docs: Add PubMed Full-Text Retrieval Phase Documentation

- Introduce a new document detailing Phase 16: PubMed Full-Text Retrieval, outlining its objectives, prerequisites, success criteria, and implementation notes.
- This phase aims to enhance evidence quality by enabling full-text retrieval from PubMed, including structured sections and search integration.
- The document serves as a comprehensive guide for developers and stakeholders involved in the implementation of this feature.

docs/development/testing.md

@@ -1,139 +0,0 @@
-# Testing Strategy
-## ensuring DeepBoner is Ironclad
-
----
-
-## Overview
-
-Our testing strategy follows a strict **Pyramid of Reliability**:
-1. **Unit Tests**: Fast, isolated logic checks (60% of tests)
-2. **Integration Tests**: Tool interactions & Agent loops (30% of tests)
-3. **E2E / Regression Tests**: Full research workflows (10% of tests)
-
-**Goal**: Ship a research agent that doesn't hallucinate, crash on API limits, or burn $100 in tokens by accident.
-
----
-
-## 1. Unit Tests (Fast & Cheap)
-
-**Location**: `tests/unit/`
-
-Focus on individual components without external network calls. Mock everything.
-
-### Key Test Cases
-
-#### Agent Logic
-- **Initialization**: Verify default config loads correctly.
-- **State Updates**: Ensure `ResearchState` updates correctly (e.g., token counts increment).
-- **Budget Checks**: Test `should_continue()` returns `False` when budget exceeded.
-- **Error Handling**: Test partial failure recovery (e.g., one tool fails, agent continues).
-
-#### Tools (Mocked)
-- **Parser Logic**: Feed raw XML/JSON to tool parsers and verify `Evidence` objects.
-- **Validation**: Ensure tools reject invalid queries (empty strings, etc.).
-
-#### Judge Prompts
-- **Schema Compliance**: Verify prompt templates generate valid JSON structure instructions.
-- **Variable Injection**: Ensure `{question}` and `{context}` are injected correctly into prompts.
-
-```python
-# Example: Testing State Logic
-def test_budget_stop():
-    state = ResearchState(tokens_used=50001, max_tokens=50000)
-    assert should_continue(state) is False
-```
-
----
-
-## 2. Integration Tests (Realistic & Mocked I/O)
-
-**Location**: `tests/integration/`
-
-Focus on the interaction between the Orchestrator, Tools, and LLM Judge. Use **VCR.py** or **Replay** patterns to record/replay API calls to save money/time.
-
-### Key Test Cases
-
-#### Search Loop
-- **Iteration Flow**: Verify agent performs Search -> Judge -> Search loop.
-- **Tool Selection**: Verify correct tools are called based on judge output (mocked judge).
-- **Context Accumulation**: Ensure findings from Iteration 1 are passed to Iteration 2.
-
-#### MCP Server Integration
-- **Server Startup**: Verify MCP server starts and exposes tools.
-- **Client Connection**: Verify agent can call tools via MCP protocol.
-
-```python
-# Example: Testing Search Loop with Mocked Tools
-async def test_search_loop_flow():
-    agent = ResearchAgent(tools=[MockPubMed(), MockWeb()])
-    report = await agent.run("test query")
-    assert agent.state.iterations > 0
-    assert len(report.sources) > 0
-```
-
----
-
-## 3. End-to-End (E2E) Tests (The "Real Deal")
-
-**Location**: `tests/e2e/`
-
-Run against **real APIs** (with strict rate limits) to verify system integrity. Run these **on demand** or **nightly**, not on every commit.
-
-### Key Test Cases
-
-#### The "Golden Query"
-Run the primary demo query: *"What existing drugs might help treat long COVID fatigue?"*
-- **Success Criteria**:
-  - Returns at least 2 valid drug candidates (e.g., CoQ10, LDN).
-  - Includes citations from PubMed.
-  - Completes within 3 iterations.
-  - JSON output matches schema.
-
-#### Deployment Smoke Test
-- **Gradio UI**: Verify UI launches and accepts input.
-- **Streaming**: Verify generator yields chunks (first chunk within 2s).
-
----
-
-## 4. Tools & Config
-
-### Pytest Configuration
-```toml
-# pyproject.toml
-[tool.pytest.ini_options]
-markers = [
-    "unit: fast, isolated tests",
-    "integration: mocked network tests",
-    "e2e: real network tests (slow, expensive)"
-]
-asyncio_mode = "auto"
-```
-
-### CI/CD Pipeline (GitHub Actions)
-1. **Lint**: `ruff check .`
-2. **Type Check**: `mypy .`
-3. **Unit**: `pytest -m unit`
-4. **Integration**: `pytest -m integration`
-5. **E2E**: (Manual trigger only)
-
----
-
-## 5. Anti-Hallucination Validation
-
-How do we test if the agent is lying?
-
-1. **Citation Check**:
-   - Regex verify that every `[PMID: 12345]` in the report exists in the `Evidence` list.
-   - Fail if a citation is "orphaned" (hallucinated ID).
-
-2. **Negative Constraints**:
-   - Test queries for fake diseases ("Ligma syndrome") -> Agent should return "No evidence found".
-
----
-
-## Checklist for Implementation
-
-- [ ] Set up `tests/` directory structure
-- [ ] Configure `pytest` and `vcrpy`
-- [ ] Create `tests/fixtures/` for mock data (PubMed XMLs)
-- [ ] Write first unit test for `ResearchState`