docs: update MCP server integration documentation and status

- Revised the documentation for the MCP server integration, confirming its implementation in Phase 12.
- Updated the priority summary to reflect the MCP server as working and compliant with Track 2 requirements.
- Enhanced testing instructions for the MCP server, including starting the server via the Gradio app and checking the MCP schema.
- Documented files created during the integration, including `src/mcp_tools.py` and `src/app.py`, along with their respective functionalities.

Files modified:
- docs/pending/00_priority_summary.md
- docs/pending/02_mcp_server_integration.md

docs/implementation/13_phase_modal_integration.md

@@ -1125,13 +1125,13 @@ Phase 13 is **COMPLETE** when:
 
 ```text
 ┌─────────────────────────────────────────────────────────────────┐
-│                        MCP Clients                               │
-│              (Claude Desktop, Cursor, etc.)                      │
+│                        MCP Clients                              │
+│              (Claude Desktop, Cursor, etc.)                     │
 └───────────────────────────┬─────────────────────────────────────┘
                             │ MCP Protocol
                             ▼
 ┌─────────────────────────────────────────────────────────────────┐
-│                     Gradio App + MCP Server                      │
+│                     Gradio App + MCP Server                     │
 │  ┌──────────────────────────────────────────────────────────┐   │
 │  │  MCP Tools: search_pubmed, search_trials, search_biorxiv │   │
 │  │             search_all, analyze_hypothesis               │   │
@@ -1152,7 +1152,7 @@ Phase 13 is **COMPLETE** when:
 └───────────┬───────────┘            └───────────────────────────┘
             │
             ▼
-┌─────────────────────────────────────────────────────────────────┐
+┌──────────────────────────────────────────────────────────────────┐
 │                    StatisticalAnalyzer                           │
 │              (src/services/statistical_analyzer.py)              │
 │                    NO agent_framework dependency                 │
@@ -1160,11 +1160,11 @@ Phase 13 is **COMPLETE** when:
 │  1. Generate code with pydantic-ai                               │
 │  2. Execute in Modal sandbox                                     │
 │  3. Return AnalysisResult                                        │
-└───────────────────────────┬─────────────────────────────────────┘
+└───────────────────────────┬──────────────────────────────────────┘
                             │
                             ▼
 ┌─────────────────────────────────────────────────────────────────┐
-│                       Modal Sandbox                              │
+│                       Modal Sandbox                             │
 │  ┌─────────────────────────────────────────────────────────┐    │
 │  │  - pandas, numpy, scipy, sklearn, statsmodels           │    │
 │  │  - Network: BLOCKED                                     │    │

docs/pending/00_priority_summary.md

@@ -6,7 +6,7 @@
 
 ## Git Contribution Analysis
 
-```
+```text
 The-Obstacle-Is-The-Way: 20+ commits (Phases 1-11, all demos, all fixes)
 MarioAderman:            3 commits (Modal, LlamaIndex, PubMed fix)
 JJ (Maintainer):         0 code commits (merge button only)
@@ -32,7 +32,7 @@ JJ (Maintainer):         0 code commits (merge button only)
 | Orchestrator | ✅ Working | `src/orchestrator.py` |
 | Gradio UI | ✅ Working | `src/app.py` |
 | Modal Code Execution | ⚠️ Built, not wired | `src/tools/code_execution.py` |
-| **MCP Server** | ❌ **MISSING** | Need to create |
+| **MCP Server** | ✅ **Working** | `src/mcp_tools.py`, `src/app.py` |
 
 ---
 
@@ -41,21 +41,22 @@ JJ (Maintainer):         0 code commits (merge button only)
 | Requirement | Have It? | Priority |
 |-------------|----------|----------|
 | Autonomous agent behavior | ✅ Yes | - |
-| Must use MCP servers as tools | ❌ **NO** | **P0** |
+| Must use MCP servers as tools | ✅ **YES** | Done (Phase 12) |
 | Must be Gradio app | ✅ Yes | - |
 | Planning/reasoning/execution | ✅ Yes | - |
 
-**Bottom Line:** Without MCP server, we're potentially disqualified from Track 2.
+**Bottom Line:** ✅ MCP server implemented in Phase 12. Track 2 compliant.
 
 ---
 
 ## 3 Things To Do (In Order)
 
-### 1. MCP Server (P0 - Required)
-- **File:** `src/mcp_server.py`
-- **Time:** 2-4 hours
+### 1. MCP Server (P0 - Required) ✅ DONE
+
+- **Files:** `src/mcp_tools.py`, `src/app.py`
+- **Status:** Implemented in Phase 12
 - **Doc:** `02_mcp_server_integration.md`
-- **Why:** Required for Track 2. No MCP = no entry.
+- **Endpoint:** `/gradio_api/mcp/`
 
 ### 2. Modal Wiring (P1 - $2,500 Prize)
 - **File:** Update `src/agents/analysis_agent.py`
@@ -95,19 +96,16 @@ JJ (Maintainer):         0 code commits (merge button only)
 ## Next Actions
 
 ```bash
-# 1. Read MCP integration doc
-cat docs/pending/02_mcp_server_integration.md
-
-# 2. Create MCP server
-# (implement based on doc)
+# 1. MCP Server - DONE ✅
+uv run python src/app.py  # Starts Gradio with MCP at /gradio_api/mcp/
 
-# 3. Test MCP works
-uv run python src/mcp_server.py
+# 2. Test MCP works
+curl http://localhost:7860/gradio_api/mcp/schema | jq
 
-# 4. Wire Modal into pipeline
+# 3. Wire Modal into pipeline
 # (see 03_modal_integration.md)
 
-# 5. Record demo video
+# 4. Record demo video
 
-# 6. Submit to MCP-1st-Birthday org
+# 5. Submit to MCP-1st-Birthday org
 ```

docs/pending/02_mcp_server_integration.md

@@ -2,6 +2,9 @@
 
 ## Priority: P0 - REQUIRED FOR TRACK 2
 
+> **✅ STATUS: IMPLEMENTED** - See `src/mcp_tools.py` and `src/app.py`
+> MCP endpoint: `/gradio_api/mcp/`
+
 ---
 
 ## What We Need
@@ -129,17 +132,25 @@ After implementing, users add to `claude_desktop_config.json`:
 
 ## Testing MCP Server
 
-1. Start the MCP server:
+1. Start the MCP server (via Gradio app):
+
 ```bash
-uv run python src/mcp_server.py
+uv run python src/app.py
 ```
 
-2. Test with Claude Desktop or MCP Inspector:
+2. Check MCP schema:
+
+```bash
+curl http://localhost:7860/gradio_api/mcp/schema | jq
+```
+
+3. Test with MCP Inspector:
+
 ```bash
-npx @anthropic/mcp-inspector
+npx @anthropic/mcp-inspector http://localhost:7860/gradio_api/mcp/sse
 ```
 
-3. Verify tools appear and work
+4. Verify tools appear and work
 
 ---
 
@@ -157,8 +168,10 @@ This proves MCP integration works.
 
 ---
 
-## Files to Create
+## Files Created
 
-- [ ] `src/mcp_server.py` - MCP server implementation
-- [ ] `examples/mcp_demo/test_mcp.py` - Test script
-- [ ] Update `README.md` with MCP usage instructions
+- [x] `src/mcp_tools.py` - MCP tool wrapper functions
+- [x] `src/app.py` - Gradio app with `mcp_server=True`
+- [x] `tests/unit/test_mcp_tools.py` - Unit tests
+- [x] `tests/integration/test_mcp_tools_live.py` - Integration tests
+- [x] `README.md` - Updated with MCP usage instructions