test START state
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && git checkout milestone-milestone_M08_docs-start && cargo test --no-run"
-   ```
-
----
-
-### PHASE 2.5: Generate test_config.json
-**Create test configuration file required by test runner**
-
-The test_config.json defines how the test runner should execute tests.
-
-**Format:**
-```json
-[
-  {
-    "name": "config_name",
-    "test_states": ["start", "end"],
-    "test_cmd": "test command with placeholders",
-    "description": "What this configuration tests"
-  }
-]
-```
-
-**Available placeholders:** `{workers}`, `{timeout}`, `{output_file}`
-
-**Basic Example (Single Crate):**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests"
-  }
-]
-```
-
-**Workspace Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --workspace --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests"
-  }
-]
-```
-
-**With Features Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --all-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests with all features"
-  },
-  {
-    "name": "no_default_features",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-default-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Tests without default features"
-  }
-]
-```
-
-**Multiple Test Targets Example:**
-```json
-[
-  {
-    "name": "unit",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --lib --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Unit tests only"
-  },
-  {
-    "name": "integration",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --test '*' --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Integration tests only"
-  },
-  {
-    "name": "doc",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --doc --no-fail-fast 2>&1 | tee /output/{output_file}",
-    "description": "Doc tests only"
-  }
-]
-```
-
-**Guidelines:**
-1. **Always include "default" configuration** that runs all tests
-2. **Discover special test modes:**
-
-   ```bash
-   # Check for feature flags
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-
-   # Check for test-specific features
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && grep -E 'test-|testing' Cargo.toml"
-
-   # Check for conditional compilation in tests
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && grep -r '#\[cfg(test)\]' src/ | head -10"
-
-   # Check for ignored tests that might need special flags
-   docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && grep -r '#\[ignore\]' . | head -20"
-   ```
-
----
-
-### PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-**Run full tests and identify environment-related issues**
-
-1. **Run tests using the test runner script:**
-
-   ```bash
-   python -m harness.test_runner.run_milestone_tests \
-     --milestone-id milestone_M08_docs \
-     --image-name test-milestone-milestone_M08_docs-temp \
-     --output-dir /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results \
-     --language rust \
-     --test-framework cargo \
-     --max-retries 1
-   ```
-
-2. **Analyze test results:**
-
-   After tests complete, examine the output log for ignored tests:
-
-   ```bash
-   # Find ignored tests
-   grep "ignored" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_M08_docs/attempt_1/end_default.log
-
-   # Find failed tests
-   grep "FAILED" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_M08_docs/attempt_1/end_default.log
-   ```
-
-3. **Classification of Rust test skip/ignore reasons:**
-
-   | Pattern | Classification | Action |
-   |---------|----------------|--------|
-   | `#[ignore]` without reason | Review | Check if intentional |
-   | `#[ignore = "requires X"]` | Depends | Check if X is environment-related |
-   | `#[ignore = "flaky"]` | Acceptable | Intentionally ignored |
-   | `#[ignore = "slow"]` | Acceptable | Run with `--include-ignored` if needed |
-   | `#[cfg(feature = "X")]` not enabled | Resolvable | Enable feature in test_config.json |
-   | Missing system library | Resolvable | Install in Dockerfile |
-   | Network-dependent test | Acceptable | Requires external resources |
-
-4. **Common Rust environment issues:**
-
-   | Error Pattern | Cause | Solution |
-   |---------------|-------|----------|
-   | `error: could not find native static library` | Missing C library | `RUN apt-get install libXXX-dev` |
-   | `error: linking with cc failed` | Missing linker deps | Install build-essential |
-   | `RUSTFLAGS` related | Build flags issue | Set `ENV RUSTFLAGS="..."` |
-   | `openssl` errors | Missing OpenSSL | Install `libssl-dev` |
-   | `pkg-config` errors | Missing pkg-config | Install `pkg-config` |
-
-5. **If resolvable environment issues found → Proceed to PHASE 4**
-   **If no resolvable issues → Proceed to PHASE 4.5**
-
----
-
-### PHASE 4: Fix Environment Issues
-**Resolve environment-related issues by updating Dockerfile**
-
-**Common fixes for Rust projects:**
-
-```dockerfile
-# Install missing system libraries
-RUN apt-get update && apt-get install -y \
-    libssl-dev \
-    pkg-config \
-    libclang-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-# Set environment variables
-ENV RUST_BACKTRACE=1
-ENV CARGO_NET_GIT_FETCH_WITH_CLI=true
-
-# Enable specific features by default
-ENV CARGO_FEATURE_FLAGS="--all-features"
-
-# Fix OpenSSL issues
-ENV OPENSSL_DIR=/usr
-ENV OPENSSL_LIB_DIR=/usr/lib/x86_64-linux-gnu
-ENV OPENSSL_INCLUDE_DIR=/usr/include
-
-# Fetch dependencies again after changes
-RUN cd /testbed && cargo fetch
-```
-
-**Iteration loop:**
-
-1. Update Dockerfile with fix
-2. Rebuild: `docker build -t test-milestone-milestone_M08_docs-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-3. Re-run tests with test runner script
-4. Check if issue is resolved by comparing results
-5. Repeat until no resolvable issues remain
-
----
-
-### PHASE 4.5: Validate Commit-Related Tests
-**Ensure tests modified by milestone commits are collected AND not ignored**
-
-1. **Run the collect_milestone_patched_tests.py script:**
-
-   ```bash
-   python -m harness.prepare_images.collect_milestone_patched_tests \
-     /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 \
-     --repo /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed \
-     --milestone milestone_M08_docs
-   ```
-
-   This script:
-   - Extracts symbol changes (added/modified/deleted tests) from each commit
-   - Aggregates patched tests at the milestone level
-   - Matches patched test IDs to actual test results (nodeids)
-   - Generates a report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_M08_docs.json`
-
-2. **Check the output JSON file:**
-
-   The output format is:
-   ```json
-   {
-     "milestone_id": "milestone_M08_docs",
-     "commits": ["abc1234", "def5678"],
-     "test_ids": {
-       "added": [...],      // Tests added by commits
-       "modified": [...],   // Tests modified by commits
-       "deleted": [...],    // Tests deleted by commits
-       "effective": [...]   // Effective tests = (added ∪ modified) - deleted
-     },
-     "collected": {
-       "patched_in_results": [...],      // ✅ Patched tests found in test results
-       "patched_not_in_results": [],     // ⚠️ MUST BE EMPTY!
-       "test_id_to_nodeid": {...},       // Mapping from test_id to nodeid
-       "status": {
-         "start": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []},
-         "end": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []}
-       },
-       "transitions": {
-         "fixed": [],        // start failed/error -> end passed
-         "broken": [],       // start passed -> end failed/error
-         "still_passing": [],
-         "still_failing": [],
-         "other": []
-       }
-     },
-     "summary": {...}
-   }
-   ```
-
-3. **⚠️ CRITICAL VALIDATION: `collected.patched_not_in_results` MUST be empty!**
-
-   This field lists patched tests that were NOT found in test results. If not empty, it means:
-   - Some patched tests failed to compile (possibly commented out incorrectly)
-   - Some patched tests were excluded from test collection
-   - The test_id to nodeid matching failed
-
-   **How to verify:**
-   ```bash
-   # Check if patched_not_in_results is empty
-   cat /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_M08_docs.json | jq '.collected.patched_not_in_results'
-   # Expected output: []
-   ```
-
-4. **If `patched_not_in_results` is NOT empty:**
-   - Identify which tests are missing from results
-   - Check if those tests were incorrectly commented out or excluded
-   - Return to PHASE 4 to fix environment issues
-   - Re-run tests and re-validate until `patched_not_in_results` is empty
-
-5. **Also verify no commit-related tests are ignored:**
-   - Check `collected.status.end.skipped` - patched tests should not be ignored
-   - If ignored due to environment issues, return to PHASE 4 to fix
-
----
-
-### PHASE 5: Finalize Dockerfile & Generate Skip Analysis
-**Set default state to START, create skip analysis report, and clean up**
-
-1. **Ensure Dockerfile sets default state to START:**
-
-   ```dockerfile
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Environment fixes (if any)
-   # RUN apt-get update && apt-get install -y ...
-   # ENV RUST_BACKTRACE=1
-
-   # Checkout to END state (for any patching if needed)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_M08_docs-end
-
-   # [If patches needed, add them here]
-
-   # Set default git state to START
-   RUN cd /testbed && git checkout milestone-milestone_M08_docs-start
-   ```
-
-2. **Final validation**
-
-3. **Generate skip analysis report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_M08_docs/attempt_1/skip_analysis.md`**
-
-4. **Clean up:**
-   ```bash
-   docker rmi test-milestone-milestone_M08_docs-temp
-   ```
-
----
-
-## RUST-SPECIFIC PATCHING
-
-### How to Apply Patches in Dockerfile
-
-⚠️ **Apply patches using patch files or sed commands in the Dockerfile. DO NOT modify /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed!**
-
-⚠️ **CRITICAL**: After applying patches, you MUST commit the changes and move the tag to preserve patches across git checkouts. Without this step, patches will be lost when switching between START and END states!
-
-⚠️ **NEVER DELETE FILES**: When applying patches, you must NEVER delete any files (e.g., using `rm`, `git rm`, or similar commands). Only modify file contents. Deleting files can break test discovery and cause unexpected issues.
-
-### Rust Compilation Error Handling
-
-**CRITICAL**: Rust is a compiled language. Unlike Python/JavaScript, ALL code must compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-**Goal**: Comment out the minimal amount of code that causes compilation errors, so that the maximum number of tests can compile and run.
-
-### Patching Strategies for Rust
-
-#### Strategy 1: Use `#[cfg]` Attributes (Preferred)
-
-The best way to handle compilation errors in Rust is to use conditional compilation:
-
-```rust
-// Original code that fails in START state:
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();  // This doesn't exist in START state
-    assert!(result.is_ok());
-}
-
-// Patched version using cfg:
-#[cfg(feature = "new_feature")]
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();
-    assert!(result.is_ok());
-}
-```
-
-**Dockerfile example:**
-```dockerfile
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start && \
-    # Add cfg attribute before test function
-    sed -i 's/#\[test\]\nfn test_new_feature/#[cfg(feature = "env_patch")]\n#[test]\nfn test_new_feature/' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add cfg guard for test_new_feature" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-```
-
-#### Strategy 2: Comment Out Test Functions
-
-When a test function uses APIs that don't exist in START state:
-
-```dockerfile
-# Comment out a specific test function (from line 45 to line 55)
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start && \
-    sed -i '45,55 s/^/\/\/ [ENV-PATCH] /' src/tests.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_new_feature for START state" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-```
-
-**Better approach using markers:**
-```dockerfile
-# Find and comment out specific test
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start && \
-    # Add /* before #[test] and */ after the closing brace
-    sed -i '/#\[test\]/,/^}$/{
-        /fn test_problematic/,/^}$/ {
-            s/^/\/\/ [ENV-PATCH] /
-        }
-    }' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_problematic" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-```
-
-#### Strategy 3: Comment Out Entire Module (Last Resort)
-
-Only when module-level code causes compilation errors:
-
-```dockerfile
-# Comment out entire test module
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start && \
-    sed -i '/^mod tests {/,/^}/ s/^/\/\/ [ENV-PATCH] /' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests module" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-```
-
-#### Strategy 4: Modify Cargo.toml Features
-
-If the issue is feature-related:
-
-```dockerfile
-# Add a feature flag for conditional compilation
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start && \
-    sed -i '/\[features\]/a env_patch = []' Cargo.toml && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add env_patch feature flag" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-```
-
-### Common Rust Compilation Error Patterns
-
-| Error Pattern | Cause | Solution |
-|---------------|-------|----------|
-| `cannot find function X in this scope` | Function doesn't exist in START | Comment out test using it |
-| `cannot find type X in this scope` | Type doesn't exist in START | Comment out test using it |
-| `trait X is not implemented for Y` | Trait impl missing in START | Comment out test using it |
-| `mismatched types` | API signature changed | Comment out test using it |
-| `unresolved import X::Y` | Module/item doesn't exist | Comment out import and tests |
-| `no method named X found` | Method doesn't exist in START | Comment out test using it |
-| `struct X has no field Y` | Field doesn't exist in START | Comment out test using it |
-| `lifetime mismatch` | Lifetime requirements changed | Comment out test using it |
-
-### Example: Full Patching Workflow
-
-```dockerfile
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Checkout to START state and apply patches
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start && \
-    # Patch 1: Comment out test that uses new API (lines 120-135)
-    sed -i '120,135 s/^/\/\/ [ENV-PATCH] /' src/api/tests.rs && \
-    # Patch 2: Comment out test that uses new struct field (lines 45-52)
-    sed -i '45,52 s/^/\/\/ [ENV-PATCH] /' tests/integration_test.rs && \
-    # Commit patches and move tag
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests using APIs not in START state" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-
-# Verify END state still compiles
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-end && cargo test --no-run
-
-# Set default to START
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start
-```
-
-### Verify Patches Persist
-
-```bash
-docker build -t test-milestone-milestone_M08_docs-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-# Test START state (verify patches applied)
-docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && cargo test --no-run"
-
-# Test END state (verify patches persist after checkout)
-docker run --rm test-milestone-milestone_M08_docs-temp bash -c "cd /testbed && git checkout milestone-milestone_M08_docs-end && cargo test --no-run"
-```
-
----
-
-## FINAL CHECKLIST
-
-### Before Completing Your Work
-Ensure you have:
-- [ ] **PHASE 0 completed**: Analyzed Rust project structure (single crate vs workspace, features, test targets)
-- [ ] Dockerfile based on `FROM nushell_nushell_0.106.0_0.108.0/base:latest`
-- [ ] **Testbed replaced**: `RUN rm -rf /testbed` + `COPY . /testbed/` included in Dockerfile
-- [ ] Both START and END states compile successfully (`cargo test --no-run`)
-- [ ] Minimal patches only (if needed)
-- [ ] No artificial skips
-- [ ] **Patches committed and tags moved** (if patches applied):
-  - [ ] Used `git add -A && git commit` after applying patches
-  - [ ] Used `git tag -f <TAG> HEAD` to move tag to patched commit
-  - [ ] Verified patches persist across `git checkout` (test switching between states)
-- [ ] **Full tests run** using test runner script with `--language rust --test-framework cargo`
-- [ ] **No resolvable environment-related issues** remaining
-- [ ] **Commit-related tests validated** using `collect_milestone_patched_tests.py`:
-  - [ ] Ran: `python -m harness.prepare_images.collect_milestone_patched_tests /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 --milestone milestone_M08_docs`
-  - [ ] **`collected.patched_not_in_results` is EMPTY** (all patched tests found in results)
-  - [ ] No patched tests in `collected.status.end.skipped` (no environment-related ignores)
-- [ ] **test_config.json** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_M08_docs/test_config.json` with correct cargo test command
-- [ ] **Skip analysis report** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_M08_docs/attempt_1/skip_analysis.md`
-- [ ] Default state is START
-- [ ] Cleaned up: `docker rmi test-milestone-milestone_M08_docs-temp`
-
----
-
-## COMMON PITFALLS TO AVOID
-
-❌ **Apply patches without committing and moving tags** - patches will be lost on `git checkout`!
-❌ **Forget to verify patches persist** - always test switching between START and END states after patching
-❌ **Modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository, use Dockerfile commands instead
-❌ **Skip PHASE 0** - understanding Rust project structure is essential
-❌ **Proceed to next phase before current phase compiles** - validate each phase before moving on
-❌ **Comment out entire files/crates** - only comment out specific functions/tests
-❌ **Forget workspace flag** - use `cargo test --workspace` for workspace projects
-❌ **Ignore feature flags** - check if tests require specific features to be enabled
-
-✅ **Always commit patches and move tags** (`git add -A && git commit && git tag -f <TAG> HEAD`)
-✅ **Test both states after applying patches** to ensure patches persist across checkout
-✅ **Document patched code** in Dockerfile comments (which functions, why)
-✅ **Use `[ENV-PATCH]` prefix** in commit messages and comments for tracking
-✅ **Use conditional compilation** (`#[cfg]`) when possible instead of commenting out
-✅ **Check all feature combinations** if the project uses feature flags

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_M08_docs.bak/test_config.json

@@ -1,12 +0,0 @@
-[
-  {
-    "name": "default",
-    "test_states": [
-      "start",
-      "end"
-    ],
-    "test_cmd": "cargo test --profile ci --workspace --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests (excluding plugins)",
-    "framework": "cargo"
-  }
-]

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_M08_docs/Dockerfile.bak

@@ -1,96 +0,0 @@
-# Build on pre-configured base image for nushell
-# Base image already has Rust 1.86.0, dependencies, and cargo build cache
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Remove the original /testbed from base image and copy local testbed
-# NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Ensure git knows this directory is safe and configure git identity for patches
-RUN git config --global --add safe.directory /testbed && \
-    git config --global user.email "env-patch@test.local" && \
-    git config --global user.name "ENV-PATCH"
-
-# Copy fix script to /tmp before git operations (so it won't be affected by checkouts)
-RUN cp /testbed/fix_reedline_api.py /tmp/fix_reedline_api.py
-
-# [ENV-PATCH] Fix multiple environment issues:
-# 1. Version mismatch: root Cargo.toml requires ^0.107.1 but crates have 0.106.x
-#    Solution: Normalize ALL version numbers (0.106.x and 0.107.x) to 0.106.0
-# 2. ureq version mismatch: Cargo.toml has ureq 3.x but code uses ureq 2.x API
-# 3. Rust version: milestone requires 1.87.0 but base image has 1.86.0
-# 4. Test compilation errors due to API/typo issues:
-#    - PipelineData::value -> PipelineData::Value (case typo in 2 files)
-#    - NuOpts experimental field doesn't exist
-#    - completion -> custom_completion field rename
-# We fix by normalizing all crate versions to 0.106.0, downgrading ureq to 2.12, and fixing/commenting broken tests
-
-# Fix END state
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-end && \
-    # Normalize ALL nu-* crate versions to 0.106.0 (handles both 0.106.x and 0.107.x)
-    find . -name "Cargo.toml" -exec sed -i 's/"0\.10[67]\.[0-9]*"/"0.106.0"/g' {} \; && \
-    # Also fix version declarations without quotes (version = 0.106.x or ^0.107.x patterns)
-    find . -name "Cargo.toml" -exec sed -i 's/= "\^0\.10[67]\.[0-9]*"/= "0.106.0"/g' {} \; && \
-    # Downgrade ureq from 3.x to 2.x (code was written for 2.x API)
-    sed -i 's/ureq = { version = "=3.0.12"/ureq = { version = "2.12"/g' Cargo.toml && \
-    # Downgrade rust-version to 1.86.0 to match base image toolchain
-    sed -i 's/rust-version = "1.87.0"/rust-version = "1.86.0"/g' Cargo.toml && \
-    # Comment out test with PipelineData::value typo (lines 143-153 in custom_value/mod.rs)
-    sed -i '143,153 s/^/\/\/ [ENV-PATCH] /' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    # Fix PipelineData::value -> PipelineData::Value typo (case fix, not logic change)
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Comment out test with NuOpts experimental field (lines 739-758 in external.rs)
-    sed -i '739,758 s/^/\/\/ [ENV-PATCH] /' tests/shell/pipeline/commands/external.rs && \
-    # Fix completion -> custom_completion field rename (field name change, not logic change)
-    sed -i 's/completion: None,/custom_completion: None,/g' crates/nu-protocol/tests/test_signature.rs && \
-    # Remove Cargo.lock to regenerate with correct versions
-    rm -f Cargo.lock && \
-    # Fix reedline API compatibility
-    python3 /tmp/fix_reedline_api.py && \
-    # Fix let chains syntax in parser.rs (not stable in Rust 1.86)
-    sed -i '1253,1259c\            if let SyntaxShape::Keyword(ref keyword, ..) = positional.shape {\n                if keyword == b"catch" {\n                    if let [nu_protocol::CompileError::NotInALoop { .. }] =\n                        \&working_set.compile_errors[compile_error_count..]\n                    {\n                        working_set.compile_errors.truncate(compile_error_count);\n                    }\n                }\n            }' crates/nu-parser/src/parser.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version mismatches and test compilation errors" && \
-    git tag -f milestone-milestone_M08_docs-end HEAD
-
-# Fix START state
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start && \
-    # Normalize ALL nu-* crate versions to 0.106.0 (handles both 0.106.x and 0.107.x)
-    find . -name "Cargo.toml" -exec sed -i 's/"0\.10[67]\.[0-9]*"/"0.106.0"/g' {} \; && \
-    # Also fix version declarations without quotes (version = 0.106.x or ^0.107.x patterns)
-    find . -name "Cargo.toml" -exec sed -i 's/= "\^0\.10[67]\.[0-9]*"/= "0.106.0"/g' {} \; && \
-    # Downgrade ureq from 3.x to 2.x (code was written for 2.x API)
-    sed -i 's/ureq = { version = "=3.0.12"/ureq = { version = "2.12"/g' Cargo.toml && \
-    # Downgrade rust-version to 1.86.0 to match base image toolchain
-    sed -i 's/rust-version = "1.87.0"/rust-version = "1.86.0"/g' Cargo.toml && \
-    # Comment out test with PipelineData::value typo (lines 143-153 in custom_value/mod.rs)
-    sed -i '143,153 s/^/\/\/ [ENV-PATCH] /' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    # Fix PipelineData::value -> PipelineData::Value typo (case fix, not logic change)
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Comment out test with NuOpts experimental field (lines 739-758 in external.rs)
-    sed -i '739,758 s/^/\/\/ [ENV-PATCH] /' tests/shell/pipeline/commands/external.rs && \
-    # Fix completion -> custom_completion field rename (field name change, not logic change)
-    sed -i 's/completion: None,/custom_completion: None,/g' crates/nu-protocol/tests/test_signature.rs && \
-    # Remove Cargo.lock to regenerate with correct versions
-    rm -f Cargo.lock && \
-    # Fix reedline API compatibility
-    python3 /tmp/fix_reedline_api.py && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix version mismatches and test compilation errors" && \
-    git tag -f milestone-milestone_M08_docs-start HEAD
-
-# Verify END state compiles
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-end && \
-    cargo test --no-run --profile ci --workspace --exclude nu_plugin_* -j 4
-
-# Set default git state to START
-RUN cd /testbed && git checkout milestone-milestone_M08_docs-start

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_core_development.1.bak/Dockerfile

@@ -1,224 +0,0 @@
-# Build on pre-configured base image
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Configure git user for commits
-RUN git config --global user.email "env-patch@test.local" && \
-    git config --global user.name "ENV Patch"
-
-# Set cargo to use fewer parallel jobs to avoid "too many open files" error
-ENV CARGO_BUILD_JOBS=4
-ENV RUST_BACKTRACE=1
-
-# Remove the original /testbed from base image and copy local testbed with milestone tags
-COPY . /testbed/
-
-# Clean any untracked files that might conflict with checkout
-RUN cd /testbed && git clean -fd
-
-# =====================================================
-# [ENV-PATCH] Apply patches for END state compilation
-# =====================================================
-
-# Checkout to END state first
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-end
-
-# [ENV-PATCH] Fix Cargo.toml - nu-mcp crate doesn't exist
-RUN cd /testbed && \
-    sed -i '/^  "crates\/nu-mcp",$/d' Cargo.toml && \
-    sed -i 's|^nu-mcp = { path = "\./crates/nu-mcp".*$|# [ENV-PATCH] nu-mcp dependency removed - crate not present|' Cargo.toml && \
-    sed -i 's|^  "dep:nu-mcp",$|  # [ENV-PATCH] "dep:nu-mcp", # crate not present|' Cargo.toml && \
-    sed -i 's|^  "nu-mcp/mcp",$|  # [ENV-PATCH] "nu-mcp/mcp", # crate not present|' Cargo.toml
-
-# [ENV-PATCH] Fix rust-toolchain.toml to use 1.86.0 instead of 1.88.0
-RUN cd /testbed && \
-    sed -i 's/channel = "1\.88\.0"/channel = "1.86.0"/' rust-toolchain.toml
-
-# [ENV-PATCH] Fix version and rust-version to match base image
-RUN cd /testbed && \
-    sed -i 's/^rust-version = "1\.88\.0"$/rust-version = "1.86.0"/' Cargo.toml && \
-    sed -i 's/^version = "0\.107\.1"$/version = "0.106.0"/' Cargo.toml && \
-    sed -i 's/version = "0\.107\.1"/version = "0.106.0"/g' Cargo.toml
-
-# [ENV-PATCH] Fix workspace dependency versions for END state
-# Keep uu_* at 0.2.2 (code uses newer APIs), downgrade other problematic deps
-RUN cd /testbed && \
-    # Downgrade rusqlite to 0.31 (code uses DatabaseName which doesn't exist in 0.37)
-    sed -i 's/^rusqlite = "0\.37"$/rusqlite = "0.31"/' Cargo.toml && \
-    # Downgrade reedline to 0.41 (code uses CutInside/YankInside which don't exist in 0.42)
-    sed -i 's/^reedline = "0\.42\.0"$/reedline = "0.41.0"/' Cargo.toml
-
-# [ENV-PATCH] Fix sqlite feature - remove nu-cli/sqlite and nu-protocol/sqlite which don't exist
-RUN cd /testbed && \
-    sed -i '/^sqlite = \[$/,/^\]$/c\sqlite = [\n  "nu-command/sqlite",\n  "nu-std/sqlite",\n  "reedline/sqlite"\n]' Cargo.toml
-
-# [ENV-PATCH] Add memchr/lean_string/byteyarn to nu-utils/Cargo.toml for downstream milestone compatibility (G05_0b8531e)
-RUN cd /testbed && \
-    sed -i '/^fancy-regex = { workspace = true }$/a byteyarn.workspace = true\nlean_string.workspace = true\nmemchr.workspace = true' crates/nu-utils/Cargo.toml
-
-# Fetch updated dependencies for END state
-RUN cd /testbed && cargo fetch
-
-# [ENV-PATCH] Fix table.rs - Duration::from_value doesn't exist, implement alternative using as_duration()
-RUN cd /testbed && \
-    perl -i -pe 'BEGIN{undef $/;} s/"batch_duration" => \{\s+match Duration::from_value\(val\.clone\(\)\)\.map_err\(ConfigError::from\) \{\s+Ok\(val\) => self\.batch_duration = val,\s+Err\(err\) => errors\.error\(err\),\s+\}\s+\}/"batch_duration" => {\n                    match val.as_duration() {\n                        Ok(nanos) if nanos >= 0 => {\n                            self.batch_duration = Duration::from_nanos(nanos as u64);\n                        }\n                        Ok(_) => errors.invalid_value(path, "a positive duration", val),\n                        Err(_) => errors.type_mismatch(path, Type::Duration, val),\n                    }\n                }/smg' crates/nu-protocol/src/config/table.rs
-
-# [ENV-PATCH] Fix reedline_config.rs - CutInside, YankInside, and ViChangeMode don't exist in reedline 0.41
-# Comment out lines 1050-1053 (vichangemode) and lines 1292-1305 (CutInside/YankInside)
-RUN cd /testbed && \
-    sed -i '1050,1053s/^/\/\/ [ENV-PATCH] /' crates/nu-cli/src/reedline_config.rs && \
-    sed -i '1292,1305s/^/\/\/ [ENV-PATCH] /' crates/nu-cli/src/reedline_config.rs
-
-# [ENV-PATCH] Fix PipelineData::value() -> PipelineData::Value() everywhere
-RUN cd /testbed && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-command/src/filesystem/umkdir.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-cli/tests/completions/support/completions_helpers.rs
-
-# [ENV-PATCH] Fix nu-plugin-core tests - PipelineData case changes
-RUN cd /testbed && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::list_stream(/PipelineData::ListStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::byte_stream(/PipelineData::ByteStream(/g' crates/nu-plugin-core/src/interface/tests.rs
-
-# [ENV-PATCH] Fix html.rs test - revert to test_examples (test_examples_with_commands doesn't exist in nu-cmd-extra)
-RUN cd /testbed && \
-    sed -i 's/use crate::test_examples_with_commands;/use crate::test_examples;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/use nu_command::ToXml;/\/\/ [ENV-PATCH] use nu_command::ToXml;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/test_examples_with_commands(ToHtml {}, \&\[&ToXml\])/test_examples(ToHtml {})/' crates/nu-cmd-extra/src/extra/formats/to/html.rs
-
-# [ENV-PATCH] Fix completer.rs - need_fallback is immutable, comment out the assignment
-RUN cd /testbed && \
-    sed -i 's/\*need_fallback = false/\/\/ [ENV-PATCH] *need_fallback = false/' crates/nu-cli/src/completions/completer.rs
-
-# [ENV-PATCH] Fix is_multiple_of - unstable feature in Rust 1.86
-RUN cd /testbed && \
-    sed -i 's/\.is_multiple_of(2)/ % 2 == 0/g' crates/nu-parser/src/parser.rs && \
-    sed -i 's/i\.is_multiple_of(self\.chunk)/i % self.chunk == 0/g' crates/nu-pretty-hex/src/pretty_hex.rs && \
-    sed -i 's/i\.is_multiple_of(self\.group \* self\.chunk)/i % (self.group * self.chunk) == 0/g' crates/nu-pretty-hex/src/pretty_hex.rs && \
-    sed -i 's/self\.cells\.len()\.is_multiple_of(num_columns)/self.cells.len() % num_columns == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/self\.cell_count\.is_multiple_of(theoretical_min_num_cols)/self.cell_count % theoretical_min_num_cols == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/self\.cell_count\.is_multiple_of(num_lines)/self.cell_count % num_lines == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/values\.len()\.is_multiple_of(2)/values.len() % 2 == 0/g' crates/nu-command/src/math/median.rs
-
-# [ENV-PATCH] Fix test_parser.rs - comment out InvalidBinaryString tests (lines 497-537)
-RUN cd /testbed && \
-    sed -i '497,537s/^/\/\/ [ENV-PATCH] /' crates/nu-parser/tests/test_parser.rs
-
-# [ENV-PATCH] Comment out test files using ConfigFileKind which doesn't exist
-RUN cd /testbed && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in this state\n\/\* /' crates/nu-command/tests/commands/config_env_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_env_default.rs && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in this state\n\/\* /' crates/nu-command/tests/commands/config_nu_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_nu_default.rs
-
-# [ENV-PATCH] Comment out NuOpts::experimental usage in external.rs
-RUN cd /testbed && \
-    sed -i 's/experimental: vec!\["pipefail"\.to_string()\],/\/\/ [ENV-PATCH] experimental: vec!["pipefail".to_string()],/' tests/shell/pipeline/commands/external.rs
-
-# [ENV-PATCH] Fix test_signature.rs - comment out 'completion: None' lines that don't exist
-RUN cd /testbed && \
-    sed -i 's/^            completion: None,$/            \/\/ [ENV-PATCH] completion: None,/' crates/nu-protocol/tests/test_signature.rs
-
-# Commit END state patches and move tag
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix Cargo.toml and code compatibility for END state" && \
-    git tag -f milestone-milestone_core_development.1-end HEAD
-
-# =====================================================
-# [ENV-PATCH] Apply patches for START state
-# =====================================================
-
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start
-
-# [ENV-PATCH] Fix rust-toolchain.toml for START state
-RUN cd /testbed && \
-    sed -i 's/channel = "1\.88\.0"/channel = "1.86.0"/' rust-toolchain.toml
-
-# [ENV-PATCH] Fix Cargo.toml for START state
-RUN cd /testbed && \
-    # Remove nu-mcp from workspace members
-    sed -i '/^  "crates\/nu-mcp",$/d' Cargo.toml && \
-    sed -i 's|^nu-mcp = { path = "\./crates/nu-mcp".*$|# [ENV-PATCH] nu-mcp dependency removed - crate not present|' Cargo.toml && \
-    sed -i 's|^  "dep:nu-mcp",$|  # [ENV-PATCH] "dep:nu-mcp", # crate not present|' Cargo.toml && \
-    sed -i 's|^  "nu-mcp/mcp",$|  # [ENV-PATCH] "nu-mcp/mcp", # crate not present|' Cargo.toml && \
-    # Fix rust-version
-    sed -i 's/^rust-version = "1\.88\.0"$/rust-version = "1.86.0"/' Cargo.toml && \
-    # Fix version
-    sed -i 's/^version = "0\.107\.1"$/version = "0.106.0"/' Cargo.toml && \
-    sed -i 's/version = "0\.107\.1"/version = "0.106.0"/g' Cargo.toml && \
-    # Downgrade rusqlite
-    sed -i 's/^rusqlite = "0\.37"$/rusqlite = "0.31"/' Cargo.toml && \
-    # Downgrade reedline
-    sed -i 's/^reedline = "0\.42\.0"$/reedline = "0.41.0"/' Cargo.toml && \
-    # Downgrade ureq to 2.12 for START state
-    sed -i 's/^ureq = { version = "=3\.0\.12"/ureq = { version = "2.12"/' Cargo.toml && \
-    # Downgrade uu_* crates to 0.0.30 for START state (code uses older APIs)
-    sed -i 's/^uu_cp = "0\.2\.2"$/uu_cp = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mkdir = "0\.2\.2"$/uu_mkdir = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mktemp = "0\.2\.2"$/uu_mktemp = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mv = "0\.2\.2"$/uu_mv = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_touch = "0\.2\.2"$/uu_touch = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_uname = "0\.2\.2"$/uu_uname = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_whoami = "0\.2\.2"$/uu_whoami = "0.0.30"/' Cargo.toml && \
-    # Fix sqlite feature
-    sed -i '/^sqlite = \[$/,/^\]$/c\sqlite = [\n  "nu-command/sqlite",\n  "nu-std/sqlite",\n  "reedline/sqlite"\n]' Cargo.toml
-
-# [ENV-PATCH] Fix nu-command/Cargo.toml for START state - fix ureq features for ureq 2.x
-RUN cd /testbed && \
-    sed -i 's|"ureq/platform-verifier"|# [ENV-PATCH] "ureq/platform-verifier" # removed - feature not in ureq 2.x|' crates/nu-command/Cargo.toml && \
-    sed -i 's|"ureq/rustls"|"ureq/tls"|' crates/nu-command/Cargo.toml
-
-# [ENV-PATCH] Add memchr/lean_string/byteyarn to nu-utils/Cargo.toml for downstream milestone compatibility (G05_0b8531e)
-RUN cd /testbed && \
-    sed -i '/^fancy-regex = { workspace = true }$/a byteyarn.workspace = true\nlean_string.workspace = true\nmemchr.workspace = true' crates/nu-utils/Cargo.toml
-
-# [ENV-PATCH] Fix test_signature.rs - comment out 'completion: None' lines that don't exist in START state
-RUN cd /testbed && \
-    sed -i 's/^            completion: None,$/            \/\/ [ENV-PATCH] completion: None,/' crates/nu-protocol/tests/test_signature.rs
-
-# [ENV-PATCH] Fix test files using APIs that don't exist in START state
-RUN cd /testbed && \
-    # Fix PipelineData::value -> PipelineData::Value in all test files
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Fix nu-plugin-core tests - PipelineData case changes
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::list_stream(/PipelineData::ListStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::byte_stream(/PipelineData::ByteStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    # Comment out test functions using ParseError::InvalidBinaryString (lines 497-537)
-    sed -i '497,537s/^/\/\/ [ENV-PATCH] /' crates/nu-parser/tests/test_parser.rs && \
-    # Comment out test files using ConfigFileKind which doesn't exist in START
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in START state\n\/\* /' crates/nu-command/tests/commands/config_env_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_env_default.rs && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in START state\n\/\* /' crates/nu-command/tests/commands/config_nu_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_nu_default.rs && \
-    # Comment out NuOpts::experimental usage in external.rs
-    sed -i 's/experimental: vec!\["pipefail"\.to_string()\],/\/\/ [ENV-PATCH] experimental: vec!["pipefail".to_string()],/' tests/shell/pipeline/commands/external.rs
-
-# [ENV-PATCH] Fix stor/insert.rs - remove EngineState parameter from process() calls in tests (START state doesn't have engine_state param yet)
-RUN cd /testbed && \
-    perl -i -pe 'BEGIN{undef $/;} s/process\(\s*&EngineState::new\(\),\s*/process(/smg' crates/nu-command/src/stor/insert.rs
-
-# [ENV-PATCH] Fix html.rs test - revert to test_examples (test_examples_with_commands doesn't exist in nu-cmd-extra)
-RUN cd /testbed && \
-    sed -i 's/use crate::test_examples_with_commands;/use crate::test_examples;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/use nu_command::ToXml;/\/\/ [ENV-PATCH] use nu_command::ToXml;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/test_examples_with_commands(ToHtml {}, \&\[&ToXml\])/test_examples(ToHtml {})/' crates/nu-cmd-extra/src/extra/formats/to/html.rs
-
-# Commit START state patches and move tag
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix Cargo.toml compatibility for START state" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-
-# Set default git state to START
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_core_development.1.bak/Dockerfile.bak

@@ -1,216 +0,0 @@
-# Build on pre-configured base image
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Configure git user for commits
-RUN git config --global user.email "env-patch@test.local" && \
-    git config --global user.name "ENV Patch"
-
-# Set cargo to use fewer parallel jobs to avoid "too many open files" error
-ENV CARGO_BUILD_JOBS=4
-ENV RUST_BACKTRACE=1
-
-# Remove the original /testbed from base image and copy local testbed with milestone tags
-COPY . /testbed/
-
-# Clean any untracked files that might conflict with checkout
-RUN cd /testbed && git clean -fd
-
-# =====================================================
-# [ENV-PATCH] Apply patches for END state compilation
-# =====================================================
-
-# Checkout to END state first
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-end
-
-# [ENV-PATCH] Fix Cargo.toml - nu-mcp crate doesn't exist
-RUN cd /testbed && \
-    sed -i '/^  "crates\/nu-mcp",$/d' Cargo.toml && \
-    sed -i 's|^nu-mcp = { path = "\./crates/nu-mcp".*$|# [ENV-PATCH] nu-mcp dependency removed - crate not present|' Cargo.toml && \
-    sed -i 's|^  "dep:nu-mcp",$|  # [ENV-PATCH] "dep:nu-mcp", # crate not present|' Cargo.toml && \
-    sed -i 's|^  "nu-mcp/mcp",$|  # [ENV-PATCH] "nu-mcp/mcp", # crate not present|' Cargo.toml
-
-# [ENV-PATCH] Fix rust-toolchain.toml to use 1.86.0 instead of 1.88.0
-RUN cd /testbed && \
-    sed -i 's/channel = "1\.88\.0"/channel = "1.86.0"/' rust-toolchain.toml
-
-# [ENV-PATCH] Fix version and rust-version to match base image
-RUN cd /testbed && \
-    sed -i 's/^rust-version = "1\.88\.0"$/rust-version = "1.86.0"/' Cargo.toml && \
-    sed -i 's/^version = "0\.107\.1"$/version = "0.106.0"/' Cargo.toml && \
-    sed -i 's/version = "0\.107\.1"/version = "0.106.0"/g' Cargo.toml
-
-# [ENV-PATCH] Fix workspace dependency versions for END state
-# Keep uu_* at 0.2.2 (code uses newer APIs), downgrade other problematic deps
-RUN cd /testbed && \
-    # Downgrade rusqlite to 0.31 (code uses DatabaseName which doesn't exist in 0.37)
-    sed -i 's/^rusqlite = "0\.37"$/rusqlite = "0.31"/' Cargo.toml && \
-    # Downgrade reedline to 0.41 (code uses CutInside/YankInside which don't exist in 0.42)
-    sed -i 's/^reedline = "0\.42\.0"$/reedline = "0.41.0"/' Cargo.toml
-
-# [ENV-PATCH] Fix sqlite feature - remove nu-cli/sqlite and nu-protocol/sqlite which don't exist
-RUN cd /testbed && \
-    sed -i '/^sqlite = \[$/,/^\]$/c\sqlite = [\n  "nu-command/sqlite",\n  "nu-std/sqlite",\n  "reedline/sqlite"\n]' Cargo.toml
-
-# Fetch updated dependencies for END state
-RUN cd /testbed && cargo fetch
-
-# [ENV-PATCH] Fix table.rs - Duration::from_value doesn't exist, implement alternative using as_duration()
-RUN cd /testbed && \
-    perl -i -pe 'BEGIN{undef $/;} s/"batch_duration" => \{\s+match Duration::from_value\(val\.clone\(\)\)\.map_err\(ConfigError::from\) \{\s+Ok\(val\) => self\.batch_duration = val,\s+Err\(err\) => errors\.error\(err\),\s+\}\s+\}/"batch_duration" => {\n                    match val.as_duration() {\n                        Ok(nanos) if nanos >= 0 => {\n                            self.batch_duration = Duration::from_nanos(nanos as u64);\n                        }\n                        Ok(_) => errors.invalid_value(path, "a positive duration", val),\n                        Err(_) => errors.type_mismatch(path, Type::Duration, val),\n                    }\n                }/smg' crates/nu-protocol/src/config/table.rs
-
-# [ENV-PATCH] Fix reedline_config.rs - CutInside, YankInside, and ViChangeMode don't exist in reedline 0.41
-# Comment out lines 1050-1053 (vichangemode) and lines 1292-1305 (CutInside/YankInside)
-RUN cd /testbed && \
-    sed -i '1050,1053s/^/\/\/ [ENV-PATCH] /' crates/nu-cli/src/reedline_config.rs && \
-    sed -i '1292,1305s/^/\/\/ [ENV-PATCH] /' crates/nu-cli/src/reedline_config.rs
-
-# [ENV-PATCH] Fix PipelineData::value() -> PipelineData::Value() everywhere
-RUN cd /testbed && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-command/src/filesystem/umkdir.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-cli/tests/completions/support/completions_helpers.rs
-
-# [ENV-PATCH] Fix nu-plugin-core tests - PipelineData case changes
-RUN cd /testbed && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::list_stream(/PipelineData::ListStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::byte_stream(/PipelineData::ByteStream(/g' crates/nu-plugin-core/src/interface/tests.rs
-
-# [ENV-PATCH] Fix html.rs test - revert to test_examples (test_examples_with_commands doesn't exist in nu-cmd-extra)
-RUN cd /testbed && \
-    sed -i 's/use crate::test_examples_with_commands;/use crate::test_examples;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/use nu_command::ToXml;/\/\/ [ENV-PATCH] use nu_command::ToXml;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/test_examples_with_commands(ToHtml {}, \&\[&ToXml\])/test_examples(ToHtml {})/' crates/nu-cmd-extra/src/extra/formats/to/html.rs
-
-# [ENV-PATCH] Fix completer.rs - need_fallback is immutable, comment out the assignment
-RUN cd /testbed && \
-    sed -i 's/\*need_fallback = false/\/\/ [ENV-PATCH] *need_fallback = false/' crates/nu-cli/src/completions/completer.rs
-
-# [ENV-PATCH] Fix is_multiple_of - unstable feature in Rust 1.86
-RUN cd /testbed && \
-    sed -i 's/\.is_multiple_of(2)/ % 2 == 0/g' crates/nu-parser/src/parser.rs && \
-    sed -i 's/i\.is_multiple_of(self\.chunk)/i % self.chunk == 0/g' crates/nu-pretty-hex/src/pretty_hex.rs && \
-    sed -i 's/i\.is_multiple_of(self\.group \* self\.chunk)/i % (self.group * self.chunk) == 0/g' crates/nu-pretty-hex/src/pretty_hex.rs && \
-    sed -i 's/self\.cells\.len()\.is_multiple_of(num_columns)/self.cells.len() % num_columns == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/self\.cell_count\.is_multiple_of(theoretical_min_num_cols)/self.cell_count % theoretical_min_num_cols == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/self\.cell_count\.is_multiple_of(num_lines)/self.cell_count % num_lines == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/values\.len()\.is_multiple_of(2)/values.len() % 2 == 0/g' crates/nu-command/src/math/median.rs
-
-# [ENV-PATCH] Fix test_parser.rs - comment out InvalidBinaryString tests (lines 497-537)
-RUN cd /testbed && \
-    sed -i '497,537s/^/\/\/ [ENV-PATCH] /' crates/nu-parser/tests/test_parser.rs
-
-# [ENV-PATCH] Comment out test files using ConfigFileKind which doesn't exist
-RUN cd /testbed && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in this state\n\/\* /' crates/nu-command/tests/commands/config_env_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_env_default.rs && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in this state\n\/\* /' crates/nu-command/tests/commands/config_nu_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_nu_default.rs
-
-# [ENV-PATCH] Comment out NuOpts::experimental usage in external.rs
-RUN cd /testbed && \
-    sed -i 's/experimental: vec!\["pipefail"\.to_string()\],/\/\/ [ENV-PATCH] experimental: vec!["pipefail".to_string()],/' tests/shell/pipeline/commands/external.rs
-
-# [ENV-PATCH] Fix test_signature.rs - comment out 'completion: None' lines that don't exist
-RUN cd /testbed && \
-    sed -i 's/^            completion: None,$/            \/\/ [ENV-PATCH] completion: None,/' crates/nu-protocol/tests/test_signature.rs
-
-# Commit END state patches and move tag
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix Cargo.toml and code compatibility for END state" && \
-    git tag -f milestone-milestone_core_development.1-end HEAD
-
-# =====================================================
-# [ENV-PATCH] Apply patches for START state
-# =====================================================
-
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start
-
-# [ENV-PATCH] Fix rust-toolchain.toml for START state
-RUN cd /testbed && \
-    sed -i 's/channel = "1\.88\.0"/channel = "1.86.0"/' rust-toolchain.toml
-
-# [ENV-PATCH] Fix Cargo.toml for START state
-RUN cd /testbed && \
-    # Remove nu-mcp from workspace members
-    sed -i '/^  "crates\/nu-mcp",$/d' Cargo.toml && \
-    sed -i 's|^nu-mcp = { path = "\./crates/nu-mcp".*$|# [ENV-PATCH] nu-mcp dependency removed - crate not present|' Cargo.toml && \
-    sed -i 's|^  "dep:nu-mcp",$|  # [ENV-PATCH] "dep:nu-mcp", # crate not present|' Cargo.toml && \
-    sed -i 's|^  "nu-mcp/mcp",$|  # [ENV-PATCH] "nu-mcp/mcp", # crate not present|' Cargo.toml && \
-    # Fix rust-version
-    sed -i 's/^rust-version = "1\.88\.0"$/rust-version = "1.86.0"/' Cargo.toml && \
-    # Fix version
-    sed -i 's/^version = "0\.107\.1"$/version = "0.106.0"/' Cargo.toml && \
-    sed -i 's/version = "0\.107\.1"/version = "0.106.0"/g' Cargo.toml && \
-    # Downgrade rusqlite
-    sed -i 's/^rusqlite = "0\.37"$/rusqlite = "0.31"/' Cargo.toml && \
-    # Downgrade reedline
-    sed -i 's/^reedline = "0\.42\.0"$/reedline = "0.41.0"/' Cargo.toml && \
-    # Downgrade ureq to 2.12 for START state
-    sed -i 's/^ureq = { version = "=3\.0\.12"/ureq = { version = "2.12"/' Cargo.toml && \
-    # Downgrade uu_* crates to 0.0.30 for START state (code uses older APIs)
-    sed -i 's/^uu_cp = "0\.2\.2"$/uu_cp = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mkdir = "0\.2\.2"$/uu_mkdir = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mktemp = "0\.2\.2"$/uu_mktemp = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mv = "0\.2\.2"$/uu_mv = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_touch = "0\.2\.2"$/uu_touch = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_uname = "0\.2\.2"$/uu_uname = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_whoami = "0\.2\.2"$/uu_whoami = "0.0.30"/' Cargo.toml && \
-    # Fix sqlite feature
-    sed -i '/^sqlite = \[$/,/^\]$/c\sqlite = [\n  "nu-command/sqlite",\n  "nu-std/sqlite",\n  "reedline/sqlite"\n]' Cargo.toml
-
-# [ENV-PATCH] Fix nu-command/Cargo.toml for START state - fix ureq features for ureq 2.x
-RUN cd /testbed && \
-    sed -i 's|"ureq/platform-verifier"|# [ENV-PATCH] "ureq/platform-verifier" # removed - feature not in ureq 2.x|' crates/nu-command/Cargo.toml && \
-    sed -i 's|"ureq/rustls"|"ureq/tls"|' crates/nu-command/Cargo.toml
-
-# [ENV-PATCH] Fix test_signature.rs - comment out 'completion: None' lines that don't exist in START state
-RUN cd /testbed && \
-    sed -i 's/^            completion: None,$/            \/\/ [ENV-PATCH] completion: None,/' crates/nu-protocol/tests/test_signature.rs
-
-# [ENV-PATCH] Fix test files using APIs that don't exist in START state
-RUN cd /testbed && \
-    # Fix PipelineData::value -> PipelineData::Value in all test files
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Fix nu-plugin-core tests - PipelineData case changes
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::list_stream(/PipelineData::ListStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::byte_stream(/PipelineData::ByteStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    # Comment out test functions using ParseError::InvalidBinaryString (lines 497-537)
-    sed -i '497,537s/^/\/\/ [ENV-PATCH] /' crates/nu-parser/tests/test_parser.rs && \
-    # Comment out test files using ConfigFileKind which doesn't exist in START
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in START state\n\/\* /' crates/nu-command/tests/commands/config_env_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_env_default.rs && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in START state\n\/\* /' crates/nu-command/tests/commands/config_nu_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_nu_default.rs && \
-    # Comment out NuOpts::experimental usage in external.rs
-    sed -i 's/experimental: vec!\["pipefail"\.to_string()\],/\/\/ [ENV-PATCH] experimental: vec!["pipefail".to_string()],/' tests/shell/pipeline/commands/external.rs
-
-# [ENV-PATCH] Fix stor/insert.rs - remove EngineState parameter from process() calls in tests (START state doesn't have engine_state param yet)
-RUN cd /testbed && \
-    perl -i -pe 'BEGIN{undef $/;} s/process\(\s*&EngineState::new\(\),\s*/process(/smg' crates/nu-command/src/stor/insert.rs
-
-# [ENV-PATCH] Fix html.rs test - revert to test_examples (test_examples_with_commands doesn't exist in nu-cmd-extra)
-RUN cd /testbed && \
-    sed -i 's/use crate::test_examples_with_commands;/use crate::test_examples;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/use nu_command::ToXml;/\/\/ [ENV-PATCH] use nu_command::ToXml;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/test_examples_with_commands(ToHtml {}, \&\[&ToXml\])/test_examples(ToHtml {})/' crates/nu-cmd-extra/src/extra/formats/to/html.rs
-
-# Commit START state patches and move tag
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix Cargo.toml compatibility for START state" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-
-# Set default git state to START
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_core_development.1.bak/env_setup_prompt.md

@@ -1,935 +0,0 @@
-You are an expert in Rust software environment configuration. Your task is to configure
-a Docker container so that a given Rust repository can successfully run its test suite
-across TWO different git states (START and END tags).
-
-## RUST TEST FRAMEWORK
-
-| Language | Framework | Test Collect Command | Report Format | **Output File Extension** |
-|----------|-----------|----------------------|---------------|---------------------------|
-| Rust | cargo | `cargo test --no-run` | Console log | **`.log`** |
-
-### Output File Format Reference
-
-When generating `test_config.json`, use the `.log` extension for `{output_file}`:
-
-| Framework | Recommended Extension | Example `{output_file}` |
-|-----------|----------------------|-------------------------|
-| cargo | `.log` | `start_default.log` |
-
-**IMPORTANT**: The test runner (`run_milestone_tests.py`) will automatically use the cargo log parser based on the `--test-framework cargo` argument.
-
-## GOAL
-Configure the environment to:
-1. Make test compilation succeed for BOTH states (START and END)
-2. Run tests successfully with the test runner script
-3. Ensure no tests are skipped due to resolvable environment issues
-4. Ensure commit-related tests (tests modified by milestone commits) are collected AND run (not skipped)
-5. Generate a skip analysis report documenting remaining skips
-
-Generate a complete, buildable Dockerfile that supports dual-state testing.
-
-**IMPORTANT**: You are building on top of a pre-configured BASE IMAGE that already has:
-- Correct Rust toolchain version (rustc, cargo, rustup)
-- All system dependencies installed (OpenSSL, pkg-config, etc.)
-- Cargo dependencies cached (via `cargo fetch`)
-- Environment paths configured (CARGO_HOME, RUSTUP_HOME, PATH)
-- Repository cloned to /testbed
-
-**IMPORTANT**: The local testbed (/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed) already contains pre-created milestone tags:
-- `milestone-milestone_core_development.1-start` (START state tag)
-- `milestone-milestone_core_development.1-end` (END state tag)
-- **DO NOT create these tags in Dockerfile** - they are already included when you `COPY . /testbed/`
-- Simply use `git checkout milestone-milestone_core_development.1-start` or `git checkout milestone-milestone_core_development.1-end` to switch states
-
-Your task is to handle **git state management and compatibility patches** only.
-
----
-
-## ⚠️ DOCKERFILE VERIFICATION CHECKLIST (CRITICAL)
-
-Before finalizing your Dockerfile, verify ALL of the following constraints:
-
-- [ ] **No Source Code Modification**: Dockerfile must not modify source code logic
-- [ ] **No Test Logic Modification**: Dockerfile must not modify test code logic
-- [ ] **No File Deletion**: Dockerfile must not delete test files or any other files
-- [ ] **No Git Checkout to Fix Errors**: Cannot use `git checkout` to revert a file to a previous state to resolve compilation errors
-
-- [ ] **Compilation Error Handling**: If compilation problems occur, follow the minimal fix principle below
-
-### Minimal Fix Principle (Compilation Errors)
-
-```
-  Compilation Error Found
-      │
-      ├─ Locate the exact error position (file:line)
-      │
-      ├─ Error Type Classification:
-      │
-      ├─ Missing type/trait/function/module
-      │   └─→ Use #[cfg(feature = "...")] to conditionally compile
-      │   └─→ Or comment out the ENTIRE function/test containing the error
-      │
-      ├─ Trait implementation mismatch
-      │   └─→ Comment out the ENTIRE impl block or function
-      │
-      ├─ Lifetime/borrow checker errors
-      │   └─→ Comment out the ENTIRE function containing the error
-      │
-      └─ Feature flag issues
-          └─→ Fix via Cargo.toml features or environment variables (NOT code changes)
-```
-
-**Core Principles:**
-1. **NEVER skip/exclude entire crates or modules** - only comment out specific functions/tests
-2. **Comment out ENTIRE functions (not single lines)** - maintain code logic integrity
-3. **Preserve ALL tests that can compile normally** - maximize test coverage
-4. **Feature flag issues → fix via Cargo.toml or ENV** - not by modifying code
-
-**Specific Rules for Rust:**
-- For `Cargo.toml`: Can modify `[features]` section or comment out individual dependency lines
-- For test code: Comment out the **entire test function** (including `#[test]` attribute), not individual lines
-- For helper functions used by tests: Comment out the **entire function** if it causes compilation errors
-- **NEVER comment out an entire file** just because one function has compilation errors
-- **NEVER exclude an entire crate/module** just because one function has compilation errors
-
----
-
-### Inputs
-
-Milestone ID: milestone_core_development.1
-Milestone Commits: ["28a796d", "459f3c0", "3e37922", "dfbd980", "f33d952", "06fa178", "bf83756", "e8579a9", "c75e7bf", "4245c67", "5478bdf", "5a7d906", "4e90eed", "c9c067a", "26464fc", "a473e3e", "ac01a64", "63ff98d", "c4dfaca", "9090431", "3c83ea7", "75a8a2c", "d54de7d", "4eb43a0", "41e718f", "b4038fe", "2b2575f"] (list of commit SHAs included in this milestone)
-Commit Changed Tests Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/commit_level/patched_tests (directory containing per-commit test changes)
-Start Tag: milestone-milestone_core_development.1-start (earlier git state - may have missing features)
-End Tag: milestone-milestone_core_development.1-end (later git state - has all features)
-Repository Path: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed (source repository on host, used as build context)
-Source Directories: ["src/", "crates/"] (directories containing source code)
-Test Directory: test (directory containing tests, default: "tests/")
-Base Image: nushell_nushell_0.106.0_0.108.0/base:latest (pre-configured image with all dependencies)
-Base Image Dockerfile: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/base/dockerfiles/Dockerfile (Dockerfile used to build the base image)
-Test Runner Script: harness.test_runner.run_milestone_tests (script to run milestone tests)
-Test Results Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results (where test results are saved)
-Work Directory: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 (harness workspace directory for this run)
-
-### Expected Outputs
-
-1. **Dockerfile**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_core_development.1/Dockerfile
-   - Build successfully on top of nushell_nushell_0.106.0_0.108.0/base:latest
-   - Support both START state (milestone-milestone_core_development.1-start) and END state (milestone-milestone_core_development.1-end)
-   - Configure environment for both states; if conflicts exist, prioritize END state
-   - Default to START state when container starts
-
-2. **Test Config**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_core_development.1/test_config.json
-   - Configure test runner to run tests as comprehensively as possible
-   - Include all test modes the repository supports (unit tests, integration tests, doc tests)
-   - Goal: maximize test coverage and collect complete test results
-
-3. **Skip Analysis Report**: /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_core_development.1/attempt_1/skip_analysis.md
-   - Analysis of all skipped/ignored tests based on test results
-   - Classification by skip reason (resolvable vs acceptable)
-   - Confirmation that no environment-related skips remain
-
----
-
-## RUST TEST COMMANDS
-
-### Cargo Test Commands
-
-```bash
-# Compile tests without running (test collection)
-cargo test --no-run
-
-# Compile tests for all targets (lib, bins, tests, examples, benches)
-cargo test --no-run --all-targets
-
-# Run all tests
-cargo test
-
-# Run tests with specific options
-cargo test --no-fail-fast -- --test-threads={workers}
-
-# Run tests with verbose output
-cargo test -- --nocapture
-
-# Run only unit tests (in src/)
-cargo test --lib
-
-# Run only integration tests (in tests/)
-cargo test --test '*'
-
-# Run tests for a specific package in a workspace
-cargo test -p package_name
-
-# Run tests for all packages in a workspace
-cargo test --workspace
-
-# Run tests with all features enabled
-cargo test --all-features
-
-# Run tests with specific features
-cargo test --features "feature1 feature2"
-
-# Run tests without default features
-cargo test --no-default-features
-
-# Run doc tests only
-cargo test --doc
-
-# List all tests without running
-cargo test -- --list
-
-# Run ignored tests
-cargo test -- --ignored
-
-# Run both normal and ignored tests
-cargo test -- --include-ignored
-```
-
-### Test Output Format
-
-Cargo test output follows this format:
-```
-running X tests
-test module::test_name ... ok
-test module::another_test ... FAILED
-test module::ignored_test ... ignored
-test module::skipped_test ... ignored, reason: "requires feature X"
-
-test result: FAILED. X passed; Y failed; Z ignored; 0 measured; 0 filtered out
-```
-
----
-
-## CRITICAL WORKFLOW (FOLLOW THIS ORDER)
-
-⚠️ **You MUST follow this exact workflow sequence:**
-
-```
-PHASE 0: Analyze Rust Project Structure
-    └── Check Cargo.toml → Identify workspace/crates → Determine features → List test targets
-
-PHASE 1: Write Initial Dockerfile & Test END State
-    └── Build minimal image → Test compilation for END state → Verify success
-
-PHASE 2: Test START State & Apply Minimal Patches (if needed)
-    └── Test START compilation → Apply patches if needed → Verify both states pass
-
-PHASE 2.5: Generate test_config.json
-    └── Create test configuration file required by test runner
-
-PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-    └── Run {test_runner_script} → Analyze ignored tests → Identify environment issues
-
-PHASE 4: Fix Environment Issues (iterate until resolved)
-    └── Update Dockerfile → Re-run tests → Verify issues are resolved
-
-PHASE 4.5: Validate Commit-Related Tests
-    └── Verify tests modified by milestone commits are collected AND not ignored
-
-PHASE 5: Finalize & Generate Skip Analysis
-    └── Set default state to START → Create skip_analysis.md → Clean up
-```
-
----
-
-### PHASE 0: Analyze Rust Project Structure
-**Understand the Rust project before proceeding**
-
-1. **Check project type (single crate vs workspace):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat Cargo.toml | head -30"
-   ```
-
-   **Single crate indicators:**
-   ```toml
-   [package]
-   name = "my_crate"
-   version = "0.1.0"
-   ```
-
-   **Workspace indicators:**
-   ```toml
-   [workspace]
-   members = [
-       "crate1",
-       "crate2",
-   ]
-   ```
-
-2. **List all crates in workspace (if applicable):**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cargo metadata --no-deps --format-version 1 | jq '.packages[].name'"
-   ```
-
-3. **Check available features:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-   ```
-
-4. **Identify test targets:**
-
-   ```bash
-   # Check for integration tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la tests/ 2>/dev/null"
-
-   # Check for unit tests in src/
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '#\[test\]' src/ | head -20"
-
-   # Check for doc tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && grep -r '```rust' src/ | head -10"
-
-   # Check for benchmark tests
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && ls -la benches/ 2>/dev/null"
-   ```
-
-5. **Check Rust toolchain requirements:**
-
-   ```bash
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "cd /testbed && cat rust-toolchain.toml rust-toolchain 2>/dev/null"
-   docker run --rm nushell_nushell_0.106.0_0.108.0/base:latest bash -c "rustc --version && cargo --version"
-   ```
-
-6. **Record your analysis:**
-
-   ```
-   PROJECT TYPE: <single_crate|workspace>
-   WORKSPACE MEMBERS: <list of crate names if workspace>
-   AVAILABLE FEATURES: <list of features>
-   TEST TARGETS: <lib|tests|examples|benches|doc>
-   RUST TOOLCHAIN: <stable|nightly|specific version>
-   ```
-
-⚠️ **DO NOT PROCEED to Phase 1 until you understand the project structure!**
-
-### IMPORTANT: Building on Base Image
-
-Since you are building on top of `nushell_nushell_0.106.0_0.108.0/base:latest`, you do NOT need to:
-- Install Rust toolchain
-- Install system dependencies
-- Run `cargo fetch` or `cargo build`
-- Configure environment paths
-
-Your Dockerfile only needs to:
-1. Checkout to the correct git states
-2. Apply minimal patches if START state has compilation issues
-
-**Temp image name**: `test-milestone-milestone_core_development.1-temp` (unique for this milestone)
-
-**CRITICAL RULES:**
-- ❌ **NEVER modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository
-- ✅ **Use a working copy for exploration** (create with `cp -r` if needed)
-- ✅ **Build using**: `docker build -t test-milestone-milestone_core_development.1-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-- ✅ **Clean up test images when done**: `docker rmi test-milestone-milestone_core_development.1-temp`
-
----
-
-### PHASE 1: Write Initial Dockerfile & Test END State
-**Start with a minimal Dockerfile based on the base image**
-
-1. **Write the initial Dockerfile:**
-
-   ```dockerfile
-   # Build on pre-configured base image
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Set umask to ensure files created in container are world-writable
-   # This prevents permission issues when test results are written to mounted volumes
-   RUN echo 'umask 000' >> /etc/bash.bashrc && \
-       echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-       chmod +x /entrypoint.sh
-   ENTRYPOINT ["/entrypoint.sh"]
-   CMD ["bash"]
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Checkout to END state (all features available)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_core_development.1-end
-   ```
-
-2. **Build and test END state compilation:**
-
-   ```bash
-   docker build -t test-milestone-milestone_core_development.1-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-   ```
-
-   Then test compilation:
-
-   ```bash
-   # For single crate
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && cargo test --no-run"
-
-   # For workspace
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && cargo test --workspace --no-run"
-
-   # With all features
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && cargo test --all-features --no-run"
-   ```
-
-3. **SUCCESS CRITERIA for END state:**
-   - Exit code 0
-   - Output shows "Compiling" and "Finished" messages
-   - NO compilation errors
-   - Test binaries are generated
-
-   ⚠️ **DO NOT PROCEED to Phase 2 until END state compiles!**
-
----
-
-### PHASE 2: Test START State & Apply Minimal Patches (if needed)
-**Handle the earlier codebase state which may lack features**
-
-1. **Test START state compilation:**
-
-   ```bash
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && git checkout milestone-milestone_core_development.1-start && cargo test --no-run"
-   ```
-
-2. **Handle results:**
-
-   **Case A: Compilation succeeds immediately**
-   ✅ Both states work! Proceed to PHASE 2.5.
-
-   **Case B: Compilation fails**
-   Apply Rust-specific minimal patches. See "RUST-SPECIFIC PATCHING" section.
-
-   ⚠️ **RUST COMPILATION**: Like Java, Rust requires ALL code to compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-3. **VALIDATION - Both states MUST compile:**
-   ```bash
-   docker build -t test-milestone-milestone_core_development.1-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-   # Test END state
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && git checkout milestone-milestone_core_development.1-end && cargo test --no-run"
-
-   # Test START state
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && git checkout milestone-milestone_core_development.1-start && cargo test --no-run"
-   ```
-
----
-
-### PHASE 2.5: Generate test_config.json
-**Create test configuration file required by test runner**
-
-The test_config.json defines how the test runner should execute tests.
-
-**Format:**
-```json
-[
-  {
-    "name": "config_name",
-    "test_states": ["start", "end"],
-    "test_cmd": "test command with placeholders",
-    "description": "What this configuration tests"
-  }
-]
-```
-
-**Available placeholders:** `{workers}`, `{timeout}`, `{output_file}`
-
-**Basic Example (Single Crate):**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests"
-  }
-]
-```
-
-**Workspace Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --workspace --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests"
-  }
-]
-```
-
-**With Features Example:**
-```json
-[
-  {
-    "name": "default",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --all-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All tests with all features"
-  },
-  {
-    "name": "no_default_features",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --no-default-features --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Tests without default features"
-  }
-]
-```
-
-**Multiple Test Targets Example:**
-```json
-[
-  {
-    "name": "unit",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --lib --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Unit tests only"
-  },
-  {
-    "name": "integration",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --test '*' --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "Integration tests only"
-  },
-  {
-    "name": "doc",
-    "test_states": ["start", "end"],
-    "test_cmd": "cargo test --doc --no-fail-fast 2>&1 | tee /output/{output_file}",
-    "description": "Doc tests only"
-  }
-]
-```
-
-**Guidelines:**
-1. **Always include "default" configuration** that runs all tests
-2. **Discover special test modes:**
-
-   ```bash
-   # Check for feature flags
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && grep -A20 '\[features\]' Cargo.toml"
-
-   # Check for test-specific features
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && grep -E 'test-|testing' Cargo.toml"
-
-   # Check for conditional compilation in tests
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && grep -r '#\[cfg(test)\]' src/ | head -10"
-
-   # Check for ignored tests that might need special flags
-   docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && grep -r '#\[ignore\]' . | head -20"
-   ```
-
----
-
-### PHASE 3: Run Tests & Analyze Ignored/Skipped Tests
-**Run full tests and identify environment-related issues**
-
-1. **Run tests using the test runner script:**
-
-   ```bash
-   python -m harness.test_runner.run_milestone_tests \
-     --milestone-id milestone_core_development.1 \
-     --image-name test-milestone-milestone_core_development.1-temp \
-     --output-dir /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results \
-     --language rust \
-     --test-framework cargo \
-     --max-retries 1
-   ```
-
-2. **Analyze test results:**
-
-   After tests complete, examine the output log for ignored tests:
-
-   ```bash
-   # Find ignored tests
-   grep "ignored" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_core_development.1/attempt_1/end_default.log
-
-   # Find failed tests
-   grep "FAILED" /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_core_development.1/attempt_1/end_default.log
-   ```
-
-3. **Classification of Rust test skip/ignore reasons:**
-
-   | Pattern | Classification | Action |
-   |---------|----------------|--------|
-   | `#[ignore]` without reason | Review | Check if intentional |
-   | `#[ignore = "requires X"]` | Depends | Check if X is environment-related |
-   | `#[ignore = "flaky"]` | Acceptable | Intentionally ignored |
-   | `#[ignore = "slow"]` | Acceptable | Run with `--include-ignored` if needed |
-   | `#[cfg(feature = "X")]` not enabled | Resolvable | Enable feature in test_config.json |
-   | Missing system library | Resolvable | Install in Dockerfile |
-   | Network-dependent test | Acceptable | Requires external resources |
-
-4. **Common Rust environment issues:**
-
-   | Error Pattern | Cause | Solution |
-   |---------------|-------|----------|
-   | `error: could not find native static library` | Missing C library | `RUN apt-get install libXXX-dev` |
-   | `error: linking with cc failed` | Missing linker deps | Install build-essential |
-   | `RUSTFLAGS` related | Build flags issue | Set `ENV RUSTFLAGS="..."` |
-   | `openssl` errors | Missing OpenSSL | Install `libssl-dev` |
-   | `pkg-config` errors | Missing pkg-config | Install `pkg-config` |
-
-5. **If resolvable environment issues found → Proceed to PHASE 4**
-   **If no resolvable issues → Proceed to PHASE 4.5**
-
----
-
-### PHASE 4: Fix Environment Issues
-**Resolve environment-related issues by updating Dockerfile**
-
-**Common fixes for Rust projects:**
-
-```dockerfile
-# Install missing system libraries
-RUN apt-get update && apt-get install -y \
-    libssl-dev \
-    pkg-config \
-    libclang-dev \
-    && rm -rf /var/lib/apt/lists/*
-
-# Set environment variables
-ENV RUST_BACKTRACE=1
-ENV CARGO_NET_GIT_FETCH_WITH_CLI=true
-
-# Enable specific features by default
-ENV CARGO_FEATURE_FLAGS="--all-features"
-
-# Fix OpenSSL issues
-ENV OPENSSL_DIR=/usr
-ENV OPENSSL_LIB_DIR=/usr/lib/x86_64-linux-gnu
-ENV OPENSSL_INCLUDE_DIR=/usr/include
-
-# Fetch dependencies again after changes
-RUN cd /testbed && cargo fetch
-```
-
-**Iteration loop:**
-
-1. Update Dockerfile with fix
-2. Rebuild: `docker build -t test-milestone-milestone_core_development.1-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed`
-3. Re-run tests with test runner script
-4. Check if issue is resolved by comparing results
-5. Repeat until no resolvable issues remain
-
----
-
-### PHASE 4.5: Validate Commit-Related Tests
-**Ensure tests modified by milestone commits are collected AND not ignored**
-
-1. **Run the collect_milestone_patched_tests.py script:**
-
-   ```bash
-   python -m harness.prepare_images.collect_milestone_patched_tests \
-     /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 \
-     --repo /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed \
-     --milestone milestone_core_development.1
-   ```
-
-   This script:
-   - Extracts symbol changes (added/modified/deleted tests) from each commit
-   - Aggregates patched tests at the milestone level
-   - Matches patched test IDs to actual test results (nodeids)
-   - Generates a report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_core_development.1.json`
-
-2. **Check the output JSON file:**
-
-   The output format is:
-   ```json
-   {
-     "milestone_id": "milestone_core_development.1",
-     "commits": ["abc1234", "def5678"],
-     "test_ids": {
-       "added": [...],      // Tests added by commits
-       "modified": [...],   // Tests modified by commits
-       "deleted": [...],    // Tests deleted by commits
-       "effective": [...]   // Effective tests = (added ∪ modified) - deleted
-     },
-     "collected": {
-       "patched_in_results": [...],      // ✅ Patched tests found in test results
-       "patched_not_in_results": [],     // ⚠️ MUST BE EMPTY!
-       "test_id_to_nodeid": {...},       // Mapping from test_id to nodeid
-       "status": {
-         "start": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []},
-         "end": {"passed": [], "failed": [], "skipped": [], "error": [], "unknown": []}
-       },
-       "transitions": {
-         "fixed": [],        // start failed/error -> end passed
-         "broken": [],       // start passed -> end failed/error
-         "still_passing": [],
-         "still_failing": [],
-         "other": []
-       }
-     },
-     "summary": {...}
-   }
-   ```
-
-3. **⚠️ CRITICAL VALIDATION: `collected.patched_not_in_results` MUST be empty!**
-
-   This field lists patched tests that were NOT found in test results. If not empty, it means:
-   - Some patched tests failed to compile (possibly commented out incorrectly)
-   - Some patched tests were excluded from test collection
-   - The test_id to nodeid matching failed
-
-   **How to verify:**
-   ```bash
-   # Check if patched_not_in_results is empty
-   cat /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/milestone_patched_tests/milestone_core_development.1.json | jq '.collected.patched_not_in_results'
-   # Expected output: []
-   ```
-
-4. **If `patched_not_in_results` is NOT empty:**
-   - Identify which tests are missing from results
-   - Check if those tests were incorrectly commented out or excluded
-   - Return to PHASE 4 to fix environment issues
-   - Re-run tests and re-validate until `patched_not_in_results` is empty
-
-5. **Also verify no commit-related tests are ignored:**
-   - Check `collected.status.end.skipped` - patched tests should not be ignored
-   - If ignored due to environment issues, return to PHASE 4 to fix
-
----
-
-### PHASE 5: Finalize Dockerfile & Generate Skip Analysis
-**Set default state to START, create skip analysis report, and clean up**
-
-1. **Ensure Dockerfile sets default state to START:**
-
-   ```dockerfile
-   FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-   # Remove the original /testbed from base image and copy local testbed
-   # NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-   RUN rm -rf /testbed
-   COPY . /testbed/
-
-   # Environment fixes (if any)
-   # RUN apt-get update && apt-get install -y ...
-   # ENV RUST_BACKTRACE=1
-
-   # Checkout to END state (for any patching if needed)
-   # Tags already exist in testbed - just checkout, don't create tags
-   RUN cd /testbed && git checkout milestone-milestone_core_development.1-end
-
-   # [If patches needed, add them here]
-
-   # Set default git state to START
-   RUN cd /testbed && git checkout milestone-milestone_core_development.1-start
-   ```
-
-2. **Final validation**
-
-3. **Generate skip analysis report at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_core_development.1/attempt_1/skip_analysis.md`**
-
-4. **Clean up:**
-   ```bash
-   docker rmi test-milestone-milestone_core_development.1-temp
-   ```
-
----
-
-## RUST-SPECIFIC PATCHING
-
-### How to Apply Patches in Dockerfile
-
-⚠️ **Apply patches using patch files or sed commands in the Dockerfile. DO NOT modify /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed!**
-
-⚠️ **CRITICAL**: After applying patches, you MUST commit the changes and move the tag to preserve patches across git checkouts. Without this step, patches will be lost when switching between START and END states!
-
-⚠️ **NEVER DELETE FILES**: When applying patches, you must NEVER delete any files (e.g., using `rm`, `git rm`, or similar commands). Only modify file contents. Deleting files can break test discovery and cause unexpected issues.
-
-### Rust Compilation Error Handling
-
-**CRITICAL**: Rust is a compiled language. Unlike Python/JavaScript, ALL code must compile successfully before ANY test can run. A single compilation error blocks the entire test suite.
-
-**Goal**: Comment out the minimal amount of code that causes compilation errors, so that the maximum number of tests can compile and run.
-
-### Patching Strategies for Rust
-
-#### Strategy 1: Use `#[cfg]` Attributes (Preferred)
-
-The best way to handle compilation errors in Rust is to use conditional compilation:
-
-```rust
-// Original code that fails in START state:
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();  // This doesn't exist in START state
-    assert!(result.is_ok());
-}
-
-// Patched version using cfg:
-#[cfg(feature = "new_feature")]
-#[test]
-fn test_new_feature() {
-    let result = new_api_function();
-    assert!(result.is_ok());
-}
-```
-
-**Dockerfile example:**
-```dockerfile
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start && \
-    # Add cfg attribute before test function
-    sed -i 's/#\[test\]\nfn test_new_feature/#[cfg(feature = "env_patch")]\n#[test]\nfn test_new_feature/' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add cfg guard for test_new_feature" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-```
-
-#### Strategy 2: Comment Out Test Functions
-
-When a test function uses APIs that don't exist in START state:
-
-```dockerfile
-# Comment out a specific test function (from line 45 to line 55)
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start && \
-    sed -i '45,55 s/^/\/\/ [ENV-PATCH] /' src/tests.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_new_feature for START state" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-```
-
-**Better approach using markers:**
-```dockerfile
-# Find and comment out specific test
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start && \
-    # Add /* before #[test] and */ after the closing brace
-    sed -i '/#\[test\]/,/^}$/{
-        /fn test_problematic/,/^}$/ {
-            s/^/\/\/ [ENV-PATCH] /
-        }
-    }' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out test_problematic" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-```
-
-#### Strategy 3: Comment Out Entire Module (Last Resort)
-
-Only when module-level code causes compilation errors:
-
-```dockerfile
-# Comment out entire test module
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start && \
-    sed -i '/^mod tests {/,/^}/ s/^/\/\/ [ENV-PATCH] /' src/lib.rs && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests module" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-```
-
-#### Strategy 4: Modify Cargo.toml Features
-
-If the issue is feature-related:
-
-```dockerfile
-# Add a feature flag for conditional compilation
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start && \
-    sed -i '/\[features\]/a env_patch = []' Cargo.toml && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add env_patch feature flag" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-```
-
-### Common Rust Compilation Error Patterns
-
-| Error Pattern | Cause | Solution |
-|---------------|-------|----------|
-| `cannot find function X in this scope` | Function doesn't exist in START | Comment out test using it |
-| `cannot find type X in this scope` | Type doesn't exist in START | Comment out test using it |
-| `trait X is not implemented for Y` | Trait impl missing in START | Comment out test using it |
-| `mismatched types` | API signature changed | Comment out test using it |
-| `unresolved import X::Y` | Module/item doesn't exist | Comment out import and tests |
-| `no method named X found` | Method doesn't exist in START | Comment out test using it |
-| `struct X has no field Y` | Field doesn't exist in START | Comment out test using it |
-| `lifetime mismatch` | Lifetime requirements changed | Comment out test using it |
-
-### Example: Full Patching Workflow
-
-```dockerfile
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Checkout to START state and apply patches
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start && \
-    # Patch 1: Comment out test that uses new API (lines 120-135)
-    sed -i '120,135 s/^/\/\/ [ENV-PATCH] /' src/api/tests.rs && \
-    # Patch 2: Comment out test that uses new struct field (lines 45-52)
-    sed -i '45,52 s/^/\/\/ [ENV-PATCH] /' tests/integration_test.rs && \
-    # Commit patches and move tag
-    git add -A && \
-    git commit -m "[ENV-PATCH] Comment out tests using APIs not in START state" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-
-# Verify END state still compiles
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-end && cargo test --no-run
-
-# Set default to START
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start
-```
-
-### Verify Patches Persist
-
-```bash
-docker build -t test-milestone-milestone_core_development.1-temp -f Dockerfile /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed
-
-# Test START state (verify patches applied)
-docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && cargo test --no-run"
-
-# Test END state (verify patches persist after checkout)
-docker run --rm test-milestone-milestone_core_development.1-temp bash -c "cd /testbed && git checkout milestone-milestone_core_development.1-end && cargo test --no-run"
-```
-
----
-
-## FINAL CHECKLIST
-
-### Before Completing Your Work
-Ensure you have:
-- [ ] **PHASE 0 completed**: Analyzed Rust project structure (single crate vs workspace, features, test targets)
-- [ ] Dockerfile based on `FROM nushell_nushell_0.106.0_0.108.0/base:latest`
-- [ ] **Testbed replaced**: `RUN rm -rf /testbed` + `COPY . /testbed/` included in Dockerfile
-- [ ] Both START and END states compile successfully (`cargo test --no-run`)
-- [ ] Minimal patches only (if needed)
-- [ ] No artificial skips
-- [ ] **Patches committed and tags moved** (if patches applied):
-  - [ ] Used `git add -A && git commit` after applying patches
-  - [ ] Used `git tag -f <TAG> HEAD` to move tag to patched commit
-  - [ ] Verified patches persist across `git checkout` (test switching between states)
-- [ ] **Full tests run** using test runner script with `--language rust --test-framework cargo`
-- [ ] **No resolvable environment-related issues** remaining
-- [ ] **Commit-related tests validated** using `collect_milestone_patched_tests.py`:
-  - [ ] Ran: `python -m harness.prepare_images.collect_milestone_patched_tests /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003 --milestone milestone_core_development.1`
-  - [ ] **`collected.patched_not_in_results` is EMPTY** (all patched tests found in results)
-  - [ ] No patched tests in `collected.status.end.skipped` (no environment-related ignores)
-- [ ] **test_config.json** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/dockerfiles/milestone_core_development.1/test_config.json` with correct cargo test command
-- [ ] **Skip analysis report** generated at `/data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/test_results/milestone_core_development.1/attempt_1/skip_analysis.md`
-- [ ] Default state is START
-- [ ] Cleaned up: `docker rmi test-milestone-milestone_core_development.1-temp`
-
----
-
-## COMMON PITFALLS TO AVOID
-
-❌ **Apply patches without committing and moving tags** - patches will be lost on `git checkout`!
-❌ **Forget to verify patches persist** - always test switching between START and END states after patching
-❌ **Modify files in /data2/gangda/agent-bench/harness_workspace/nushell_nushell_0.106.0_0.108.0/baseline_rerun_stage4_003/testbed** - this is the source repository, use Dockerfile commands instead
-❌ **Skip PHASE 0** - understanding Rust project structure is essential
-❌ **Proceed to next phase before current phase compiles** - validate each phase before moving on
-❌ **Comment out entire files/crates** - only comment out specific functions/tests
-❌ **Forget workspace flag** - use `cargo test --workspace` for workspace projects
-❌ **Ignore feature flags** - check if tests require specific features to be enabled
-
-✅ **Always commit patches and move tags** (`git add -A && git commit && git tag -f <TAG> HEAD`)
-✅ **Test both states after applying patches** to ensure patches persist across checkout
-✅ **Document patched code** in Dockerfile comments (which functions, why)
-✅ **Use `[ENV-PATCH]` prefix** in commit messages and comments for tracking
-✅ **Use conditional compilation** (`#[cfg]`) when possible instead of commenting out
-✅ **Check all feature combinations** if the project uses feature flags

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_core_development.1.bak/test_config.json

@@ -1,12 +0,0 @@
-[
-  {
-    "name": "default",
-    "test_states": [
-      "start",
-      "end"
-    ],
-    "test_cmd": "cd /testbed && cargo test --workspace --profile ci --no-fail-fast -- --test-threads={workers} 2>&1 | tee /output/{output_file}",
-    "description": "All workspace tests excluding plugin crates with CI profile",
-    "framework": "cargo"
-  }
-]

nushell_nushell_0.106.0_0.108.0/dockerfiles/milestone_core_development.1/Dockerfile.bak

@@ -1,216 +0,0 @@
-# Build on pre-configured base image
-FROM nushell_nushell_0.106.0_0.108.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Configure git user for commits
-RUN git config --global user.email "env-patch@test.local" && \
-    git config --global user.name "ENV Patch"
-
-# Set cargo to use fewer parallel jobs to avoid "too many open files" error
-ENV CARGO_BUILD_JOBS=4
-ENV RUST_BACKTRACE=1
-
-# Remove the original /testbed from base image and copy local testbed with milestone tags
-COPY . /testbed/
-
-# Clean any untracked files that might conflict with checkout
-RUN cd /testbed && git clean -fd
-
-# =====================================================
-# [ENV-PATCH] Apply patches for END state compilation
-# =====================================================
-
-# Checkout to END state first
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-end
-
-# [ENV-PATCH] Fix Cargo.toml - nu-mcp crate doesn't exist
-RUN cd /testbed && \
-    sed -i '/^  "crates\/nu-mcp",$/d' Cargo.toml && \
-    sed -i 's|^nu-mcp = { path = "\./crates/nu-mcp".*$|# [ENV-PATCH] nu-mcp dependency removed - crate not present|' Cargo.toml && \
-    sed -i 's|^  "dep:nu-mcp",$|  # [ENV-PATCH] "dep:nu-mcp", # crate not present|' Cargo.toml && \
-    sed -i 's|^  "nu-mcp/mcp",$|  # [ENV-PATCH] "nu-mcp/mcp", # crate not present|' Cargo.toml
-
-# [ENV-PATCH] Fix rust-toolchain.toml to use 1.86.0 instead of 1.88.0
-RUN cd /testbed && \
-    sed -i 's/channel = "1\.88\.0"/channel = "1.86.0"/' rust-toolchain.toml
-
-# [ENV-PATCH] Fix version and rust-version to match base image
-RUN cd /testbed && \
-    sed -i 's/^rust-version = "1\.88\.0"$/rust-version = "1.86.0"/' Cargo.toml && \
-    sed -i 's/^version = "0\.107\.1"$/version = "0.106.0"/' Cargo.toml && \
-    sed -i 's/version = "0\.107\.1"/version = "0.106.0"/g' Cargo.toml
-
-# [ENV-PATCH] Fix workspace dependency versions for END state
-# Keep uu_* at 0.2.2 (code uses newer APIs), downgrade other problematic deps
-RUN cd /testbed && \
-    # Downgrade rusqlite to 0.31 (code uses DatabaseName which doesn't exist in 0.37)
-    sed -i 's/^rusqlite = "0\.37"$/rusqlite = "0.31"/' Cargo.toml && \
-    # Downgrade reedline to 0.41 (code uses CutInside/YankInside which don't exist in 0.42)
-    sed -i 's/^reedline = "0\.42\.0"$/reedline = "0.41.0"/' Cargo.toml
-
-# [ENV-PATCH] Fix sqlite feature - remove nu-cli/sqlite and nu-protocol/sqlite which don't exist
-RUN cd /testbed && \
-    sed -i '/^sqlite = \[$/,/^\]$/c\sqlite = [\n  "nu-command/sqlite",\n  "nu-std/sqlite",\n  "reedline/sqlite"\n]' Cargo.toml
-
-# Fetch updated dependencies for END state
-RUN cd /testbed && cargo fetch
-
-# [ENV-PATCH] Fix table.rs - Duration::from_value doesn't exist, implement alternative using as_duration()
-RUN cd /testbed && \
-    perl -i -pe 'BEGIN{undef $/;} s/"batch_duration" => \{\s+match Duration::from_value\(val\.clone\(\)\)\.map_err\(ConfigError::from\) \{\s+Ok\(val\) => self\.batch_duration = val,\s+Err\(err\) => errors\.error\(err\),\s+\}\s+\}/"batch_duration" => {\n                    match val.as_duration() {\n                        Ok(nanos) if nanos >= 0 => {\n                            self.batch_duration = Duration::from_nanos(nanos as u64);\n                        }\n                        Ok(_) => errors.invalid_value(path, "a positive duration", val),\n                        Err(_) => errors.type_mismatch(path, Type::Duration, val),\n                    }\n                }/smg' crates/nu-protocol/src/config/table.rs
-
-# [ENV-PATCH] Fix reedline_config.rs - CutInside, YankInside, and ViChangeMode don't exist in reedline 0.41
-# Comment out lines 1050-1053 (vichangemode) and lines 1292-1305 (CutInside/YankInside)
-RUN cd /testbed && \
-    sed -i '1050,1053s/^/\/\/ [ENV-PATCH] /' crates/nu-cli/src/reedline_config.rs && \
-    sed -i '1292,1305s/^/\/\/ [ENV-PATCH] /' crates/nu-cli/src/reedline_config.rs
-
-# [ENV-PATCH] Fix PipelineData::value() -> PipelineData::Value() everywhere
-RUN cd /testbed && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-command/src/filesystem/umkdir.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-cli/tests/completions/support/completions_helpers.rs
-
-# [ENV-PATCH] Fix nu-plugin-core tests - PipelineData case changes
-RUN cd /testbed && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::list_stream(/PipelineData::ListStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::byte_stream(/PipelineData::ByteStream(/g' crates/nu-plugin-core/src/interface/tests.rs
-
-# [ENV-PATCH] Fix html.rs test - revert to test_examples (test_examples_with_commands doesn't exist in nu-cmd-extra)
-RUN cd /testbed && \
-    sed -i 's/use crate::test_examples_with_commands;/use crate::test_examples;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/use nu_command::ToXml;/\/\/ [ENV-PATCH] use nu_command::ToXml;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/test_examples_with_commands(ToHtml {}, \&\[&ToXml\])/test_examples(ToHtml {})/' crates/nu-cmd-extra/src/extra/formats/to/html.rs
-
-# [ENV-PATCH] Fix completer.rs - need_fallback is immutable, comment out the assignment
-RUN cd /testbed && \
-    sed -i 's/\*need_fallback = false/\/\/ [ENV-PATCH] *need_fallback = false/' crates/nu-cli/src/completions/completer.rs
-
-# [ENV-PATCH] Fix is_multiple_of - unstable feature in Rust 1.86
-RUN cd /testbed && \
-    sed -i 's/\.is_multiple_of(2)/ % 2 == 0/g' crates/nu-parser/src/parser.rs && \
-    sed -i 's/i\.is_multiple_of(self\.chunk)/i % self.chunk == 0/g' crates/nu-pretty-hex/src/pretty_hex.rs && \
-    sed -i 's/i\.is_multiple_of(self\.group \* self\.chunk)/i % (self.group * self.chunk) == 0/g' crates/nu-pretty-hex/src/pretty_hex.rs && \
-    sed -i 's/self\.cells\.len()\.is_multiple_of(num_columns)/self.cells.len() % num_columns == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/self\.cell_count\.is_multiple_of(theoretical_min_num_cols)/self.cell_count % theoretical_min_num_cols == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/self\.cell_count\.is_multiple_of(num_lines)/self.cell_count % num_lines == 0/g' crates/nu-term-grid/src/grid.rs && \
-    sed -i 's/values\.len()\.is_multiple_of(2)/values.len() % 2 == 0/g' crates/nu-command/src/math/median.rs
-
-# [ENV-PATCH] Fix test_parser.rs - comment out InvalidBinaryString tests (lines 497-537)
-RUN cd /testbed && \
-    sed -i '497,537s/^/\/\/ [ENV-PATCH] /' crates/nu-parser/tests/test_parser.rs
-
-# [ENV-PATCH] Comment out test files using ConfigFileKind which doesn't exist
-RUN cd /testbed && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in this state\n\/\* /' crates/nu-command/tests/commands/config_env_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_env_default.rs && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in this state\n\/\* /' crates/nu-command/tests/commands/config_nu_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_nu_default.rs
-
-# [ENV-PATCH] Comment out NuOpts::experimental usage in external.rs
-RUN cd /testbed && \
-    sed -i 's/experimental: vec!\["pipefail"\.to_string()\],/\/\/ [ENV-PATCH] experimental: vec!["pipefail".to_string()],/' tests/shell/pipeline/commands/external.rs
-
-# [ENV-PATCH] Fix test_signature.rs - comment out 'completion: None' lines that don't exist
-RUN cd /testbed && \
-    sed -i 's/^            completion: None,$/            \/\/ [ENV-PATCH] completion: None,/' crates/nu-protocol/tests/test_signature.rs
-
-# Commit END state patches and move tag
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix Cargo.toml and code compatibility for END state" && \
-    git tag -f milestone-milestone_core_development.1-end HEAD
-
-# =====================================================
-# [ENV-PATCH] Apply patches for START state
-# =====================================================
-
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start
-
-# [ENV-PATCH] Fix rust-toolchain.toml for START state
-RUN cd /testbed && \
-    sed -i 's/channel = "1\.88\.0"/channel = "1.86.0"/' rust-toolchain.toml
-
-# [ENV-PATCH] Fix Cargo.toml for START state
-RUN cd /testbed && \
-    # Remove nu-mcp from workspace members
-    sed -i '/^  "crates\/nu-mcp",$/d' Cargo.toml && \
-    sed -i 's|^nu-mcp = { path = "\./crates/nu-mcp".*$|# [ENV-PATCH] nu-mcp dependency removed - crate not present|' Cargo.toml && \
-    sed -i 's|^  "dep:nu-mcp",$|  # [ENV-PATCH] "dep:nu-mcp", # crate not present|' Cargo.toml && \
-    sed -i 's|^  "nu-mcp/mcp",$|  # [ENV-PATCH] "nu-mcp/mcp", # crate not present|' Cargo.toml && \
-    # Fix rust-version
-    sed -i 's/^rust-version = "1\.88\.0"$/rust-version = "1.86.0"/' Cargo.toml && \
-    # Fix version
-    sed -i 's/^version = "0\.107\.1"$/version = "0.106.0"/' Cargo.toml && \
-    sed -i 's/version = "0\.107\.1"/version = "0.106.0"/g' Cargo.toml && \
-    # Downgrade rusqlite
-    sed -i 's/^rusqlite = "0\.37"$/rusqlite = "0.31"/' Cargo.toml && \
-    # Downgrade reedline
-    sed -i 's/^reedline = "0\.42\.0"$/reedline = "0.41.0"/' Cargo.toml && \
-    # Downgrade ureq to 2.12 for START state
-    sed -i 's/^ureq = { version = "=3\.0\.12"/ureq = { version = "2.12"/' Cargo.toml && \
-    # Downgrade uu_* crates to 0.0.30 for START state (code uses older APIs)
-    sed -i 's/^uu_cp = "0\.2\.2"$/uu_cp = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mkdir = "0\.2\.2"$/uu_mkdir = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mktemp = "0\.2\.2"$/uu_mktemp = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_mv = "0\.2\.2"$/uu_mv = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_touch = "0\.2\.2"$/uu_touch = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_uname = "0\.2\.2"$/uu_uname = "0.0.30"/' Cargo.toml && \
-    sed -i 's/^uu_whoami = "0\.2\.2"$/uu_whoami = "0.0.30"/' Cargo.toml && \
-    # Fix sqlite feature
-    sed -i '/^sqlite = \[$/,/^\]$/c\sqlite = [\n  "nu-command/sqlite",\n  "nu-std/sqlite",\n  "reedline/sqlite"\n]' Cargo.toml
-
-# [ENV-PATCH] Fix nu-command/Cargo.toml for START state - fix ureq features for ureq 2.x
-RUN cd /testbed && \
-    sed -i 's|"ureq/platform-verifier"|# [ENV-PATCH] "ureq/platform-verifier" # removed - feature not in ureq 2.x|' crates/nu-command/Cargo.toml && \
-    sed -i 's|"ureq/rustls"|"ureq/tls"|' crates/nu-command/Cargo.toml
-
-# [ENV-PATCH] Fix test_signature.rs - comment out 'completion: None' lines that don't exist in START state
-RUN cd /testbed && \
-    sed -i 's/^            completion: None,$/            \/\/ [ENV-PATCH] completion: None,/' crates/nu-protocol/tests/test_signature.rs
-
-# [ENV-PATCH] Fix test files using APIs that don't exist in START state
-RUN cd /testbed && \
-    # Fix PipelineData::value -> PipelineData::Value in all test files
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-plugin-test-support/tests/custom_value/mod.rs && \
-    sed -i 's/PipelineData::value(/PipelineData::Value(/' crates/nu-cli/tests/completions/support/completions_helpers.rs && \
-    # Fix nu-plugin-core tests - PipelineData case changes
-    sed -i 's/PipelineData::value(/PipelineData::Value(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::list_stream(/PipelineData::ListStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    sed -i 's/PipelineData::byte_stream(/PipelineData::ByteStream(/g' crates/nu-plugin-core/src/interface/tests.rs && \
-    # Comment out test functions using ParseError::InvalidBinaryString (lines 497-537)
-    sed -i '497,537s/^/\/\/ [ENV-PATCH] /' crates/nu-parser/tests/test_parser.rs && \
-    # Comment out test files using ConfigFileKind which doesn't exist in START
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in START state\n\/\* /' crates/nu-command/tests/commands/config_env_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_env_default.rs && \
-    sed -i '1s/^/\/\/ [ENV-PATCH] Entire file commented out - uses APIs not in START state\n\/\* /' crates/nu-command/tests/commands/config_nu_default.rs && \
-    echo '*/' >> crates/nu-command/tests/commands/config_nu_default.rs && \
-    # Comment out NuOpts::experimental usage in external.rs
-    sed -i 's/experimental: vec!\["pipefail"\.to_string()\],/\/\/ [ENV-PATCH] experimental: vec!["pipefail".to_string()],/' tests/shell/pipeline/commands/external.rs
-
-# [ENV-PATCH] Fix stor/insert.rs - remove EngineState parameter from process() calls in tests (START state doesn't have engine_state param yet)
-RUN cd /testbed && \
-    perl -i -pe 'BEGIN{undef $/;} s/process\(\s*&EngineState::new\(\),\s*/process(/smg' crates/nu-command/src/stor/insert.rs
-
-# [ENV-PATCH] Fix html.rs test - revert to test_examples (test_examples_with_commands doesn't exist in nu-cmd-extra)
-RUN cd /testbed && \
-    sed -i 's/use crate::test_examples_with_commands;/use crate::test_examples;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/use nu_command::ToXml;/\/\/ [ENV-PATCH] use nu_command::ToXml;/' crates/nu-cmd-extra/src/extra/formats/to/html.rs && \
-    sed -i 's/test_examples_with_commands(ToHtml {}, \&\[&ToXml\])/test_examples(ToHtml {})/' crates/nu-cmd-extra/src/extra/formats/to/html.rs
-
-# Commit START state patches and move tag
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Fix Cargo.toml compatibility for START state" && \
-    git tag -f milestone-milestone_core_development.1-start HEAD
-
-# Set default git state to START
-RUN cd /testbed && git checkout milestone-milestone_core_development.1-start

scikit-learn_scikit-learn_1.5.2_1.6.0/dockerfiles/M06/Dockerfile.bak

@@ -1,213 +0,0 @@
-# Build on pre-configured base image
-FROM scikit-learn_scikit-learn_1.5.2_1.6.0/base:latest
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# [ENV-PATCH] Install array_api_compat and array_api_strict for array API tests
-# These are required by test_label_encoder_array_api_compliance and test_isin
-RUN pip install array_api_compat array_api_strict
-
-# Configure git identity for commits
-RUN git config --global user.email "env-patch@localhost" && \
-    git config --global user.name "ENV Patch"
-
-# Remove the original /testbed from base image and copy local testbed
-# NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# Checkout to END state first (all features available)
-# Tags already exist in testbed - just checkout, don't create tags
-RUN cd /testbed && git checkout milestone-M06-end
-
-# [ENV-PATCH] Fix test_base.py import error - is_clusterer doesn't exist at this state
-# Wrap the is_clusterer import in try-except using Python script
-RUN cd /testbed && python3 << 'EOF'
-import re
-
-# Read the file
-with open('sklearn/tests/test_base.py', 'r') as f:
-    content = f.read()
-
-# Replace the import - remove is_clusterer from the import block
-old_import = '''from sklearn.base import (
-    BaseEstimator,
-    OutlierMixin,
-    TransformerMixin,
-    clone,
-    is_classifier,
-    is_clusterer,
-    is_regressor,
-)'''
-new_import = '''from sklearn.base import (
-    BaseEstimator,
-    OutlierMixin,
-    TransformerMixin,
-    clone,
-    is_classifier,
-    is_regressor,
-)
-
-# [ENV-PATCH] Conditional import for is_clusterer - may not exist in all versions
-try:
-    from sklearn.base import is_clusterer
-except ImportError:
-    is_clusterer = None'''
-
-content = content.replace(old_import, new_import)
-
-# Add skipif decorator to test_is_clusterer
-old_test = '''def test_is_clusterer(estimator, expected_result):
-    assert is_clusterer(estimator) == expected_result'''
-new_test = '''@pytest.mark.skipif(is_clusterer is None, reason="[ENV-PATCH] is_clusterer not available in this version")
-def test_is_clusterer(estimator, expected_result):
-    assert is_clusterer(estimator) == expected_result'''
-
-content = content.replace(old_test, new_test)
-
-# Write back
-with open('sklearn/tests/test_base.py', 'w') as f:
-    f.write(content)
-print('Patched test_base.py successfully')
-EOF
-
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Make is_clusterer import conditional in test_base.py" && \
-    git tag -f milestone-M06-end HEAD
-
-# Apply patches to START state (including test_array_api.py fix)
-RUN cd /testbed && git checkout milestone-M06-start && python3 << 'EOF'
-import re
-
-# ===== Patch 1: test_base.py =====
-with open('sklearn/tests/test_base.py', 'r') as f:
-    content = f.read()
-
-old_import = '''from sklearn.base import (
-    BaseEstimator,
-    OutlierMixin,
-    TransformerMixin,
-    clone,
-    is_classifier,
-    is_clusterer,
-    is_regressor,
-)'''
-new_import = '''from sklearn.base import (
-    BaseEstimator,
-    OutlierMixin,
-    TransformerMixin,
-    clone,
-    is_classifier,
-    is_regressor,
-)
-
-# [ENV-PATCH] Conditional import for is_clusterer - may not exist in all versions
-try:
-    from sklearn.base import is_clusterer
-except ImportError:
-    is_clusterer = None'''
-
-content = content.replace(old_import, new_import)
-
-old_test = '''def test_is_clusterer(estimator, expected_result):
-    assert is_clusterer(estimator) == expected_result'''
-new_test = '''@pytest.mark.skipif(is_clusterer is None, reason="[ENV-PATCH] is_clusterer not available in this version")
-def test_is_clusterer(estimator, expected_result):
-    assert is_clusterer(estimator) == expected_result'''
-
-content = content.replace(old_test, new_test)
-
-with open('sklearn/tests/test_base.py', 'w') as f:
-    f.write(content)
-print('Patched test_base.py successfully')
-
-# ===== Patch 2: test_array_api.py =====
-with open('sklearn/utils/tests/test_array_api.py', 'r') as f:
-    content = f.read()
-
-# Make _isin import conditional
-old_import_block = '''from sklearn.utils._array_api import (
-    _ArrayAPIWrapper,
-    _asarray_with_order,
-    _atol_for_type,
-    _average,
-    _convert_to_numpy,
-    _estimator_with_converted_arrays,
-    _is_numpy_namespace,
-    _isin,
-    _nanmax,
-    _nanmin,
-    _NumPyAPIWrapper,
-    _ravel,
-    device,
-    get_namespace,
-    get_namespace_and_device,
-    indexing_dtype,
-    supported_float_dtypes,
-    yield_namespace_device_dtype_combinations,
-)'''
-
-new_import_block = '''from sklearn.utils._array_api import (
-    _ArrayAPIWrapper,
-    _asarray_with_order,
-    _atol_for_type,
-    _average,
-    _convert_to_numpy,
-    _estimator_with_converted_arrays,
-    _is_numpy_namespace,
-    _nanmax,
-    _nanmin,
-    _NumPyAPIWrapper,
-    _ravel,
-    device,
-    get_namespace,
-    get_namespace_and_device,
-    indexing_dtype,
-    supported_float_dtypes,
-    yield_namespace_device_dtype_combinations,
-)
-
-# [ENV-PATCH] Conditional import for _isin - may not exist in all versions
-try:
-    from sklearn.utils._array_api import _isin
-except ImportError:
-    _isin = None'''
-
-content = content.replace(old_import_block, new_import_block)
-
-# Add skipif decorator to test_isin
-# Find the line with decorators and the function definition
-old_test_def = '''@pytest.mark.parametrize("element_size", [6, 10, 14])
-@pytest.mark.parametrize("int_dtype", ["int16", "int32", "int64", "uint8"])
-def test_isin(
-    array_namespace, device, _, invert, assume_unique, element_size, int_dtype
-):'''
-
-new_test_def = '''@pytest.mark.skipif(_isin is None, reason="[ENV-PATCH] _isin not available in this version")
-@pytest.mark.parametrize("element_size", [6, 10, 14])
-@pytest.mark.parametrize("int_dtype", ["int16", "int32", "int64", "uint8"])
-def test_isin(
-    array_namespace, device, _, invert, assume_unique, element_size, int_dtype
-):'''
-
-content = content.replace(old_test_def, new_test_def)
-
-with open('sklearn/utils/tests/test_array_api.py', 'w') as f:
-    f.write(content)
-print('Patched test_array_api.py successfully')
-EOF
-
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Make is_clusterer and _isin imports conditional" && \
-    git tag -f milestone-M06-start HEAD
-
-# Rebuild scikit-learn for START state (default)
-RUN cd /testbed && pip install --no-build-isolation --editable .

scikit-learn_scikit-learn_1.5.2_1.6.0/dockerfiles/M12.1/Dockerfile.bak

@@ -1,259 +0,0 @@
-# Build on pre-configured base image
-FROM scikit-learn_scikit-learn_1.5.2_1.6.0/base:latest
-
-# Configure git identity for commits
-RUN git config --global user.email "env-patch@milestone.local" && \
-    git config --global user.name "Milestone Environment Patch"
-
-# Set umask to ensure files created in container are world-writable
-# This prevents permission issues when test results are written to mounted volumes
-RUN echo 'umask 000' >> /etc/bash.bashrc && \
-    echo '#!/bin/bash\numask 000\nexec "$@"' > /entrypoint.sh && \
-    chmod +x /entrypoint.sh
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["bash"]
-
-# Remove the original /testbed from base image and copy local testbed
-# NOTE: The testbed already contains milestone tags - DO NOT create them with `git tag`
-RUN rm -rf /testbed
-COPY . /testbed/
-
-# ============================================================================
-# [ENV-PATCH] Create stub modules/functions to allow test collection
-# These APIs are from OTHER milestones but test files import them
-# Stubs raise NotImplementedError when called, but allow test collection
-# ============================================================================
-
-# Checkout to END state first to apply patches
-RUN cd /testbed && git checkout milestone-M12.1-end
-
-# 1. Create sklearn/utils/_test_common package (needed by test_ridge.py, test_pca.py, etc.)
-RUN mkdir -p /testbed/sklearn/utils/_test_common && \
-    echo '"""Stub module for _test_common package"""' > /testbed/sklearn/utils/_test_common/__init__.py && \
-    cat > /testbed/sklearn/utils/_test_common/instance_generator.py << 'STUBEOF'
-"""[ENV-PATCH] Stub module for instance_generator - API not in M12.1"""
-
-def _get_check_estimator_ids(obj):
-    """Returns string representation for pytest ids"""
-    if hasattr(obj, '__name__'):
-        return obj.__name__
-    return str(obj)
-
-def _construct_instances(*args, **kwargs):
-    """Stub: not available in this milestone"""
-    return []
-STUBEOF
-
-# 2. Add get_tags to sklearn/utils/__init__.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/__init__.py && \
-    echo '# [ENV-PATCH] Stub for get_tags - API not in M12.1' >> sklearn/utils/__init__.py && \
-    echo 'def get_tags(estimator):' >> sklearn/utils/__init__.py && \
-    echo '    """Stub: get_tags not available in this milestone"""' >> sklearn/utils/__init__.py && \
-    echo '    from sklearn.utils._tags import _safe_tags' >> sklearn/utils/__init__.py && \
-    echo '    return _safe_tags(estimator)' >> sklearn/utils/__init__.py
-
-# 3. Add _yield_masked_array_for_each_param to sklearn/model_selection/_search.py
-RUN cd /testbed && \
-    echo '' >> sklearn/model_selection/_search.py && \
-    echo '# [ENV-PATCH] Stub for _yield_masked_array_for_each_param - API not in M12.1' >> sklearn/model_selection/_search.py && \
-    echo 'def _yield_masked_array_for_each_param(*args, **kwargs):' >> sklearn/model_selection/_search.py && \
-    echo '    """Stub: _yield_masked_array_for_each_param not available in this milestone"""' >> sklearn/model_selection/_search.py && \
-    echo '    raise NotImplementedError("_yield_masked_array_for_each_param not available in M12.1")' >> sklearn/model_selection/_search.py
-
-# 4. Add is_clusterer to sklearn/base.py
-RUN cd /testbed && \
-    echo '' >> sklearn/base.py && \
-    echo '# [ENV-PATCH] Stub for is_clusterer - API not in M12.1' >> sklearn/base.py && \
-    echo 'def is_clusterer(estimator):' >> sklearn/base.py && \
-    echo '    """Stub: is_clusterer not available in this milestone"""' >> sklearn/base.py && \
-    echo '    raise NotImplementedError("is_clusterer not available in M12.1")' >> sklearn/base.py
-
-# 5. Add check_classifier_not_supporting_multiclass to sklearn/utils/estimator_checks.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/estimator_checks.py && \
-    echo '# [ENV-PATCH] Stub for check_classifier_not_supporting_multiclass - API not in M12.1' >> sklearn/utils/estimator_checks.py && \
-    echo 'def check_classifier_not_supporting_multiclass(*args, **kwargs):' >> sklearn/utils/estimator_checks.py && \
-    echo '    """Stub: check_classifier_not_supporting_multiclass not available in this milestone"""' >> sklearn/utils/estimator_checks.py && \
-    echo '    raise NotImplementedError("check_classifier_not_supporting_multiclass not available in M12.1")' >> sklearn/utils/estimator_checks.py
-
-# 6. Add assert_docstring_consistency to sklearn/utils/_testing.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/_testing.py && \
-    echo '# [ENV-PATCH] Stub for assert_docstring_consistency - API not in M12.1' >> sklearn/utils/_testing.py && \
-    echo 'def assert_docstring_consistency(*args, **kwargs):' >> sklearn/utils/_testing.py && \
-    echo '    """Stub: assert_docstring_consistency not available in this milestone"""' >> sklearn/utils/_testing.py && \
-    echo '    raise NotImplementedError("assert_docstring_consistency not available in M12.1")' >> sklearn/utils/_testing.py
-
-# 7. Add validate_data and _check_n_features to sklearn/utils/validation.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/validation.py && \
-    echo '# [ENV-PATCH] Stub for validate_data - API not in M12.1' >> sklearn/utils/validation.py && \
-    echo 'def validate_data(*args, **kwargs):' >> sklearn/utils/validation.py && \
-    echo '    """Stub: validate_data not available in this milestone"""' >> sklearn/utils/validation.py && \
-    echo '    raise NotImplementedError("validate_data not available in M12.1")' >> sklearn/utils/validation.py && \
-    echo '' >> sklearn/utils/validation.py && \
-    echo '# [ENV-PATCH] Stub for _check_n_features - API not in M12.1' >> sklearn/utils/validation.py && \
-    echo 'def _check_n_features(*args, **kwargs):' >> sklearn/utils/validation.py && \
-    echo '    """Stub: _check_n_features not available in this milestone"""' >> sklearn/utils/validation.py && \
-    echo '    raise NotImplementedError("_check_n_features not available in M12.1")' >> sklearn/utils/validation.py
-
-# 8. Add multiple stubs to sklearn/utils/estimator_checks.py
-# These are needed for test_estimator_checks.py to collect
-RUN cd /testbed && \
-    cat >> sklearn/utils/estimator_checks.py << 'STUBEOF'
-
-# [ENV-PATCH] Stub functions for test collection compatibility - APIs not in M12.1
-class _NotAnArray:
-    """Stub class for _NotAnArray - API not in M12.1"""
-    pass
-
-def check_estimator_cloneable(*args, **kwargs):
-    """Stub: check_estimator_cloneable not available in this milestone"""
-    raise NotImplementedError("check_estimator_cloneable not available in M12.1")
-
-def check_estimator_repr(*args, **kwargs):
-    """Stub: check_estimator_repr not available in this milestone"""
-    raise NotImplementedError("check_estimator_repr not available in M12.1")
-
-def check_estimator_tags_renamed(*args, **kwargs):
-    """Stub: check_estimator_tags_renamed not available in this milestone"""
-    raise NotImplementedError("check_estimator_tags_renamed not available in M12.1")
-STUBEOF
-
-# 9. Add skip_if_no_numpydoc decorator to sklearn/utils/_testing.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/_testing.py && \
-    echo '# [ENV-PATCH] Stub for skip_if_no_numpydoc - API not in M12.1' >> sklearn/utils/_testing.py && \
-    echo 'import pytest as _pytest' >> sklearn/utils/_testing.py && \
-    echo 'def skip_if_no_numpydoc(func):' >> sklearn/utils/_testing.py && \
-    echo '    """Stub decorator: skip_if_no_numpydoc not available in this milestone"""' >> sklearn/utils/_testing.py && \
-    echo '    return _pytest.mark.skip(reason="[ENV-PATCH] skip_if_no_numpydoc not available")(func)' >> sklearn/utils/_testing.py
-
-# Commit patches to END state and move tag
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add stub modules for test collection compatibility" && \
-    git tag -f milestone-M12.1-end HEAD
-
-# Clean build directory and rebuild scikit-learn for END state
-RUN cd /testbed && rm -rf build/ && pip install --no-build-isolation --editable .
-
-# ============================================================================
-# Now apply same patches to START state
-# ============================================================================
-
-RUN cd /testbed && git checkout milestone-M12.1-start
-
-# Apply the same stubs to START state
-# 1. Create sklearn/utils/_test_common package
-RUN mkdir -p /testbed/sklearn/utils/_test_common && \
-    echo '"""Stub module for _test_common package"""' > /testbed/sklearn/utils/_test_common/__init__.py && \
-    cat > /testbed/sklearn/utils/_test_common/instance_generator.py << 'STUBEOF'
-"""[ENV-PATCH] Stub module for instance_generator - API not in M12.1"""
-
-def _get_check_estimator_ids(obj):
-    """Returns string representation for pytest ids"""
-    if hasattr(obj, '__name__'):
-        return obj.__name__
-    return str(obj)
-
-def _construct_instances(*args, **kwargs):
-    """Stub: not available in this milestone"""
-    return []
-STUBEOF
-
-# 2. Add get_tags to sklearn/utils/__init__.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/__init__.py && \
-    echo '# [ENV-PATCH] Stub for get_tags - API not in M12.1' >> sklearn/utils/__init__.py && \
-    echo 'def get_tags(estimator):' >> sklearn/utils/__init__.py && \
-    echo '    """Stub: get_tags not available in this milestone"""' >> sklearn/utils/__init__.py && \
-    echo '    from sklearn.utils._tags import _safe_tags' >> sklearn/utils/__init__.py && \
-    echo '    return _safe_tags(estimator)' >> sklearn/utils/__init__.py
-
-# 3. Add _yield_masked_array_for_each_param to sklearn/model_selection/_search.py
-RUN cd /testbed && \
-    echo '' >> sklearn/model_selection/_search.py && \
-    echo '# [ENV-PATCH] Stub for _yield_masked_array_for_each_param - API not in M12.1' >> sklearn/model_selection/_search.py && \
-    echo 'def _yield_masked_array_for_each_param(*args, **kwargs):' >> sklearn/model_selection/_search.py && \
-    echo '    """Stub: _yield_masked_array_for_each_param not available in this milestone"""' >> sklearn/model_selection/_search.py && \
-    echo '    raise NotImplementedError("_yield_masked_array_for_each_param not available in M12.1")' >> sklearn/model_selection/_search.py
-
-# 4. Add is_clusterer to sklearn/base.py
-RUN cd /testbed && \
-    echo '' >> sklearn/base.py && \
-    echo '# [ENV-PATCH] Stub for is_clusterer - API not in M12.1' >> sklearn/base.py && \
-    echo 'def is_clusterer(estimator):' >> sklearn/base.py && \
-    echo '    """Stub: is_clusterer not available in this milestone"""' >> sklearn/base.py && \
-    echo '    raise NotImplementedError("is_clusterer not available in M12.1")' >> sklearn/base.py
-
-# 5. Add check_classifier_not_supporting_multiclass to sklearn/utils/estimator_checks.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/estimator_checks.py && \
-    echo '# [ENV-PATCH] Stub for check_classifier_not_supporting_multiclass - API not in M12.1' >> sklearn/utils/estimator_checks.py && \
-    echo 'def check_classifier_not_supporting_multiclass(*args, **kwargs):' >> sklearn/utils/estimator_checks.py && \
-    echo '    """Stub: check_classifier_not_supporting_multiclass not available in this milestone"""' >> sklearn/utils/estimator_checks.py && \
-    echo '    raise NotImplementedError("check_classifier_not_supporting_multiclass not available in M12.1")' >> sklearn/utils/estimator_checks.py
-
-# 6. Add assert_docstring_consistency to sklearn/utils/_testing.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/_testing.py && \
-    echo '# [ENV-PATCH] Stub for assert_docstring_consistency - API not in M12.1' >> sklearn/utils/_testing.py && \
-    echo 'def assert_docstring_consistency(*args, **kwargs):' >> sklearn/utils/_testing.py && \
-    echo '    """Stub: assert_docstring_consistency not available in this milestone"""' >> sklearn/utils/_testing.py && \
-    echo '    raise NotImplementedError("assert_docstring_consistency not available in M12.1")' >> sklearn/utils/_testing.py
-
-# 7. Add validate_data and _check_n_features to sklearn/utils/validation.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/validation.py && \
-    echo '# [ENV-PATCH] Stub for validate_data - API not in M12.1' >> sklearn/utils/validation.py && \
-    echo 'def validate_data(*args, **kwargs):' >> sklearn/utils/validation.py && \
-    echo '    """Stub: validate_data not available in this milestone"""' >> sklearn/utils/validation.py && \
-    echo '    raise NotImplementedError("validate_data not available in M12.1")' >> sklearn/utils/validation.py && \
-    echo '' >> sklearn/utils/validation.py && \
-    echo '# [ENV-PATCH] Stub for _check_n_features - API not in M12.1' >> sklearn/utils/validation.py && \
-    echo 'def _check_n_features(*args, **kwargs):' >> sklearn/utils/validation.py && \
-    echo '    """Stub: _check_n_features not available in this milestone"""' >> sklearn/utils/validation.py && \
-    echo '    raise NotImplementedError("_check_n_features not available in M12.1")' >> sklearn/utils/validation.py
-
-# 8. Add multiple stubs to sklearn/utils/estimator_checks.py
-# These are needed for test_estimator_checks.py to collect
-RUN cd /testbed && \
-    cat >> sklearn/utils/estimator_checks.py << 'STUBEOF'
-
-# [ENV-PATCH] Stub functions for test collection compatibility - APIs not in M12.1
-class _NotAnArray:
-    """Stub class for _NotAnArray - API not in M12.1"""
-    pass
-
-def check_estimator_cloneable(*args, **kwargs):
-    """Stub: check_estimator_cloneable not available in this milestone"""
-    raise NotImplementedError("check_estimator_cloneable not available in M12.1")
-
-def check_estimator_repr(*args, **kwargs):
-    """Stub: check_estimator_repr not available in this milestone"""
-    raise NotImplementedError("check_estimator_repr not available in M12.1")
-
-def check_estimator_tags_renamed(*args, **kwargs):
-    """Stub: check_estimator_tags_renamed not available in this milestone"""
-    raise NotImplementedError("check_estimator_tags_renamed not available in M12.1")
-STUBEOF
-
-# 9. Add skip_if_no_numpydoc decorator to sklearn/utils/_testing.py
-RUN cd /testbed && \
-    echo '' >> sklearn/utils/_testing.py && \
-    echo '# [ENV-PATCH] Stub for skip_if_no_numpydoc - API not in M12.1' >> sklearn/utils/_testing.py && \
-    echo 'import pytest as _pytest' >> sklearn/utils/_testing.py && \
-    echo 'def skip_if_no_numpydoc(func):' >> sklearn/utils/_testing.py && \
-    echo '    """Stub decorator: skip_if_no_numpydoc not available in this milestone"""' >> sklearn/utils/_testing.py && \
-    echo '    return _pytest.mark.skip(reason="[ENV-PATCH] skip_if_no_numpydoc not available")(func)' >> sklearn/utils/_testing.py
-
-# Commit patches to START state and move tag
-RUN cd /testbed && \
-    git add -A && \
-    git commit -m "[ENV-PATCH] Add stub modules for test collection compatibility" && \
-    git tag -f milestone-M12.1-start HEAD
-
-# Clean build directory and rebuild scikit-learn for START state
-RUN cd /testbed && rm -rf build/ && pip install --no-build-isolation --editable .