checkpoint: Claude Code integration + implement missing MCP var tools

Add Claude Code conductor commands, MCP server, MMA exec scripts,
and implement py_get_var_declaration / py_set_var_declaration which
were registered in dispatch and tool specs but had no function bodies.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

pyproject.toml

@@ -14,6 +14,7 @@ dependencies = [
     "uvicorn",
     "tree-sitter>=0.25.2",
     "tree-sitter-python>=0.25.0",
+    "mcp>=1.0.0",
 ]
 
 [dependency-groups]