NAT training data for fix-git task - includes positive and negative examples with explicit differentiation

examples/negative_hallucinated.json

@@ -0,0 +1,261 @@
+[
+  {
+    "role": "system",
+    "content": "\n<role>\nYou are a Lead Software Engineer with full terminal access. Solve technical tasks by analyzing, planning, coding, and executing. You have unrestricted access to install packages, run commands, and deploy applications.\n</role>\n\n<operating_environment>\n- **System**: Linux (in Docker) (x86_64)\n- **Current Date**: 2025-12-20\n- Commands execute inside Docker; notes save to host.\n</operating_environment>\n\n<available_tools>\nYou have access to the following tools (call as functions, not shell commands):\n\n**Terminal Execution:**\n- shell_exec(id, command, block=True/False) - Execute shell commands. Use block=True for quick commands, block=False for long-running processes\n- shell_write_content_to_file(content, file_path) - Write text content directly to a file (preferred for creating Python scripts)\n- shell_view(id) - Check output from a non-blocking session\n- shell_wait(id, wait_seconds) - Wait for output from a non-blocking session\n- shell_write_to_process(id, command) - Send input to an interactive non-blocking process\n- shell_kill_process(id) - Terminate a non-blocking process\n\n**Note Taking:**\n- create_note(title, content) - Create a new note for tracking requirements or plans\n- append_note(title, content) - Add content to an existing note\n- read_note(title) - Read the contents of a note\n</available_tools>\n\n<mandatory_instructions>\n\nAUTONOMOUS MODE (CRITICAL)\n- You are COMPLETELY AUTONOMOUS - the user will NOT respond to any questions\n- NEVER ask for confirmation, clarification, or help - execute immediately\n- Your job is to COMPLETE the task, not describe what could be done\n- Make reasonable assumptions and proceed - the user is NOT available\n- Complete the ENTIRE task in one go - there is NO back-and-forth\n- If something is unclear, make the BEST decision and continue\n- NEVER say \"I would need...\" or \"Please provide...\" - figure it out yourself\n- NEVER stop mid-task waiting for input - push through to completion\n- NEVER end with \"here's what you should do\" or \"the solution is...\" - EXECUTE IT YOURSELF\n- After making ANY change (upgrade package, fix code, etc.): IMMEDIATELY run the original failing command to verify it works\n- Your final response should show SUCCESSFUL EXECUTION, not instructions for the user\n- When the task is complete, respond with a brief summary (NO tool call)\n\nPROHIBITIONS\n1. No questions to user - EXECUTE IMMEDIATELY (user will NEVER respond)\n2. No `python3 -c` for complex code - use shell_write_content_to_file\n3. No retrying same failing command - use DIFFERENT approach\n4. No placeholders like <your_token> in commands - find actual values yourself\n5. No writing own solution when task says \"use script X\" - use that script\n6. No guessing CLI args - run `--help` FIRST and READ the output\n7. No running scripts you haven't verified exist - check with `ls -la script.sh` FIRST\n8. No repetitive output - NEVER generate 10+ similar lines (like many echo \"\" statements)\n9. No assuming files were created - after shell_write_content_to_file, verify with `ls -la` and `head`\n10. No ending with suggestions - if you say \"you should run X\", RUN X YOURSELF\n\n</mandatory_instructions>\n\n<error_handling>\nWhen encountering errors:\n- Read the FULL error message carefully\n- Identify the root cause before attempting fixes\n- Try different approaches if the first fix doesn't work\n- Never repeat the same failing command more than twice\n\nNEVER:\n- Ask user for help - solve it yourself\n- Give up without trying multiple approaches\n- Provide partial solutions - complete the task fully\n</error_handling>\n\n<terminal_tips>\nFILE CREATION:\n- Python files: shell_write_content_to_file (never python -c for complex code)\n- Always use single-quoted delimiter ('EOF' not EOF) to prevent expansion\n- ALWAYS use absolute paths: /app/filename.txt, NEVER ./filename.txt or relative paths\n- After creating file: MANDATORY verify with `ls -la /absolute/path/to/file && head -20 /absolute/path/to/file`\n- If verification shows correct content, STOP retrying and move on\n- BEFORE running ANY script: verify it exists with `ls -la script.sh`\n- If \"No such file\": the file was NOT created - create it again, verify, then run\n\nCLI & CUSTOM TOOLS:\n- CLI tools: run --help first, read subcommand help too\n- Custom tools (.c, .py files): cat the source, understand the format before using\n- If custom binary crashes: you're using wrong format, READ the source code\n\nAPIS & JSON:\n- curl -v to see status, parse response JSON, use returned IDs\n- Empty output = failure, not success\n- For JSON body: prefer Python requests over curl with inline JSON\n\nTEST FILES:\n- Before running: inspect with `cat test_file.py | head -50` to understand structure\n- Look for test framework clues: pytest (def test_*), unittest (TestCase), main block\n- If test file runs silently (no output, exit 0): tests didn't execute, use proper runner\n- Default to pytest if unsure: `python -m pytest test_file.py -v`\n- Valid test output shows: test collection, execution (PASSED/FAILED), summary\n\nGENERAL:\n- File paths: ALWAYS /app/ not ./\n- Non-interactive: use -y, -f flags\n- Long tasks: shell_exec(id=\"x\", command=\"...\", block=False)\n</terminal_tips>\n\n\n<training_mode>\nYou are being shown a CORRECT example of how to solve this task.\nGenerate tool calls that follow the exact format shown, with only the required parameters.\nDo NOT add extra parameters like message_title, message_description, or type.\nWhen the task is complete, respond with a brief summary (NO tool call).\n</training_mode>\n\n\n<training_mode>\nWARNING: The following is an INCORRECT example that demonstrates common mistakes.\nThis trajectory contains errors such as:\n- Adding unnecessary parameters (message_title, message_description)\n- Looping on the same commands after task completion\n- Using wrong command formats\nLearn to AVOID these patterns.\n</training_mode>\n"
+  },
+  {
+    "role": "user",
+    "content": "Task instruction: I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.\n"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_knQ3jekwQbmH18tEraAurQ",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"id\": \"survey\", \"command\": \"pwd && ls -la && git status && git log --oneline -10\", \"block\": true, \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "/app/personal-site\ntotal 92\ndrwxr-xr-x 12 root root  4096 Sep 13 17:54 .\ndrwxr-xr-x  1 root root  4096 Sep 13 17:54 ..\ndrwxr-xr-x  8 root root  4096 Sep 13 17:54 .git\n-rw-r--r--  1 root root   100 Sep 13 17:54 .gitignore\n-rw-r--r--  1 root root    14 Sep 13 17:54 CNAME\n-rw-r--r--  1 root root    42 Sep 13 17:54 Gemfile\n-rw-r--r--  1 root root   152 Sep 13 17:54 _config.yml\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _includes\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _layouts\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _posters\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _publications\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 biblib\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 css\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 fonts\n-rw-r--r--  1 root root    47 Sep 13 17:54 index.md\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 js\n-rw-r--r--  1 root root  2382 Sep 13 17:54 make_pubs.py\n-rw-r--r--  1 root root 19618 Sep 13 17:54 me.bib\ndrwxr-xr-x  4 root root  4096 Sep 13 17:54 resources\nOn branch master\nnothing to commit, working tree clean\nd7d3e4b off the job market woo\nc4e38a1 Add code link for BLADE\n6f46fa0 CV Update\ndd7e395 Adds BLADE to bib\n2cd355a n+1 (for the last time???)\n8eaf505 Add BLADE\ncc2ec78 Underline\nd71094e Underline Conferences\n232b279 Remove posters\n3fdf5f5 Add NeurIPS\n",
+    "tool_call_id": "tooluse_knQ3jekwQbmH18tEraAurQ"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_4iDH7hGfTUeXFA7cPOkChA",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git branch -a && git reflog --all | head -20\", \"id\": \"branches\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "* master\nd7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master\n650dba4 HEAD@{1}: commit: Move to Stanford\nc4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1\nd7d3e4b refs/heads/master@{0}: reset: moving to d7d3e4b\nb0d59cd refs/heads/master@{1}: clone: from https://github.com/TheMikeMerrill/personal-site.git\nd7d3e4b HEAD@{3}: reset: moving to d7d3e4b\nb0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git\n",
+    "tool_call_id": "tooluse_4iDH7hGfTUeXFA7cPOkChA"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_CtXkzknuSIKAnwcISlgcLw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show 650dba4 --stat\", \"id\": \"show_commit\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "commit 650dba427e0a9dcd118f41a4c5e35c8017550a5a\nAuthor: Test User <test@example.com>\nDate:   Sat Sep 13 17:54:33 2025 +0000\n\n    Move to Stanford\n\n _includes/about.md    |  4 ++--\n _layouts/default.html | 32 +++++++++++++++++---------------\n 2 files changed, 19 insertions(+), 17 deletions(-)\n",
+    "tool_call_id": "tooluse_CtXkzknuSIKAnwcISlgcLw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_LPRQbhhVTd2QYSJBnkUI_g",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git log --oneline --graph --all --decorate\", \"id\": \"git_graph\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "* d7d3e4b (HEAD -> master) off the job market woo\n* c4e38a1 Add code link for BLADE\n* 6f46fa0 CV Update\n* dd7e395 Adds BLADE to bib\n* 2cd355a n+1 (for the last time???)\n* 8eaf505 Add BLADE\n* cc2ec78 Underline\n* d71094e Underline Conferences\n* 232b279 Remove posters\n* 3fdf5f5 Add NeurIPS\n* 8c4731d Add EMNLP acceptance\n* f54f66b Add GR link\n* 18d2430 Add other links\n* 1dd055e Ignore Gemfile, etc\n* 5c77a6d Dont overwrite\n* c7d2f95 Delete unsused files\n* 20b05d9 Remove more unused files\n* 2d144f7 Add yamls for new papers\n* 7882f2d Don't track _site\n* cd2b8de Add new papers\n* 26dc65c Fix author\n* bc1962c Interests update\n* 257eba8 More space for interests\n* ff6a94a Bib update\n* 97c4a55 Underline bold\n* a320806 Other fixes, new paper\n* 2cb7243 New PDFs\n* 7321328 PDF update\n* f1e3860 Deletions\n* 7b4d171 Update Bio\n* 073117a Another update\n* cb63517 Another CV Updatee\n* 192ae7b update headshot\n* 7fb9365 Update about and contact\n* 54ef19d CV Update\n* b0fb76a Add GR\n* 6adfab9 n plus one\n* 8a5509d Needs to be a string\n* e2f686e Add Gemfile\n* fa098ef properly handle class\n* a8fffe9 Add cv\n* 01d029a Add biblib/__pycache__/ to .gitignore\n* a06e285 Update file paths for personal site and add new PhD experience\n* cef1969 ingore\n* 76398c6 CV Update\n* 7fe50ca Include asterix\n* a8ff8fb fix venue name\n* c0e24b9 Adds Neurips Paper\n* 8379341 CV Update\n* c2ca090 Typos\n* 115a23a Re order interests\n* b2f98e3 Annual update of interests\n* 3b6f690 Make thumbnails larger\n* 177c92f Add note field\n* 2a49416 Annual update to bio\n* e3abd37 Add epj paper\n* 5ddf58a New papers capitalized\n* 5b770eb New papers\n* 199bc67 CV Update\n* 79d1ef2 Removed consultling line\n* b00b8a4 Format\n* 4ebe937 Consulting\n* 93cd578 CV, about, and interests update\n* 218ead3 Third year now!\n* 8aac2ab snark removed\n* a404b45 Added new paper\n* 43117c7 Forgot thumbnail and pdf\n* 36a7b51 New paper!\n* ef5ebab Added old research statement for UW\n* fbe500f Added old research statement\n* 883942a Fall 2020 Changes\n* 6336a21 Added work statement\n* ec13894 Fixed column layout\n*   45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| *   8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll\n| |\\  \n| | * 018fcf4 Migrated to Jekyll\n| |/  \n* / dd1ae17 Empty commit\n|/  \n* dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)\n*   c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| * 09cafdd Changed name (for real!)\n* | b3ae4f0 Changed name (for real!)\n|/  \n* 719ac48 Added Tim\n* edbd5ac Changed name\n* dfbe936 Updated CV\n* bdbb55c Changed interests\n*   c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| *   3972ef7 Merge pull request #1 from TheMikeMerrill/deployment\n| |\\  \n| | * 4798881 Fixed HR Link\n| * | b4ee987 Create CNAME\n| |/  \n* / 35707d9 Added .nojekyl\n|/  \n* a1f4a2d Updated Resume\n* b2d01e3 Add files via upload\n* 5f9aeab Add files via upload\n* a1d746d Delete README.md\n* 02ed510 Initial commit\n",
+    "tool_call_id": "tooluse_LPRQbhhVTd2QYSJBnkUI_g"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_OnGuotRKQomBbm76fjCu6g",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git merge 650dba4 --no-ff -m \\\"Merge Stanford changes into master\\\"\", \"id\": \"merge\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Auto-merging _includes/about.md\nCONFLICT (content): Merge conflict in _includes/about.md\nAutomatic merge failed; fix conflicts and then commit the result.\n",
+    "tool_call_id": "tooluse_OnGuotRKQomBbm76fjCu6g"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_fOc3OYEFSLO6XtoriHX7ow",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"cat _includes/about.md\", \"id\": \"check_conflict\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "<<<<<<< HEAD\nI am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).\n\n Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \n=======\nI am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \n>>>>>>> 650dba4\n",
+    "tool_call_id": "tooluse_fOc3OYEFSLO6XtoriHX7ow"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_WFCgaZrNQAu09OZ5_hatYw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show 650dba4:_includes/about.md\", \"id\": \"show_new\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ",
+    "tool_call_id": "tooluse_WFCgaZrNQAu09OZ5_hatYw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_sM2iI0_UQ4Cu4hzVJOvFXA",
+        "type": "function",
+        "function": {
+          "name": "shell_write_content_to_file",
+          "arguments": "{\"file_path\": \"/app/personal-site/_includes/about.md\", \"content\": \"I am a Postdoctoral Researcher at Stanford CS.\\n\\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Content successfully written to '/app/personal-site/_includes/about.md' in Docker container.",
+    "tool_call_id": "tooluse_sM2iI0_UQ4Cu4hzVJOvFXA"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_Jm-YnY8BQlWDaYuyR2YQXg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"cat /app/personal-site/_includes/about.md\", \"id\": \"verify_resolved\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ",
+    "tool_call_id": "tooluse_Jm-YnY8BQlWDaYuyR2YQXg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_byHaUbWvQl6tR5-d7S_HPg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git add _includes/about.md && git status\", \"id\": \"add_file\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "On branch master\nAll conflicts fixed but you are still merging.\n  (use \"git commit\" to conclude merge)\n\nChanges to be committed:\n\tmodified:   _includes/about.md\n\tmodified:   _layouts/default.html\n\n",
+    "tool_call_id": "tooluse_byHaUbWvQl6tR5-d7S_HPg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_6RkKTjhDRAOoXLNVNSDj_w",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git commit -m \\\"Merge Stanford changes into master\\\"\", \"id\": \"commit_merge\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "[master 4c70b8e] Merge Stanford changes into master\n",
+    "tool_call_id": "tooluse_6RkKTjhDRAOoXLNVNSDj_w"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_gwQcfYwcTRWm282ZmB-uZw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git log --oneline -5 && git status\", \"id\": \"verify_complete\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "4c70b8e Merge Stanford changes into master\n650dba4 Move to Stanford\nd7d3e4b off the job market woo\nc4e38a1 Add code link for BLADE\n6f46fa0 CV Update\nOn branch master\nnothing to commit, working tree clean\n",
+    "tool_call_id": "tooluse_gwQcfYwcTRWm282ZmB-uZw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_L2F6_fAQQs6hphmbsLfBcg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show HEAD --stat\", \"id\": \"show_merge\", \"message_title\": \"Survey\", \"message_description\": \"Performing system survey\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "commit 4c70b8e770cbd0be32f1368427feced776266306\nMerge: d7d3e4b 650dba4\nAuthor: Test User <test@example.com>\nDate:   Sat Dec 20 11:20:54 2025 +0000\n\n    Merge Stanford changes into master\n\n _includes/about.md    |  4 ++--\n _layouts/default.html | 32 +++++++++++++++++---------------\n 2 files changed, 19 insertions(+), 17 deletions(-)\n",
+    "tool_call_id": "tooluse_L2F6_fAQQs6hphmbsLfBcg"
+  },
+  {
+    "role": "assistant",
+    "content": "Task completed successfully.\n\nI recovered the lost commit (650dba4 - \"Move to Stanford\") and merged it into master. The merge included:\n- Updated _includes/about.md with the Stanford position\n- Updated _layouts/default.html with layout changes\n\nThe working tree is now clean with all changes properly merged."
+  }
+]

examples/negative_hallucinated_text.txt

@@ -0,0 +1,439 @@
+<|im_start|>system
+
+<role>
+You are a Lead Software Engineer with full terminal access. Solve technical tasks by analyzing, planning, coding, and executing. You have unrestricted access to install packages, run commands, and deploy applications.
+</role>
+
+<operating_environment>
+- **System**: Linux (in Docker) (x86_64)
+- **Current Date**: 2025-12-20
+- Commands execute inside Docker; notes save to host.
+</operating_environment>
+
+<available_tools>
+You have access to the following tools (call as functions, not shell commands):
+
+**Terminal Execution:**
+- shell_exec(id, command, block=True/False) - Execute shell commands. Use block=True for quick commands, block=False for long-running processes
+- shell_write_content_to_file(content, file_path) - Write text content directly to a file (preferred for creating Python scripts)
+- shell_view(id) - Check output from a non-blocking session
+- shell_wait(id, wait_seconds) - Wait for output from a non-blocking session
+- shell_write_to_process(id, command) - Send input to an interactive non-blocking process
+- shell_kill_process(id) - Terminate a non-blocking process
+
+**Note Taking:**
+- create_note(title, content) - Create a new note for tracking requirements or plans
+- append_note(title, content) - Add content to an existing note
+- read_note(title) - Read the contents of a note
+</available_tools>
+
+<mandatory_instructions>
+
+AUTONOMOUS MODE (CRITICAL)
+- You are COMPLETELY AUTONOMOUS - the user will NOT respond to any questions
+- NEVER ask for confirmation, clarification, or help - execute immediately
+- Your job is to COMPLETE the task, not describe what could be done
+- Make reasonable assumptions and proceed - the user is NOT available
+- Complete the ENTIRE task in one go - there is NO back-and-forth
+- If something is unclear, make the BEST decision and continue
+- NEVER say "I would need..." or "Please provide..." - figure it out yourself
+- NEVER stop mid-task waiting for input - push through to completion
+- NEVER end with "here's what you should do" or "the solution is..." - EXECUTE IT YOURSELF
+- After making ANY change (upgrade package, fix code, etc.): IMMEDIATELY run the original failing command to verify it works
+- Your final response should show SUCCESSFUL EXECUTION, not instructions for the user
+- When the task is complete, respond with a brief summary (NO tool call)
+
+PROHIBITIONS
+1. No questions to user - EXECUTE IMMEDIATELY (user will NEVER respond)
+2. No `python3 -c` for complex code - use shell_write_content_to_file
+3. No retrying same failing command - use DIFFERENT approach
+4. No placeholders like <your_token> in commands - find actual values yourself
+5. No writing own solution when task says "use script X" - use that script
+6. No guessing CLI args - run `--help` FIRST and READ the output
+7. No running scripts you haven't verified exist - check with `ls -la script.sh` FIRST
+8. No repetitive output - NEVER generate 10+ similar lines (like many echo "" statements)
+9. No assuming files were created - after shell_write_content_to_file, verify with `ls -la` and `head`
+10. No ending with suggestions - if you say "you should run X", RUN X YOURSELF
+
+</mandatory_instructions>
+
+<error_handling>
+When encountering errors:
+- Read the FULL error message carefully
+- Identify the root cause before attempting fixes
+- Try different approaches if the first fix doesn't work
+- Never repeat the same failing command more than twice
+
+NEVER:
+- Ask user for help - solve it yourself
+- Give up without trying multiple approaches
+- Provide partial solutions - complete the task fully
+</error_handling>
+
+<terminal_tips>
+FILE CREATION:
+- Python files: shell_write_content_to_file (never python -c for complex code)
+- Always use single-quoted delimiter ('EOF' not EOF) to prevent expansion
+- ALWAYS use absolute paths: /app/filename.txt, NEVER ./filename.txt or relative paths
+- After creating file: MANDATORY verify with `ls -la /absolute/path/to/file && head -20 /absolute/path/to/file`
+- If verification shows correct content, STOP retrying and move on
+- BEFORE running ANY script: verify it exists with `ls -la script.sh`
+- If "No such file": the file was NOT created - create it again, verify, then run
+
+CLI & CUSTOM TOOLS:
+- CLI tools: run --help first, read subcommand help too
+- Custom tools (.c, .py files): cat the source, understand the format before using
+- If custom binary crashes: you're using wrong format, READ the source code
+
+APIS & JSON:
+- curl -v to see status, parse response JSON, use returned IDs
+- Empty output = failure, not success
+- For JSON body: prefer Python requests over curl with inline JSON
+
+TEST FILES:
+- Before running: inspect with `cat test_file.py | head -50` to understand structure
+- Look for test framework clues: pytest (def test_*), unittest (TestCase), main block
+- If test file runs silently (no output, exit 0): tests didn't execute, use proper runner
+- Default to pytest if unsure: `python -m pytest test_file.py -v`
+- Valid test output shows: test collection, execution (PASSED/FAILED), summary
+
+GENERAL:
+- File paths: ALWAYS /app/ not ./
+- Non-interactive: use -y, -f flags
+- Long tasks: shell_exec(id="x", command="...", block=False)
+</terminal_tips>
+
+
+<training_mode>
+You are being shown a CORRECT example of how to solve this task.
+Generate tool calls that follow the exact format shown, with only the required parameters.
+Do NOT add extra parameters like message_title, message_description, or type.
+When the task is complete, respond with a brief summary (NO tool call).
+</training_mode>
+
+
+<training_mode>
+WARNING: The following is an INCORRECT example that demonstrates common mistakes.
+This trajectory contains errors such as:
+- Adding unnecessary parameters (message_title, message_description)
+- Looping on the same commands after task completion
+- Using wrong command formats
+Learn to AVOID these patterns.
+</training_mode>
+<|im_end|>
+<|im_start|>user
+Task instruction: I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.
+<|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"id": "survey", "command": "pwd && ls -la && git status && git log --oneline -10", "block": true, "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+/app/personal-site
+total 92
+drwxr-xr-x 12 root root  4096 Sep 13 17:54 .
+drwxr-xr-x  1 root root  4096 Sep 13 17:54 ..
+drwxr-xr-x  8 root root  4096 Sep 13 17:54 .git
+-rw-r--r--  1 root root   100 Sep 13 17:54 .gitignore
+-rw-r--r--  1 root root    14 Sep 13 17:54 CNAME
+-rw-r--r--  1 root root    42 Sep 13 17:54 Gemfile
+-rw-r--r--  1 root root   152 Sep 13 17:54 _config.yml
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 _includes
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 _layouts
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 _posters
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 _publications
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 biblib
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 css
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 fonts
+-rw-r--r--  1 root root    47 Sep 13 17:54 index.md
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 js
+-rw-r--r--  1 root root  2382 Sep 13 17:54 make_pubs.py
+-rw-r--r--  1 root root 19618 Sep 13 17:54 me.bib
+drwxr-xr-x  4 root root  4096 Sep 13 17:54 resources
+On branch master
+nothing to commit, working tree clean
+d7d3e4b off the job market woo
+c4e38a1 Add code link for BLADE
+6f46fa0 CV Update
+dd7e395 Adds BLADE to bib
+2cd355a n+1 (for the last time???)
+8eaf505 Add BLADE
+cc2ec78 Underline
+d71094e Underline Conferences
+232b279 Remove posters
+3fdf5f5 Add NeurIPS
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git branch -a && git reflog --all | head -20", "id": "branches", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+* master
+d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
+650dba4 HEAD@{1}: commit: Move to Stanford
+c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
+d7d3e4b refs/heads/master@{0}: reset: moving to d7d3e4b
+b0d59cd refs/heads/master@{1}: clone: from https://github.com/TheMikeMerrill/personal-site.git
+d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
+b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git show 650dba4 --stat", "id": "show_commit", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+commit 650dba427e0a9dcd118f41a4c5e35c8017550a5a
+Author: Test User <test@example.com>
+Date:   Sat Sep 13 17:54:33 2025 +0000
+
+    Move to Stanford
+
+ _includes/about.md    |  4 ++--
+ _layouts/default.html | 32 +++++++++++++++++---------------
+ 2 files changed, 19 insertions(+), 17 deletions(-)
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git log --oneline --graph --all --decorate", "id": "git_graph", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+* d7d3e4b (HEAD -> master) off the job market woo
+* c4e38a1 Add code link for BLADE
+* 6f46fa0 CV Update
+* dd7e395 Adds BLADE to bib
+* 2cd355a n+1 (for the last time???)
+* 8eaf505 Add BLADE
+* cc2ec78 Underline
+* d71094e Underline Conferences
+* 232b279 Remove posters
+* 3fdf5f5 Add NeurIPS
+* 8c4731d Add EMNLP acceptance
+* f54f66b Add GR link
+* 18d2430 Add other links
+* 1dd055e Ignore Gemfile, etc
+* 5c77a6d Dont overwrite
+* c7d2f95 Delete unsused files
+* 20b05d9 Remove more unused files
+* 2d144f7 Add yamls for new papers
+* 7882f2d Don't track _site
+* cd2b8de Add new papers
+* 26dc65c Fix author
+* bc1962c Interests update
+* 257eba8 More space for interests
+* ff6a94a Bib update
+* 97c4a55 Underline bold
+* a320806 Other fixes, new paper
+* 2cb7243 New PDFs
+* 7321328 PDF update
+* f1e3860 Deletions
+* 7b4d171 Update Bio
+* 073117a Another update
+* cb63517 Another CV Updatee
+* 192ae7b update headshot
+* 7fb9365 Update about and contact
+* 54ef19d CV Update
+* b0fb76a Add GR
+* 6adfab9 n plus one
+* 8a5509d Needs to be a string
+* e2f686e Add Gemfile
+* fa098ef properly handle class
+* a8fffe9 Add cv
+* 01d029a Add biblib/__pycache__/ to .gitignore
+* a06e285 Update file paths for personal site and add new PhD experience
+* cef1969 ingore
+* 76398c6 CV Update
+* 7fe50ca Include asterix
+* a8ff8fb fix venue name
+* c0e24b9 Adds Neurips Paper
+* 8379341 CV Update
+* c2ca090 Typos
+* 115a23a Re order interests
+* b2f98e3 Annual update of interests
+* 3b6f690 Make thumbnails larger
+* 177c92f Add note field
+* 2a49416 Annual update to bio
+* e3abd37 Add epj paper
+* 5ddf58a New papers capitalized
+* 5b770eb New papers
+* 199bc67 CV Update
+* 79d1ef2 Removed consultling line
+* b00b8a4 Format
+* 4ebe937 Consulting
+* 93cd578 CV, about, and interests update
+* 218ead3 Third year now!
+* 8aac2ab snark removed
+* a404b45 Added new paper
+* 43117c7 Forgot thumbnail and pdf
+* 36a7b51 New paper!
+* ef5ebab Added old research statement for UW
+* fbe500f Added old research statement
+* 883942a Fall 2020 Changes
+* 6336a21 Added work statement
+* ec13894 Fixed column layout
+*   45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
+|\  
+| *   8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
+| |\  
+| | * 018fcf4 Migrated to Jekyll
+| |/  
+* / dd1ae17 Empty commit
+|/  
+* dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
+*   c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
+|\  
+| * 09cafdd Changed name (for real!)
+* | b3ae4f0 Changed name (for real!)
+|/  
+* 719ac48 Added Tim
+* edbd5ac Changed name
+* dfbe936 Updated CV
+* bdbb55c Changed interests
+*   c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
+|\  
+| *   3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
+| |\  
+| | * 4798881 Fixed HR Link
+| * | b4ee987 Create CNAME
+| |/  
+* / 35707d9 Added .nojekyl
+|/  
+* a1f4a2d Updated Resume
+* b2d01e3 Add files via upload
+* 5f9aeab Add files via upload
+* a1d746d Delete README.md
+* 02ed510 Initial commit
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git merge 650dba4 --no-ff -m \"Merge Stanford changes into master\"", "id": "merge", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+Auto-merging _includes/about.md
+CONFLICT (content): Merge conflict in _includes/about.md
+Automatic merge failed; fix conflicts and then commit the result.
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "cat _includes/about.md", "id": "check_conflict", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+<<<<<<< HEAD
+I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).
+
+ Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
+=======
+I am a Postdoctoral Researcher at Stanford CS.
+
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
+>>>>>>> 650dba4
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git show 650dba4:_includes/about.md", "id": "show_new", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+I am a Postdoctoral Researcher at Stanford CS.
+
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_write_content_to_file", "arguments": {"file_path": "/app/personal-site/_includes/about.md", "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+Content successfully written to '/app/personal-site/_includes/about.md' in Docker container.
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "cat /app/personal-site/_includes/about.md", "id": "verify_resolved", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+I am a Postdoctoral Researcher at Stanford CS.
+
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git add _includes/about.md && git status", "id": "add_file", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+On branch master
+All conflicts fixed but you are still merging.
+  (use "git commit" to conclude merge)
+
+Changes to be committed:
+	modified:   _includes/about.md
+	modified:   _layouts/default.html
+
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git commit -m \"Merge Stanford changes into master\"", "id": "commit_merge", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+[master 4c70b8e] Merge Stanford changes into master
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git log --oneline -5 && git status", "id": "verify_complete", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+4c70b8e Merge Stanford changes into master
+650dba4 Move to Stanford
+d7d3e4b off the job market woo
+c4e38a1 Add code link for BLADE
+6f46fa0 CV Update
+On branch master
+nothing to commit, working tree clean
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git show HEAD --stat", "id": "show_merge", "message_title": "Survey", "message_description": "Performing system survey"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+commit 4c70b8e770cbd0be32f1368427feced776266306
+Merge: d7d3e4b 650dba4
+Author: Test User <test@example.com>
+Date:   Sat Dec 20 11:20:54 2025 +0000
+
+    Merge Stanford changes into master
+
+ _includes/about.md    |  4 ++--
+ _layouts/default.html | 32 +++++++++++++++++---------------
+ 2 files changed, 19 insertions(+), 17 deletions(-)
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<think>
+
+</think>
+
+Task completed successfully.
+
+I recovered the lost commit (650dba4 - "Move to Stanford") and merged it into master. The merge included:
+- Updated _includes/about.md with the Stanford position
+- Updated _layouts/default.html with layout changes
+
+The working tree is now clean with all changes properly merged.<|im_end|>

examples/negative_looping.json

@@ -0,0 +1,290 @@
+[
+  {
+    "role": "system",
+    "content": "\n<role>\nYou are a Lead Software Engineer with full terminal access. Solve technical tasks by analyzing, planning, coding, and executing. You have unrestricted access to install packages, run commands, and deploy applications.\n</role>\n\n<operating_environment>\n- **System**: Linux (in Docker) (x86_64)\n- **Current Date**: 2025-12-20\n- Commands execute inside Docker; notes save to host.\n</operating_environment>\n\n<available_tools>\nYou have access to the following tools (call as functions, not shell commands):\n\n**Terminal Execution:**\n- shell_exec(id, command, block=True/False) - Execute shell commands. Use block=True for quick commands, block=False for long-running processes\n- shell_write_content_to_file(content, file_path) - Write text content directly to a file (preferred for creating Python scripts)\n- shell_view(id) - Check output from a non-blocking session\n- shell_wait(id, wait_seconds) - Wait for output from a non-blocking session\n- shell_write_to_process(id, command) - Send input to an interactive non-blocking process\n- shell_kill_process(id) - Terminate a non-blocking process\n\n**Note Taking:**\n- create_note(title, content) - Create a new note for tracking requirements or plans\n- append_note(title, content) - Add content to an existing note\n- read_note(title) - Read the contents of a note\n</available_tools>\n\n<mandatory_instructions>\n\nAUTONOMOUS MODE (CRITICAL)\n- You are COMPLETELY AUTONOMOUS - the user will NOT respond to any questions\n- NEVER ask for confirmation, clarification, or help - execute immediately\n- Your job is to COMPLETE the task, not describe what could be done\n- Make reasonable assumptions and proceed - the user is NOT available\n- Complete the ENTIRE task in one go - there is NO back-and-forth\n- If something is unclear, make the BEST decision and continue\n- NEVER say \"I would need...\" or \"Please provide...\" - figure it out yourself\n- NEVER stop mid-task waiting for input - push through to completion\n- NEVER end with \"here's what you should do\" or \"the solution is...\" - EXECUTE IT YOURSELF\n- After making ANY change (upgrade package, fix code, etc.): IMMEDIATELY run the original failing command to verify it works\n- Your final response should show SUCCESSFUL EXECUTION, not instructions for the user\n- When the task is complete, respond with a brief summary (NO tool call)\n\nPROHIBITIONS\n1. No questions to user - EXECUTE IMMEDIATELY (user will NEVER respond)\n2. No `python3 -c` for complex code - use shell_write_content_to_file\n3. No retrying same failing command - use DIFFERENT approach\n4. No placeholders like <your_token> in commands - find actual values yourself\n5. No writing own solution when task says \"use script X\" - use that script\n6. No guessing CLI args - run `--help` FIRST and READ the output\n7. No running scripts you haven't verified exist - check with `ls -la script.sh` FIRST\n8. No repetitive output - NEVER generate 10+ similar lines (like many echo \"\" statements)\n9. No assuming files were created - after shell_write_content_to_file, verify with `ls -la` and `head`\n10. No ending with suggestions - if you say \"you should run X\", RUN X YOURSELF\n\n</mandatory_instructions>\n\n<error_handling>\nWhen encountering errors:\n- Read the FULL error message carefully\n- Identify the root cause before attempting fixes\n- Try different approaches if the first fix doesn't work\n- Never repeat the same failing command more than twice\n\nNEVER:\n- Ask user for help - solve it yourself\n- Give up without trying multiple approaches\n- Provide partial solutions - complete the task fully\n</error_handling>\n\n<terminal_tips>\nFILE CREATION:\n- Python files: shell_write_content_to_file (never python -c for complex code)\n- Always use single-quoted delimiter ('EOF' not EOF) to prevent expansion\n- ALWAYS use absolute paths: /app/filename.txt, NEVER ./filename.txt or relative paths\n- After creating file: MANDATORY verify with `ls -la /absolute/path/to/file && head -20 /absolute/path/to/file`\n- If verification shows correct content, STOP retrying and move on\n- BEFORE running ANY script: verify it exists with `ls -la script.sh`\n- If \"No such file\": the file was NOT created - create it again, verify, then run\n\nCLI & CUSTOM TOOLS:\n- CLI tools: run --help first, read subcommand help too\n- Custom tools (.c, .py files): cat the source, understand the format before using\n- If custom binary crashes: you're using wrong format, READ the source code\n\nAPIS & JSON:\n- curl -v to see status, parse response JSON, use returned IDs\n- Empty output = failure, not success\n- For JSON body: prefer Python requests over curl with inline JSON\n\nTEST FILES:\n- Before running: inspect with `cat test_file.py | head -50` to understand structure\n- Look for test framework clues: pytest (def test_*), unittest (TestCase), main block\n- If test file runs silently (no output, exit 0): tests didn't execute, use proper runner\n- Default to pytest if unsure: `python -m pytest test_file.py -v`\n- Valid test output shows: test collection, execution (PASSED/FAILED), summary\n\nGENERAL:\n- File paths: ALWAYS /app/ not ./\n- Non-interactive: use -y, -f flags\n- Long tasks: shell_exec(id=\"x\", command=\"...\", block=False)\n</terminal_tips>\n\n\n<training_mode>\nYou are being shown a CORRECT example of how to solve this task.\nGenerate tool calls that follow the exact format shown, with only the required parameters.\nDo NOT add extra parameters like message_title, message_description, or type.\nWhen the task is complete, respond with a brief summary (NO tool call).\n</training_mode>\n\n\n<training_mode>\nWARNING: The following is an INCORRECT example that demonstrates common mistakes.\nThis trajectory contains errors such as:\n- Adding unnecessary parameters (message_title, message_description)\n- Looping on the same commands after task completion\n- Using wrong command formats\nLearn to AVOID these patterns.\n</training_mode>\n"
+  },
+  {
+    "role": "user",
+    "content": "Task instruction: I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.\n"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_knQ3jekwQbmH18tEraAurQ",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"id\": \"survey\", \"command\": \"pwd && ls -la && git status && git log --oneline -10\", \"block\": true}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "/app/personal-site\ntotal 92\ndrwxr-xr-x 12 root root  4096 Sep 13 17:54 .\ndrwxr-xr-x  1 root root  4096 Sep 13 17:54 ..\ndrwxr-xr-x  8 root root  4096 Sep 13 17:54 .git\n-rw-r--r--  1 root root   100 Sep 13 17:54 .gitignore\n-rw-r--r--  1 root root    14 Sep 13 17:54 CNAME\n-rw-r--r--  1 root root    42 Sep 13 17:54 Gemfile\n-rw-r--r--  1 root root   152 Sep 13 17:54 _config.yml\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _includes\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _layouts\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _posters\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _publications\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 biblib\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 css\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 fonts\n-rw-r--r--  1 root root    47 Sep 13 17:54 index.md\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 js\n-rw-r--r--  1 root root  2382 Sep 13 17:54 make_pubs.py\n-rw-r--r--  1 root root 19618 Sep 13 17:54 me.bib\ndrwxr-xr-x  4 root root  4096 Sep 13 17:54 resources\nOn branch master\nnothing to commit, working tree clean\nd7d3e4b off the job market woo\nc4e38a1 Add code link for BLADE\n6f46fa0 CV Update\ndd7e395 Adds BLADE to bib\n2cd355a n+1 (for the last time???)\n8eaf505 Add BLADE\ncc2ec78 Underline\nd71094e Underline Conferences\n232b279 Remove posters\n3fdf5f5 Add NeurIPS\n",
+    "tool_call_id": "tooluse_knQ3jekwQbmH18tEraAurQ"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_4iDH7hGfTUeXFA7cPOkChA",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git branch -a && git reflog --all | head -20\", \"id\": \"branches\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "* master\nd7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master\n650dba4 HEAD@{1}: commit: Move to Stanford\nc4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1\nd7d3e4b refs/heads/master@{0}: reset: moving to d7d3e4b\nb0d59cd refs/heads/master@{1}: clone: from https://github.com/TheMikeMerrill/personal-site.git\nd7d3e4b HEAD@{3}: reset: moving to d7d3e4b\nb0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git\n",
+    "tool_call_id": "tooluse_4iDH7hGfTUeXFA7cPOkChA"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_CtXkzknuSIKAnwcISlgcLw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show 650dba4 --stat\", \"id\": \"show_commit\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "commit 650dba427e0a9dcd118f41a4c5e35c8017550a5a\nAuthor: Test User <test@example.com>\nDate:   Sat Sep 13 17:54:33 2025 +0000\n\n    Move to Stanford\n\n _includes/about.md    |  4 ++--\n _layouts/default.html | 32 +++++++++++++++++---------------\n 2 files changed, 19 insertions(+), 17 deletions(-)\n",
+    "tool_call_id": "tooluse_CtXkzknuSIKAnwcISlgcLw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_LPRQbhhVTd2QYSJBnkUI_g",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git log --oneline --graph --all --decorate\", \"id\": \"git_graph\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "* d7d3e4b (HEAD -> master) off the job market woo\n* c4e38a1 Add code link for BLADE\n* 6f46fa0 CV Update\n* dd7e395 Adds BLADE to bib\n* 2cd355a n+1 (for the last time???)\n* 8eaf505 Add BLADE\n* cc2ec78 Underline\n* d71094e Underline Conferences\n* 232b279 Remove posters\n* 3fdf5f5 Add NeurIPS\n* 8c4731d Add EMNLP acceptance\n* f54f66b Add GR link\n* 18d2430 Add other links\n* 1dd055e Ignore Gemfile, etc\n* 5c77a6d Dont overwrite\n* c7d2f95 Delete unsused files\n* 20b05d9 Remove more unused files\n* 2d144f7 Add yamls for new papers\n* 7882f2d Don't track _site\n* cd2b8de Add new papers\n* 26dc65c Fix author\n* bc1962c Interests update\n* 257eba8 More space for interests\n* ff6a94a Bib update\n* 97c4a55 Underline bold\n* a320806 Other fixes, new paper\n* 2cb7243 New PDFs\n* 7321328 PDF update\n* f1e3860 Deletions\n* 7b4d171 Update Bio\n* 073117a Another update\n* cb63517 Another CV Updatee\n* 192ae7b update headshot\n* 7fb9365 Update about and contact\n* 54ef19d CV Update\n* b0fb76a Add GR\n* 6adfab9 n plus one\n* 8a5509d Needs to be a string\n* e2f686e Add Gemfile\n* fa098ef properly handle class\n* a8fffe9 Add cv\n* 01d029a Add biblib/__pycache__/ to .gitignore\n* a06e285 Update file paths for personal site and add new PhD experience\n* cef1969 ingore\n* 76398c6 CV Update\n* 7fe50ca Include asterix\n* a8ff8fb fix venue name\n* c0e24b9 Adds Neurips Paper\n* 8379341 CV Update\n* c2ca090 Typos\n* 115a23a Re order interests\n* b2f98e3 Annual update of interests\n* 3b6f690 Make thumbnails larger\n* 177c92f Add note field\n* 2a49416 Annual update to bio\n* e3abd37 Add epj paper\n* 5ddf58a New papers capitalized\n* 5b770eb New papers\n* 199bc67 CV Update\n* 79d1ef2 Removed consultling line\n* b00b8a4 Format\n* 4ebe937 Consulting\n* 93cd578 CV, about, and interests update\n* 218ead3 Third year now!\n* 8aac2ab snark removed\n* a404b45 Added new paper\n* 43117c7 Forgot thumbnail and pdf\n* 36a7b51 New paper!\n* ef5ebab Added old research statement for UW\n* fbe500f Added old research statement\n* 883942a Fall 2020 Changes\n* 6336a21 Added work statement\n* ec13894 Fixed column layout\n*   45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| *   8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll\n| |\\  \n| | * 018fcf4 Migrated to Jekyll\n| |/  \n* / dd1ae17 Empty commit\n|/  \n* dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)\n*   c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| * 09cafdd Changed name (for real!)\n* | b3ae4f0 Changed name (for real!)\n|/  \n* 719ac48 Added Tim\n* edbd5ac Changed name\n* dfbe936 Updated CV\n* bdbb55c Changed interests\n*   c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| *   3972ef7 Merge pull request #1 from TheMikeMerrill/deployment\n| |\\  \n| | * 4798881 Fixed HR Link\n| * | b4ee987 Create CNAME\n| |/  \n* / 35707d9 Added .nojekyl\n|/  \n* a1f4a2d Updated Resume\n* b2d01e3 Add files via upload\n* 5f9aeab Add files via upload\n* a1d746d Delete README.md\n* 02ed510 Initial commit\n",
+    "tool_call_id": "tooluse_LPRQbhhVTd2QYSJBnkUI_g"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_OnGuotRKQomBbm76fjCu6g",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git merge 650dba4 --no-ff -m \\\"Merge Stanford changes into master\\\"\", \"id\": \"merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Auto-merging _includes/about.md\nCONFLICT (content): Merge conflict in _includes/about.md\nAutomatic merge failed; fix conflicts and then commit the result.\n",
+    "tool_call_id": "tooluse_OnGuotRKQomBbm76fjCu6g"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_fOc3OYEFSLO6XtoriHX7ow",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"cat _includes/about.md\", \"id\": \"check_conflict\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "<<<<<<< HEAD\nI am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).\n\n Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \n=======\nI am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \n>>>>>>> 650dba4\n",
+    "tool_call_id": "tooluse_fOc3OYEFSLO6XtoriHX7ow"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_WFCgaZrNQAu09OZ5_hatYw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show 650dba4:_includes/about.md\", \"id\": \"show_new\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ",
+    "tool_call_id": "tooluse_WFCgaZrNQAu09OZ5_hatYw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_sM2iI0_UQ4Cu4hzVJOvFXA",
+        "type": "function",
+        "function": {
+          "name": "shell_write_content_to_file",
+          "arguments": "{\"file_path\": \"/app/personal-site/_includes/about.md\", \"content\": \"I am a Postdoctoral Researcher at Stanford CS.\\n\\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Content successfully written to '/app/personal-site/_includes/about.md' in Docker container.",
+    "tool_call_id": "tooluse_sM2iI0_UQ4Cu4hzVJOvFXA"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_Jm-YnY8BQlWDaYuyR2YQXg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"cat /app/personal-site/_includes/about.md\", \"id\": \"verify_resolved\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ",
+    "tool_call_id": "tooluse_Jm-YnY8BQlWDaYuyR2YQXg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_byHaUbWvQl6tR5-d7S_HPg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git add _includes/about.md && git status\", \"id\": \"add_file\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "On branch master\nAll conflicts fixed but you are still merging.\n  (use \"git commit\" to conclude merge)\n\nChanges to be committed:\n\tmodified:   _includes/about.md\n\tmodified:   _layouts/default.html\n\n",
+    "tool_call_id": "tooluse_byHaUbWvQl6tR5-d7S_HPg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_6RkKTjhDRAOoXLNVNSDj_w",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git commit -m \\\"Merge Stanford changes into master\\\"\", \"id\": \"commit_merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "[master 4c70b8e] Merge Stanford changes into master\n",
+    "tool_call_id": "tooluse_6RkKTjhDRAOoXLNVNSDj_w"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_gwQcfYwcTRWm282ZmB-uZw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git log --oneline -5 && git status\", \"id\": \"verify_complete\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "4c70b8e Merge Stanford changes into master\n650dba4 Move to Stanford\nd7d3e4b off the job market woo\nc4e38a1 Add code link for BLADE\n6f46fa0 CV Update\nOn branch master\nnothing to commit, working tree clean\n",
+    "tool_call_id": "tooluse_gwQcfYwcTRWm282ZmB-uZw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_L2F6_fAQQs6hphmbsLfBcg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show HEAD --stat\", \"id\": \"show_merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "commit 4c70b8e770cbd0be32f1368427feced776266306\nMerge: d7d3e4b 650dba4\nAuthor: Test User <test@example.com>\nDate:   Sat Dec 20 11:20:54 2025 +0000\n\n    Merge Stanford changes into master\n\n _includes/about.md    |  4 ++--\n _layouts/default.html | 32 +++++++++++++++++---------------\n 2 files changed, 19 insertions(+), 17 deletions(-)\n",
+    "tool_call_id": "tooluse_L2F6_fAQQs6hphmbsLfBcg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "loop_call_1",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"id\": \"loop_merge\", \"command\": \"git merge 650dba4 --no-ff -m \\\"Merge Stanford changes into master\\\"\", \"block\": true}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Already up to date.",
+    "tool_call_id": "loop_call_1"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "loop_call_2",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"id\": \"loop_status\", \"command\": \"git status\", \"block\": true}"
+        }
+      }
+    ]
+  }
+]

examples/negative_wrong_cmd.json

@@ -0,0 +1,261 @@
+[
+  {
+    "role": "system",
+    "content": "\n<role>\nYou are a Lead Software Engineer with full terminal access. Solve technical tasks by analyzing, planning, coding, and executing. You have unrestricted access to install packages, run commands, and deploy applications.\n</role>\n\n<operating_environment>\n- **System**: Linux (in Docker) (x86_64)\n- **Current Date**: 2025-12-20\n- Commands execute inside Docker; notes save to host.\n</operating_environment>\n\n<available_tools>\nYou have access to the following tools (call as functions, not shell commands):\n\n**Terminal Execution:**\n- shell_exec(id, command, block=True/False) - Execute shell commands. Use block=True for quick commands, block=False for long-running processes\n- shell_write_content_to_file(content, file_path) - Write text content directly to a file (preferred for creating Python scripts)\n- shell_view(id) - Check output from a non-blocking session\n- shell_wait(id, wait_seconds) - Wait for output from a non-blocking session\n- shell_write_to_process(id, command) - Send input to an interactive non-blocking process\n- shell_kill_process(id) - Terminate a non-blocking process\n\n**Note Taking:**\n- create_note(title, content) - Create a new note for tracking requirements or plans\n- append_note(title, content) - Add content to an existing note\n- read_note(title) - Read the contents of a note\n</available_tools>\n\n<mandatory_instructions>\n\nAUTONOMOUS MODE (CRITICAL)\n- You are COMPLETELY AUTONOMOUS - the user will NOT respond to any questions\n- NEVER ask for confirmation, clarification, or help - execute immediately\n- Your job is to COMPLETE the task, not describe what could be done\n- Make reasonable assumptions and proceed - the user is NOT available\n- Complete the ENTIRE task in one go - there is NO back-and-forth\n- If something is unclear, make the BEST decision and continue\n- NEVER say \"I would need...\" or \"Please provide...\" - figure it out yourself\n- NEVER stop mid-task waiting for input - push through to completion\n- NEVER end with \"here's what you should do\" or \"the solution is...\" - EXECUTE IT YOURSELF\n- After making ANY change (upgrade package, fix code, etc.): IMMEDIATELY run the original failing command to verify it works\n- Your final response should show SUCCESSFUL EXECUTION, not instructions for the user\n- When the task is complete, respond with a brief summary (NO tool call)\n\nPROHIBITIONS\n1. No questions to user - EXECUTE IMMEDIATELY (user will NEVER respond)\n2. No `python3 -c` for complex code - use shell_write_content_to_file\n3. No retrying same failing command - use DIFFERENT approach\n4. No placeholders like <your_token> in commands - find actual values yourself\n5. No writing own solution when task says \"use script X\" - use that script\n6. No guessing CLI args - run `--help` FIRST and READ the output\n7. No running scripts you haven't verified exist - check with `ls -la script.sh` FIRST\n8. No repetitive output - NEVER generate 10+ similar lines (like many echo \"\" statements)\n9. No assuming files were created - after shell_write_content_to_file, verify with `ls -la` and `head`\n10. No ending with suggestions - if you say \"you should run X\", RUN X YOURSELF\n\n</mandatory_instructions>\n\n<error_handling>\nWhen encountering errors:\n- Read the FULL error message carefully\n- Identify the root cause before attempting fixes\n- Try different approaches if the first fix doesn't work\n- Never repeat the same failing command more than twice\n\nNEVER:\n- Ask user for help - solve it yourself\n- Give up without trying multiple approaches\n- Provide partial solutions - complete the task fully\n</error_handling>\n\n<terminal_tips>\nFILE CREATION:\n- Python files: shell_write_content_to_file (never python -c for complex code)\n- Always use single-quoted delimiter ('EOF' not EOF) to prevent expansion\n- ALWAYS use absolute paths: /app/filename.txt, NEVER ./filename.txt or relative paths\n- After creating file: MANDATORY verify with `ls -la /absolute/path/to/file && head -20 /absolute/path/to/file`\n- If verification shows correct content, STOP retrying and move on\n- BEFORE running ANY script: verify it exists with `ls -la script.sh`\n- If \"No such file\": the file was NOT created - create it again, verify, then run\n\nCLI & CUSTOM TOOLS:\n- CLI tools: run --help first, read subcommand help too\n- Custom tools (.c, .py files): cat the source, understand the format before using\n- If custom binary crashes: you're using wrong format, READ the source code\n\nAPIS & JSON:\n- curl -v to see status, parse response JSON, use returned IDs\n- Empty output = failure, not success\n- For JSON body: prefer Python requests over curl with inline JSON\n\nTEST FILES:\n- Before running: inspect with `cat test_file.py | head -50` to understand structure\n- Look for test framework clues: pytest (def test_*), unittest (TestCase), main block\n- If test file runs silently (no output, exit 0): tests didn't execute, use proper runner\n- Default to pytest if unsure: `python -m pytest test_file.py -v`\n- Valid test output shows: test collection, execution (PASSED/FAILED), summary\n\nGENERAL:\n- File paths: ALWAYS /app/ not ./\n- Non-interactive: use -y, -f flags\n- Long tasks: shell_exec(id=\"x\", command=\"...\", block=False)\n</terminal_tips>\n\n\n<training_mode>\nYou are being shown a CORRECT example of how to solve this task.\nGenerate tool calls that follow the exact format shown, with only the required parameters.\nDo NOT add extra parameters like message_title, message_description, or type.\nWhen the task is complete, respond with a brief summary (NO tool call).\n</training_mode>\n\n\n<training_mode>\nWARNING: The following is an INCORRECT example that demonstrates common mistakes.\nThis trajectory contains errors such as:\n- Adding unnecessary parameters (message_title, message_description)\n- Looping on the same commands after task completion\n- Using wrong command formats\nLearn to AVOID these patterns.\n</training_mode>\n"
+  },
+  {
+    "role": "user",
+    "content": "Task instruction: I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.\n"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_knQ3jekwQbmH18tEraAurQ",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"id\": \"survey\", \"command\": \"survey\", \"block\": true}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "/app/personal-site\ntotal 92\ndrwxr-xr-x 12 root root  4096 Sep 13 17:54 .\ndrwxr-xr-x  1 root root  4096 Sep 13 17:54 ..\ndrwxr-xr-x  8 root root  4096 Sep 13 17:54 .git\n-rw-r--r--  1 root root   100 Sep 13 17:54 .gitignore\n-rw-r--r--  1 root root    14 Sep 13 17:54 CNAME\n-rw-r--r--  1 root root    42 Sep 13 17:54 Gemfile\n-rw-r--r--  1 root root   152 Sep 13 17:54 _config.yml\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _includes\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _layouts\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _posters\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _publications\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 biblib\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 css\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 fonts\n-rw-r--r--  1 root root    47 Sep 13 17:54 index.md\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 js\n-rw-r--r--  1 root root  2382 Sep 13 17:54 make_pubs.py\n-rw-r--r--  1 root root 19618 Sep 13 17:54 me.bib\ndrwxr-xr-x  4 root root  4096 Sep 13 17:54 resources\nOn branch master\nnothing to commit, working tree clean\nd7d3e4b off the job market woo\nc4e38a1 Add code link for BLADE\n6f46fa0 CV Update\ndd7e395 Adds BLADE to bib\n2cd355a n+1 (for the last time???)\n8eaf505 Add BLADE\ncc2ec78 Underline\nd71094e Underline Conferences\n232b279 Remove posters\n3fdf5f5 Add NeurIPS\n",
+    "tool_call_id": "tooluse_knQ3jekwQbmH18tEraAurQ"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_4iDH7hGfTUeXFA7cPOkChA",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"branches\", \"id\": \"branches\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "* master\nd7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master\n650dba4 HEAD@{1}: commit: Move to Stanford\nc4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1\nd7d3e4b refs/heads/master@{0}: reset: moving to d7d3e4b\nb0d59cd refs/heads/master@{1}: clone: from https://github.com/TheMikeMerrill/personal-site.git\nd7d3e4b HEAD@{3}: reset: moving to d7d3e4b\nb0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git\n",
+    "tool_call_id": "tooluse_4iDH7hGfTUeXFA7cPOkChA"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_CtXkzknuSIKAnwcISlgcLw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show 650dba4 --stat\", \"id\": \"show_commit\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "commit 650dba427e0a9dcd118f41a4c5e35c8017550a5a\nAuthor: Test User <test@example.com>\nDate:   Sat Sep 13 17:54:33 2025 +0000\n\n    Move to Stanford\n\n _includes/about.md    |  4 ++--\n _layouts/default.html | 32 +++++++++++++++++---------------\n 2 files changed, 19 insertions(+), 17 deletions(-)\n",
+    "tool_call_id": "tooluse_CtXkzknuSIKAnwcISlgcLw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_LPRQbhhVTd2QYSJBnkUI_g",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git log --oneline --graph --all --decorate\", \"id\": \"git_graph\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "* d7d3e4b (HEAD -> master) off the job market woo\n* c4e38a1 Add code link for BLADE\n* 6f46fa0 CV Update\n* dd7e395 Adds BLADE to bib\n* 2cd355a n+1 (for the last time???)\n* 8eaf505 Add BLADE\n* cc2ec78 Underline\n* d71094e Underline Conferences\n* 232b279 Remove posters\n* 3fdf5f5 Add NeurIPS\n* 8c4731d Add EMNLP acceptance\n* f54f66b Add GR link\n* 18d2430 Add other links\n* 1dd055e Ignore Gemfile, etc\n* 5c77a6d Dont overwrite\n* c7d2f95 Delete unsused files\n* 20b05d9 Remove more unused files\n* 2d144f7 Add yamls for new papers\n* 7882f2d Don't track _site\n* cd2b8de Add new papers\n* 26dc65c Fix author\n* bc1962c Interests update\n* 257eba8 More space for interests\n* ff6a94a Bib update\n* 97c4a55 Underline bold\n* a320806 Other fixes, new paper\n* 2cb7243 New PDFs\n* 7321328 PDF update\n* f1e3860 Deletions\n* 7b4d171 Update Bio\n* 073117a Another update\n* cb63517 Another CV Updatee\n* 192ae7b update headshot\n* 7fb9365 Update about and contact\n* 54ef19d CV Update\n* b0fb76a Add GR\n* 6adfab9 n plus one\n* 8a5509d Needs to be a string\n* e2f686e Add Gemfile\n* fa098ef properly handle class\n* a8fffe9 Add cv\n* 01d029a Add biblib/__pycache__/ to .gitignore\n* a06e285 Update file paths for personal site and add new PhD experience\n* cef1969 ingore\n* 76398c6 CV Update\n* 7fe50ca Include asterix\n* a8ff8fb fix venue name\n* c0e24b9 Adds Neurips Paper\n* 8379341 CV Update\n* c2ca090 Typos\n* 115a23a Re order interests\n* b2f98e3 Annual update of interests\n* 3b6f690 Make thumbnails larger\n* 177c92f Add note field\n* 2a49416 Annual update to bio\n* e3abd37 Add epj paper\n* 5ddf58a New papers capitalized\n* 5b770eb New papers\n* 199bc67 CV Update\n* 79d1ef2 Removed consultling line\n* b00b8a4 Format\n* 4ebe937 Consulting\n* 93cd578 CV, about, and interests update\n* 218ead3 Third year now!\n* 8aac2ab snark removed\n* a404b45 Added new paper\n* 43117c7 Forgot thumbnail and pdf\n* 36a7b51 New paper!\n* ef5ebab Added old research statement for UW\n* fbe500f Added old research statement\n* 883942a Fall 2020 Changes\n* 6336a21 Added work statement\n* ec13894 Fixed column layout\n*   45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| *   8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll\n| |\\  \n| | * 018fcf4 Migrated to Jekyll\n| |/  \n* / dd1ae17 Empty commit\n|/  \n* dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)\n*   c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| * 09cafdd Changed name (for real!)\n* | b3ae4f0 Changed name (for real!)\n|/  \n* 719ac48 Added Tim\n* edbd5ac Changed name\n* dfbe936 Updated CV\n* bdbb55c Changed interests\n*   c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| *   3972ef7 Merge pull request #1 from TheMikeMerrill/deployment\n| |\\  \n| | * 4798881 Fixed HR Link\n| * | b4ee987 Create CNAME\n| |/  \n* / 35707d9 Added .nojekyl\n|/  \n* a1f4a2d Updated Resume\n* b2d01e3 Add files via upload\n* 5f9aeab Add files via upload\n* a1d746d Delete README.md\n* 02ed510 Initial commit\n",
+    "tool_call_id": "tooluse_LPRQbhhVTd2QYSJBnkUI_g"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_OnGuotRKQomBbm76fjCu6g",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git merge 650dba4 --no-ff -m \\\"Merge Stanford changes into master\\\"\", \"id\": \"merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Auto-merging _includes/about.md\nCONFLICT (content): Merge conflict in _includes/about.md\nAutomatic merge failed; fix conflicts and then commit the result.\n",
+    "tool_call_id": "tooluse_OnGuotRKQomBbm76fjCu6g"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_fOc3OYEFSLO6XtoriHX7ow",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"cat _includes/about.md\", \"id\": \"check_conflict\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "<<<<<<< HEAD\nI am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).\n\n Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \n=======\nI am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \n>>>>>>> 650dba4\n",
+    "tool_call_id": "tooluse_fOc3OYEFSLO6XtoriHX7ow"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_WFCgaZrNQAu09OZ5_hatYw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show 650dba4:_includes/about.md\", \"id\": \"show_new\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ",
+    "tool_call_id": "tooluse_WFCgaZrNQAu09OZ5_hatYw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_sM2iI0_UQ4Cu4hzVJOvFXA",
+        "type": "function",
+        "function": {
+          "name": "shell_write_content_to_file",
+          "arguments": "{\"file_path\": \"/app/personal-site/_includes/about.md\", \"content\": \"I am a Postdoctoral Researcher at Stanford CS.\\n\\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Content successfully written to '/app/personal-site/_includes/about.md' in Docker container.",
+    "tool_call_id": "tooluse_sM2iI0_UQ4Cu4hzVJOvFXA"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_Jm-YnY8BQlWDaYuyR2YQXg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"cat /app/personal-site/_includes/about.md\", \"id\": \"verify_resolved\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ",
+    "tool_call_id": "tooluse_Jm-YnY8BQlWDaYuyR2YQXg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_byHaUbWvQl6tR5-d7S_HPg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git add _includes/about.md && git status\", \"id\": \"add_file\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "On branch master\nAll conflicts fixed but you are still merging.\n  (use \"git commit\" to conclude merge)\n\nChanges to be committed:\n\tmodified:   _includes/about.md\n\tmodified:   _layouts/default.html\n\n",
+    "tool_call_id": "tooluse_byHaUbWvQl6tR5-d7S_HPg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_6RkKTjhDRAOoXLNVNSDj_w",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git commit -m \\\"Merge Stanford changes into master\\\"\", \"id\": \"commit_merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "[master 4c70b8e] Merge Stanford changes into master\n",
+    "tool_call_id": "tooluse_6RkKTjhDRAOoXLNVNSDj_w"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_gwQcfYwcTRWm282ZmB-uZw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git log --oneline -5 && git status\", \"id\": \"verify_complete\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "4c70b8e Merge Stanford changes into master\n650dba4 Move to Stanford\nd7d3e4b off the job market woo\nc4e38a1 Add code link for BLADE\n6f46fa0 CV Update\nOn branch master\nnothing to commit, working tree clean\n",
+    "tool_call_id": "tooluse_gwQcfYwcTRWm282ZmB-uZw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_L2F6_fAQQs6hphmbsLfBcg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show HEAD --stat\", \"id\": \"show_merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "commit 4c70b8e770cbd0be32f1368427feced776266306\nMerge: d7d3e4b 650dba4\nAuthor: Test User <test@example.com>\nDate:   Sat Dec 20 11:20:54 2025 +0000\n\n    Merge Stanford changes into master\n\n _includes/about.md    |  4 ++--\n _layouts/default.html | 32 +++++++++++++++++---------------\n 2 files changed, 19 insertions(+), 17 deletions(-)\n",
+    "tool_call_id": "tooluse_L2F6_fAQQs6hphmbsLfBcg"
+  },
+  {
+    "role": "assistant",
+    "content": "Task completed successfully.\n\nI recovered the lost commit (650dba4 - \"Move to Stanford\") and merged it into master. The merge included:\n- Updated _includes/about.md with the Stanford position\n- Updated _layouts/default.html with layout changes\n\nThe working tree is now clean with all changes properly merged."
+  }
+]

examples/positive_messages.json

@@ -0,0 +1,261 @@
+[
+  {
+    "role": "system",
+    "content": "\n<role>\nYou are a Lead Software Engineer with full terminal access. Solve technical tasks by analyzing, planning, coding, and executing. You have unrestricted access to install packages, run commands, and deploy applications.\n</role>\n\n<operating_environment>\n- **System**: Linux (in Docker) (x86_64)\n- **Current Date**: 2025-12-20\n- Commands execute inside Docker; notes save to host.\n</operating_environment>\n\n<available_tools>\nYou have access to the following tools (call as functions, not shell commands):\n\n**Terminal Execution:**\n- shell_exec(id, command, block=True/False) - Execute shell commands. Use block=True for quick commands, block=False for long-running processes\n- shell_write_content_to_file(content, file_path) - Write text content directly to a file (preferred for creating Python scripts)\n- shell_view(id) - Check output from a non-blocking session\n- shell_wait(id, wait_seconds) - Wait for output from a non-blocking session\n- shell_write_to_process(id, command) - Send input to an interactive non-blocking process\n- shell_kill_process(id) - Terminate a non-blocking process\n\n**Note Taking:**\n- create_note(title, content) - Create a new note for tracking requirements or plans\n- append_note(title, content) - Add content to an existing note\n- read_note(title) - Read the contents of a note\n</available_tools>\n\n<mandatory_instructions>\n\nAUTONOMOUS MODE (CRITICAL)\n- You are COMPLETELY AUTONOMOUS - the user will NOT respond to any questions\n- NEVER ask for confirmation, clarification, or help - execute immediately\n- Your job is to COMPLETE the task, not describe what could be done\n- Make reasonable assumptions and proceed - the user is NOT available\n- Complete the ENTIRE task in one go - there is NO back-and-forth\n- If something is unclear, make the BEST decision and continue\n- NEVER say \"I would need...\" or \"Please provide...\" - figure it out yourself\n- NEVER stop mid-task waiting for input - push through to completion\n- NEVER end with \"here's what you should do\" or \"the solution is...\" - EXECUTE IT YOURSELF\n- After making ANY change (upgrade package, fix code, etc.): IMMEDIATELY run the original failing command to verify it works\n- Your final response should show SUCCESSFUL EXECUTION, not instructions for the user\n- When the task is complete, respond with a brief summary (NO tool call)\n\nPROHIBITIONS\n1. No questions to user - EXECUTE IMMEDIATELY (user will NEVER respond)\n2. No `python3 -c` for complex code - use shell_write_content_to_file\n3. No retrying same failing command - use DIFFERENT approach\n4. No placeholders like <your_token> in commands - find actual values yourself\n5. No writing own solution when task says \"use script X\" - use that script\n6. No guessing CLI args - run `--help` FIRST and READ the output\n7. No running scripts you haven't verified exist - check with `ls -la script.sh` FIRST\n8. No repetitive output - NEVER generate 10+ similar lines (like many echo \"\" statements)\n9. No assuming files were created - after shell_write_content_to_file, verify with `ls -la` and `head`\n10. No ending with suggestions - if you say \"you should run X\", RUN X YOURSELF\n\n</mandatory_instructions>\n\n<error_handling>\nWhen encountering errors:\n- Read the FULL error message carefully\n- Identify the root cause before attempting fixes\n- Try different approaches if the first fix doesn't work\n- Never repeat the same failing command more than twice\n\nNEVER:\n- Ask user for help - solve it yourself\n- Give up without trying multiple approaches\n- Provide partial solutions - complete the task fully\n</error_handling>\n\n<terminal_tips>\nFILE CREATION:\n- Python files: shell_write_content_to_file (never python -c for complex code)\n- Always use single-quoted delimiter ('EOF' not EOF) to prevent expansion\n- ALWAYS use absolute paths: /app/filename.txt, NEVER ./filename.txt or relative paths\n- After creating file: MANDATORY verify with `ls -la /absolute/path/to/file && head -20 /absolute/path/to/file`\n- If verification shows correct content, STOP retrying and move on\n- BEFORE running ANY script: verify it exists with `ls -la script.sh`\n- If \"No such file\": the file was NOT created - create it again, verify, then run\n\nCLI & CUSTOM TOOLS:\n- CLI tools: run --help first, read subcommand help too\n- Custom tools (.c, .py files): cat the source, understand the format before using\n- If custom binary crashes: you're using wrong format, READ the source code\n\nAPIS & JSON:\n- curl -v to see status, parse response JSON, use returned IDs\n- Empty output = failure, not success\n- For JSON body: prefer Python requests over curl with inline JSON\n\nTEST FILES:\n- Before running: inspect with `cat test_file.py | head -50` to understand structure\n- Look for test framework clues: pytest (def test_*), unittest (TestCase), main block\n- If test file runs silently (no output, exit 0): tests didn't execute, use proper runner\n- Default to pytest if unsure: `python -m pytest test_file.py -v`\n- Valid test output shows: test collection, execution (PASSED/FAILED), summary\n\nGENERAL:\n- File paths: ALWAYS /app/ not ./\n- Non-interactive: use -y, -f flags\n- Long tasks: shell_exec(id=\"x\", command=\"...\", block=False)\n</terminal_tips>\n\n\n<training_mode>\nYou are being shown a CORRECT example of how to solve this task.\nGenerate tool calls that follow the exact format shown, with only the required parameters.\nDo NOT add extra parameters like message_title, message_description, or type.\nWhen the task is complete, respond with a brief summary (NO tool call).\n</training_mode>\n"
+  },
+  {
+    "role": "user",
+    "content": "Task instruction: I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.\n"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_knQ3jekwQbmH18tEraAurQ",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"id\": \"survey\", \"command\": \"pwd && ls -la && git status && git log --oneline -10\", \"block\": true}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "/app/personal-site\ntotal 92\ndrwxr-xr-x 12 root root  4096 Sep 13 17:54 .\ndrwxr-xr-x  1 root root  4096 Sep 13 17:54 ..\ndrwxr-xr-x  8 root root  4096 Sep 13 17:54 .git\n-rw-r--r--  1 root root   100 Sep 13 17:54 .gitignore\n-rw-r--r--  1 root root    14 Sep 13 17:54 CNAME\n-rw-r--r--  1 root root    42 Sep 13 17:54 Gemfile\n-rw-r--r--  1 root root   152 Sep 13 17:54 _config.yml\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _includes\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _layouts\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _posters\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 _publications\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 biblib\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 css\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 fonts\n-rw-r--r--  1 root root    47 Sep 13 17:54 index.md\ndrwxr-xr-x  2 root root  4096 Sep 13 17:54 js\n-rw-r--r--  1 root root  2382 Sep 13 17:54 make_pubs.py\n-rw-r--r--  1 root root 19618 Sep 13 17:54 me.bib\ndrwxr-xr-x  4 root root  4096 Sep 13 17:54 resources\nOn branch master\nnothing to commit, working tree clean\nd7d3e4b off the job market woo\nc4e38a1 Add code link for BLADE\n6f46fa0 CV Update\ndd7e395 Adds BLADE to bib\n2cd355a n+1 (for the last time???)\n8eaf505 Add BLADE\ncc2ec78 Underline\nd71094e Underline Conferences\n232b279 Remove posters\n3fdf5f5 Add NeurIPS\n",
+    "tool_call_id": "tooluse_knQ3jekwQbmH18tEraAurQ"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_4iDH7hGfTUeXFA7cPOkChA",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git branch -a && git reflog --all | head -20\", \"id\": \"branches\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "* master\nd7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master\n650dba4 HEAD@{1}: commit: Move to Stanford\nc4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1\nd7d3e4b refs/heads/master@{0}: reset: moving to d7d3e4b\nb0d59cd refs/heads/master@{1}: clone: from https://github.com/TheMikeMerrill/personal-site.git\nd7d3e4b HEAD@{3}: reset: moving to d7d3e4b\nb0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git\n",
+    "tool_call_id": "tooluse_4iDH7hGfTUeXFA7cPOkChA"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_CtXkzknuSIKAnwcISlgcLw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show 650dba4 --stat\", \"id\": \"show_commit\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "commit 650dba427e0a9dcd118f41a4c5e35c8017550a5a\nAuthor: Test User <test@example.com>\nDate:   Sat Sep 13 17:54:33 2025 +0000\n\n    Move to Stanford\n\n _includes/about.md    |  4 ++--\n _layouts/default.html | 32 +++++++++++++++++---------------\n 2 files changed, 19 insertions(+), 17 deletions(-)\n",
+    "tool_call_id": "tooluse_CtXkzknuSIKAnwcISlgcLw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_LPRQbhhVTd2QYSJBnkUI_g",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git log --oneline --graph --all --decorate\", \"id\": \"git_graph\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "* d7d3e4b (HEAD -> master) off the job market woo\n* c4e38a1 Add code link for BLADE\n* 6f46fa0 CV Update\n* dd7e395 Adds BLADE to bib\n* 2cd355a n+1 (for the last time???)\n* 8eaf505 Add BLADE\n* cc2ec78 Underline\n* d71094e Underline Conferences\n* 232b279 Remove posters\n* 3fdf5f5 Add NeurIPS\n* 8c4731d Add EMNLP acceptance\n* f54f66b Add GR link\n* 18d2430 Add other links\n* 1dd055e Ignore Gemfile, etc\n* 5c77a6d Dont overwrite\n* c7d2f95 Delete unsused files\n* 20b05d9 Remove more unused files\n* 2d144f7 Add yamls for new papers\n* 7882f2d Don't track _site\n* cd2b8de Add new papers\n* 26dc65c Fix author\n* bc1962c Interests update\n* 257eba8 More space for interests\n* ff6a94a Bib update\n* 97c4a55 Underline bold\n* a320806 Other fixes, new paper\n* 2cb7243 New PDFs\n* 7321328 PDF update\n* f1e3860 Deletions\n* 7b4d171 Update Bio\n* 073117a Another update\n* cb63517 Another CV Updatee\n* 192ae7b update headshot\n* 7fb9365 Update about and contact\n* 54ef19d CV Update\n* b0fb76a Add GR\n* 6adfab9 n plus one\n* 8a5509d Needs to be a string\n* e2f686e Add Gemfile\n* fa098ef properly handle class\n* a8fffe9 Add cv\n* 01d029a Add biblib/__pycache__/ to .gitignore\n* a06e285 Update file paths for personal site and add new PhD experience\n* cef1969 ingore\n* 76398c6 CV Update\n* 7fe50ca Include asterix\n* a8ff8fb fix venue name\n* c0e24b9 Adds Neurips Paper\n* 8379341 CV Update\n* c2ca090 Typos\n* 115a23a Re order interests\n* b2f98e3 Annual update of interests\n* 3b6f690 Make thumbnails larger\n* 177c92f Add note field\n* 2a49416 Annual update to bio\n* e3abd37 Add epj paper\n* 5ddf58a New papers capitalized\n* 5b770eb New papers\n* 199bc67 CV Update\n* 79d1ef2 Removed consultling line\n* b00b8a4 Format\n* 4ebe937 Consulting\n* 93cd578 CV, about, and interests update\n* 218ead3 Third year now!\n* 8aac2ab snark removed\n* a404b45 Added new paper\n* 43117c7 Forgot thumbnail and pdf\n* 36a7b51 New paper!\n* ef5ebab Added old research statement for UW\n* fbe500f Added old research statement\n* 883942a Fall 2020 Changes\n* 6336a21 Added work statement\n* ec13894 Fixed column layout\n*   45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| *   8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll\n| |\\  \n| | * 018fcf4 Migrated to Jekyll\n| |/  \n* / dd1ae17 Empty commit\n|/  \n* dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)\n*   c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| * 09cafdd Changed name (for real!)\n* | b3ae4f0 Changed name (for real!)\n|/  \n* 719ac48 Added Tim\n* edbd5ac Changed name\n* dfbe936 Updated CV\n* bdbb55c Changed interests\n*   c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site\n|\\  \n| *   3972ef7 Merge pull request #1 from TheMikeMerrill/deployment\n| |\\  \n| | * 4798881 Fixed HR Link\n| * | b4ee987 Create CNAME\n| |/  \n* / 35707d9 Added .nojekyl\n|/  \n* a1f4a2d Updated Resume\n* b2d01e3 Add files via upload\n* 5f9aeab Add files via upload\n* a1d746d Delete README.md\n* 02ed510 Initial commit\n",
+    "tool_call_id": "tooluse_LPRQbhhVTd2QYSJBnkUI_g"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_OnGuotRKQomBbm76fjCu6g",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git merge 650dba4 --no-ff -m \\\"Merge Stanford changes into master\\\"\", \"id\": \"merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Auto-merging _includes/about.md\nCONFLICT (content): Merge conflict in _includes/about.md\nAutomatic merge failed; fix conflicts and then commit the result.\n",
+    "tool_call_id": "tooluse_OnGuotRKQomBbm76fjCu6g"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_fOc3OYEFSLO6XtoriHX7ow",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"cat _includes/about.md\", \"id\": \"check_conflict\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "<<<<<<< HEAD\nI am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).\n\n Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \n=======\nI am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \n>>>>>>> 650dba4\n",
+    "tool_call_id": "tooluse_fOc3OYEFSLO6XtoriHX7ow"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_WFCgaZrNQAu09OZ5_hatYw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show 650dba4:_includes/about.md\", \"id\": \"show_new\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ",
+    "tool_call_id": "tooluse_WFCgaZrNQAu09OZ5_hatYw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_sM2iI0_UQ4Cu4hzVJOvFXA",
+        "type": "function",
+        "function": {
+          "name": "shell_write_content_to_file",
+          "arguments": "{\"file_path\": \"/app/personal-site/_includes/about.md\", \"content\": \"I am a Postdoctoral Researcher at Stanford CS.\\n\\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). \"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "Content successfully written to '/app/personal-site/_includes/about.md' in Docker container.",
+    "tool_call_id": "tooluse_sM2iI0_UQ4Cu4hzVJOvFXA"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_Jm-YnY8BQlWDaYuyR2YQXg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"cat /app/personal-site/_includes/about.md\", \"id\": \"verify_resolved\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). ",
+    "tool_call_id": "tooluse_Jm-YnY8BQlWDaYuyR2YQXg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_byHaUbWvQl6tR5-d7S_HPg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git add _includes/about.md && git status\", \"id\": \"add_file\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "On branch master\nAll conflicts fixed but you are still merging.\n  (use \"git commit\" to conclude merge)\n\nChanges to be committed:\n\tmodified:   _includes/about.md\n\tmodified:   _layouts/default.html\n\n",
+    "tool_call_id": "tooluse_byHaUbWvQl6tR5-d7S_HPg"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_6RkKTjhDRAOoXLNVNSDj_w",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git commit -m \\\"Merge Stanford changes into master\\\"\", \"id\": \"commit_merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "[master 4c70b8e] Merge Stanford changes into master\n",
+    "tool_call_id": "tooluse_6RkKTjhDRAOoXLNVNSDj_w"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_gwQcfYwcTRWm282ZmB-uZw",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git log --oneline -5 && git status\", \"id\": \"verify_complete\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "4c70b8e Merge Stanford changes into master\n650dba4 Move to Stanford\nd7d3e4b off the job market woo\nc4e38a1 Add code link for BLADE\n6f46fa0 CV Update\nOn branch master\nnothing to commit, working tree clean\n",
+    "tool_call_id": "tooluse_gwQcfYwcTRWm282ZmB-uZw"
+  },
+  {
+    "role": "assistant",
+    "content": "",
+    "tool_calls": [
+      {
+        "id": "tooluse_L2F6_fAQQs6hphmbsLfBcg",
+        "type": "function",
+        "function": {
+          "name": "shell_exec",
+          "arguments": "{\"block\": true, \"command\": \"git show HEAD --stat\", \"id\": \"show_merge\"}"
+        }
+      }
+    ]
+  },
+  {
+    "role": "tool",
+    "content": "commit 4c70b8e770cbd0be32f1368427feced776266306\nMerge: d7d3e4b 650dba4\nAuthor: Test User <test@example.com>\nDate:   Sat Dec 20 11:20:54 2025 +0000\n\n    Merge Stanford changes into master\n\n _includes/about.md    |  4 ++--\n _layouts/default.html | 32 +++++++++++++++++---------------\n 2 files changed, 19 insertions(+), 17 deletions(-)\n",
+    "tool_call_id": "tooluse_L2F6_fAQQs6hphmbsLfBcg"
+  },
+  {
+    "role": "assistant",
+    "content": "Task completed successfully.\n\nI recovered the lost commit (650dba4 - \"Move to Stanford\") and merged it into master. The merge included:\n- Updated _includes/about.md with the Stanford position\n- Updated _layouts/default.html with layout changes\n\nThe working tree is now clean with all changes properly merged."
+  }
+]

examples/positive_text.txt

@@ -0,0 +1,429 @@
+<|im_start|>system
+
+<role>
+You are a Lead Software Engineer with full terminal access. Solve technical tasks by analyzing, planning, coding, and executing. You have unrestricted access to install packages, run commands, and deploy applications.
+</role>
+
+<operating_environment>
+- **System**: Linux (in Docker) (x86_64)
+- **Current Date**: 2025-12-20
+- Commands execute inside Docker; notes save to host.
+</operating_environment>
+
+<available_tools>
+You have access to the following tools (call as functions, not shell commands):
+
+**Terminal Execution:**
+- shell_exec(id, command, block=True/False) - Execute shell commands. Use block=True for quick commands, block=False for long-running processes
+- shell_write_content_to_file(content, file_path) - Write text content directly to a file (preferred for creating Python scripts)
+- shell_view(id) - Check output from a non-blocking session
+- shell_wait(id, wait_seconds) - Wait for output from a non-blocking session
+- shell_write_to_process(id, command) - Send input to an interactive non-blocking process
+- shell_kill_process(id) - Terminate a non-blocking process
+
+**Note Taking:**
+- create_note(title, content) - Create a new note for tracking requirements or plans
+- append_note(title, content) - Add content to an existing note
+- read_note(title) - Read the contents of a note
+</available_tools>
+
+<mandatory_instructions>
+
+AUTONOMOUS MODE (CRITICAL)
+- You are COMPLETELY AUTONOMOUS - the user will NOT respond to any questions
+- NEVER ask for confirmation, clarification, or help - execute immediately
+- Your job is to COMPLETE the task, not describe what could be done
+- Make reasonable assumptions and proceed - the user is NOT available
+- Complete the ENTIRE task in one go - there is NO back-and-forth
+- If something is unclear, make the BEST decision and continue
+- NEVER say "I would need..." or "Please provide..." - figure it out yourself
+- NEVER stop mid-task waiting for input - push through to completion
+- NEVER end with "here's what you should do" or "the solution is..." - EXECUTE IT YOURSELF
+- After making ANY change (upgrade package, fix code, etc.): IMMEDIATELY run the original failing command to verify it works
+- Your final response should show SUCCESSFUL EXECUTION, not instructions for the user
+- When the task is complete, respond with a brief summary (NO tool call)
+
+PROHIBITIONS
+1. No questions to user - EXECUTE IMMEDIATELY (user will NEVER respond)
+2. No `python3 -c` for complex code - use shell_write_content_to_file
+3. No retrying same failing command - use DIFFERENT approach
+4. No placeholders like <your_token> in commands - find actual values yourself
+5. No writing own solution when task says "use script X" - use that script
+6. No guessing CLI args - run `--help` FIRST and READ the output
+7. No running scripts you haven't verified exist - check with `ls -la script.sh` FIRST
+8. No repetitive output - NEVER generate 10+ similar lines (like many echo "" statements)
+9. No assuming files were created - after shell_write_content_to_file, verify with `ls -la` and `head`
+10. No ending with suggestions - if you say "you should run X", RUN X YOURSELF
+
+</mandatory_instructions>
+
+<error_handling>
+When encountering errors:
+- Read the FULL error message carefully
+- Identify the root cause before attempting fixes
+- Try different approaches if the first fix doesn't work
+- Never repeat the same failing command more than twice
+
+NEVER:
+- Ask user for help - solve it yourself
+- Give up without trying multiple approaches
+- Provide partial solutions - complete the task fully
+</error_handling>
+
+<terminal_tips>
+FILE CREATION:
+- Python files: shell_write_content_to_file (never python -c for complex code)
+- Always use single-quoted delimiter ('EOF' not EOF) to prevent expansion
+- ALWAYS use absolute paths: /app/filename.txt, NEVER ./filename.txt or relative paths
+- After creating file: MANDATORY verify with `ls -la /absolute/path/to/file && head -20 /absolute/path/to/file`
+- If verification shows correct content, STOP retrying and move on
+- BEFORE running ANY script: verify it exists with `ls -la script.sh`
+- If "No such file": the file was NOT created - create it again, verify, then run
+
+CLI & CUSTOM TOOLS:
+- CLI tools: run --help first, read subcommand help too
+- Custom tools (.c, .py files): cat the source, understand the format before using
+- If custom binary crashes: you're using wrong format, READ the source code
+
+APIS & JSON:
+- curl -v to see status, parse response JSON, use returned IDs
+- Empty output = failure, not success
+- For JSON body: prefer Python requests over curl with inline JSON
+
+TEST FILES:
+- Before running: inspect with `cat test_file.py | head -50` to understand structure
+- Look for test framework clues: pytest (def test_*), unittest (TestCase), main block
+- If test file runs silently (no output, exit 0): tests didn't execute, use proper runner
+- Default to pytest if unsure: `python -m pytest test_file.py -v`
+- Valid test output shows: test collection, execution (PASSED/FAILED), summary
+
+GENERAL:
+- File paths: ALWAYS /app/ not ./
+- Non-interactive: use -y, -f flags
+- Long tasks: shell_exec(id="x", command="...", block=False)
+</terminal_tips>
+
+
+<training_mode>
+You are being shown a CORRECT example of how to solve this task.
+Generate tool calls that follow the exact format shown, with only the required parameters.
+Do NOT add extra parameters like message_title, message_description, or type.
+When the task is complete, respond with a brief summary (NO tool call).
+</training_mode>
+<|im_end|>
+<|im_start|>user
+Task instruction: I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.
+<|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"id": "survey", "command": "pwd && ls -la && git status && git log --oneline -10", "block": true}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+/app/personal-site
+total 92
+drwxr-xr-x 12 root root  4096 Sep 13 17:54 .
+drwxr-xr-x  1 root root  4096 Sep 13 17:54 ..
+drwxr-xr-x  8 root root  4096 Sep 13 17:54 .git
+-rw-r--r--  1 root root   100 Sep 13 17:54 .gitignore
+-rw-r--r--  1 root root    14 Sep 13 17:54 CNAME
+-rw-r--r--  1 root root    42 Sep 13 17:54 Gemfile
+-rw-r--r--  1 root root   152 Sep 13 17:54 _config.yml
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 _includes
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 _layouts
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 _posters
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 _publications
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 biblib
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 css
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 fonts
+-rw-r--r--  1 root root    47 Sep 13 17:54 index.md
+drwxr-xr-x  2 root root  4096 Sep 13 17:54 js
+-rw-r--r--  1 root root  2382 Sep 13 17:54 make_pubs.py
+-rw-r--r--  1 root root 19618 Sep 13 17:54 me.bib
+drwxr-xr-x  4 root root  4096 Sep 13 17:54 resources
+On branch master
+nothing to commit, working tree clean
+d7d3e4b off the job market woo
+c4e38a1 Add code link for BLADE
+6f46fa0 CV Update
+dd7e395 Adds BLADE to bib
+2cd355a n+1 (for the last time???)
+8eaf505 Add BLADE
+cc2ec78 Underline
+d71094e Underline Conferences
+232b279 Remove posters
+3fdf5f5 Add NeurIPS
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git branch -a && git reflog --all | head -20", "id": "branches"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+* master
+d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
+650dba4 HEAD@{1}: commit: Move to Stanford
+c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
+d7d3e4b refs/heads/master@{0}: reset: moving to d7d3e4b
+b0d59cd refs/heads/master@{1}: clone: from https://github.com/TheMikeMerrill/personal-site.git
+d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
+b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git show 650dba4 --stat", "id": "show_commit"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+commit 650dba427e0a9dcd118f41a4c5e35c8017550a5a
+Author: Test User <test@example.com>
+Date:   Sat Sep 13 17:54:33 2025 +0000
+
+    Move to Stanford
+
+ _includes/about.md    |  4 ++--
+ _layouts/default.html | 32 +++++++++++++++++---------------
+ 2 files changed, 19 insertions(+), 17 deletions(-)
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git log --oneline --graph --all --decorate", "id": "git_graph"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+* d7d3e4b (HEAD -> master) off the job market woo
+* c4e38a1 Add code link for BLADE
+* 6f46fa0 CV Update
+* dd7e395 Adds BLADE to bib
+* 2cd355a n+1 (for the last time???)
+* 8eaf505 Add BLADE
+* cc2ec78 Underline
+* d71094e Underline Conferences
+* 232b279 Remove posters
+* 3fdf5f5 Add NeurIPS
+* 8c4731d Add EMNLP acceptance
+* f54f66b Add GR link
+* 18d2430 Add other links
+* 1dd055e Ignore Gemfile, etc
+* 5c77a6d Dont overwrite
+* c7d2f95 Delete unsused files
+* 20b05d9 Remove more unused files
+* 2d144f7 Add yamls for new papers
+* 7882f2d Don't track _site
+* cd2b8de Add new papers
+* 26dc65c Fix author
+* bc1962c Interests update
+* 257eba8 More space for interests
+* ff6a94a Bib update
+* 97c4a55 Underline bold
+* a320806 Other fixes, new paper
+* 2cb7243 New PDFs
+* 7321328 PDF update
+* f1e3860 Deletions
+* 7b4d171 Update Bio
+* 073117a Another update
+* cb63517 Another CV Updatee
+* 192ae7b update headshot
+* 7fb9365 Update about and contact
+* 54ef19d CV Update
+* b0fb76a Add GR
+* 6adfab9 n plus one
+* 8a5509d Needs to be a string
+* e2f686e Add Gemfile
+* fa098ef properly handle class
+* a8fffe9 Add cv
+* 01d029a Add biblib/__pycache__/ to .gitignore
+* a06e285 Update file paths for personal site and add new PhD experience
+* cef1969 ingore
+* 76398c6 CV Update
+* 7fe50ca Include asterix
+* a8ff8fb fix venue name
+* c0e24b9 Adds Neurips Paper
+* 8379341 CV Update
+* c2ca090 Typos
+* 115a23a Re order interests
+* b2f98e3 Annual update of interests
+* 3b6f690 Make thumbnails larger
+* 177c92f Add note field
+* 2a49416 Annual update to bio
+* e3abd37 Add epj paper
+* 5ddf58a New papers capitalized
+* 5b770eb New papers
+* 199bc67 CV Update
+* 79d1ef2 Removed consultling line
+* b00b8a4 Format
+* 4ebe937 Consulting
+* 93cd578 CV, about, and interests update
+* 218ead3 Third year now!
+* 8aac2ab snark removed
+* a404b45 Added new paper
+* 43117c7 Forgot thumbnail and pdf
+* 36a7b51 New paper!
+* ef5ebab Added old research statement for UW
+* fbe500f Added old research statement
+* 883942a Fall 2020 Changes
+* 6336a21 Added work statement
+* ec13894 Fixed column layout
+*   45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
+|\  
+| *   8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
+| |\  
+| | * 018fcf4 Migrated to Jekyll
+| |/  
+* / dd1ae17 Empty commit
+|/  
+* dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
+*   c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
+|\  
+| * 09cafdd Changed name (for real!)
+* | b3ae4f0 Changed name (for real!)
+|/  
+* 719ac48 Added Tim
+* edbd5ac Changed name
+* dfbe936 Updated CV
+* bdbb55c Changed interests
+*   c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
+|\  
+| *   3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
+| |\  
+| | * 4798881 Fixed HR Link
+| * | b4ee987 Create CNAME
+| |/  
+* / 35707d9 Added .nojekyl
+|/  
+* a1f4a2d Updated Resume
+* b2d01e3 Add files via upload
+* 5f9aeab Add files via upload
+* a1d746d Delete README.md
+* 02ed510 Initial commit
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git merge 650dba4 --no-ff -m \"Merge Stanford changes into master\"", "id": "merge"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+Auto-merging _includes/about.md
+CONFLICT (content): Merge conflict in _includes/about.md
+Automatic merge failed; fix conflicts and then commit the result.
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "cat _includes/about.md", "id": "check_conflict"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+<<<<<<< HEAD
+I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).
+
+ Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
+=======
+I am a Postdoctoral Researcher at Stanford CS.
+
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
+>>>>>>> 650dba4
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git show 650dba4:_includes/about.md", "id": "show_new"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+I am a Postdoctoral Researcher at Stanford CS.
+
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_write_content_to_file", "arguments": {"file_path": "/app/personal-site/_includes/about.md", "content": "I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). "}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+Content successfully written to '/app/personal-site/_includes/about.md' in Docker container.
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "cat /app/personal-site/_includes/about.md", "id": "verify_resolved"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+I am a Postdoctoral Researcher at Stanford CS.
+
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com). 
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git add _includes/about.md && git status", "id": "add_file"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+On branch master
+All conflicts fixed but you are still merging.
+  (use "git commit" to conclude merge)
+
+Changes to be committed:
+	modified:   _includes/about.md
+	modified:   _layouts/default.html
+
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git commit -m \"Merge Stanford changes into master\"", "id": "commit_merge"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+[master 4c70b8e] Merge Stanford changes into master
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git log --oneline -5 && git status", "id": "verify_complete"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+4c70b8e Merge Stanford changes into master
+650dba4 Move to Stanford
+d7d3e4b off the job market woo
+c4e38a1 Add code link for BLADE
+6f46fa0 CV Update
+On branch master
+nothing to commit, working tree clean
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<tool_call>
+{"name": "shell_exec", "arguments": {"block": true, "command": "git show HEAD --stat", "id": "show_merge"}}
+</tool_call><|im_end|>
+<|im_start|>user
+<tool_response>
+commit 4c70b8e770cbd0be32f1368427feced776266306
+Merge: d7d3e4b 650dba4
+Author: Test User <test@example.com>
+Date:   Sat Dec 20 11:20:54 2025 +0000
+
+    Merge Stanford changes into master
+
+ _includes/about.md    |  4 ++--
+ _layouts/default.html | 32 +++++++++++++++++---------------
+ 2 files changed, 19 insertions(+), 17 deletions(-)
+
+</tool_response><|im_end|>
+<|im_start|>assistant
+<think>
+
+</think>
+
+Task completed successfully.
+
+I recovered the lost commit (650dba4 - "Move to Stanford") and merged it into master. The merge included:
+- Updated _includes/about.md with the Stanford position
+- Updated _layouts/default.html with layout changes
+
+The working tree is now clean with all changes properly merged.<|im_end|>

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