chore(F.15): FastMCP 3.x upgrade + legacy cleanup — v3.5.0

- Upgrade fastmcp from >=2.14.0,<3.0.0 to >=3.0.0,<4.0.0
- Remove server_multi.py (legacy multi-endpoint server)
- Remove core/project_manager.py (legacy project manager)
- Refactor HealthMonitor to use SiteManager exclusively
- Replace _tool_manager._tools with tracked _tool_counts dict
- Clean core/__init__.py exports
- Update CHANGELOG, CLAUDE.md, tests
- Auto-format fixes (black + ruff)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

core/endpoints/registry.py

@@ -149,11 +149,7 @@ class EndpointRegistry:
             tool_count = 0
 
             if mcp:
-                # Try to get tool count from FastMCP
-                try:
-                    tool_count = len(mcp._tool_manager._tools)
-                except AttributeError:
-                    pass
+                tool_count = self.factory._tool_counts.get(path, 0)
 
             endpoints.append(
                 EndpointInfo(