fix(mcp): wire run_powershell and MCP server for Windows/Scoop environment

- Add .mcp.json at project root (correct location for claude mcp add)
- Add mcp_env.toml: project-scoped PATH/env config for subprocess execution
- shell_runner.py: load mcp_env.toml, add stdin=DEVNULL to fix git hang
- mcp_server.py: call mcp_client.configure() at startup (fix ACCESS DENIED)
- conductor skill files: enforce run_powershell over Bash, tool use hierarchy
- CLAUDE.md: document Bash unreliability on Windows, run_powershell preference

scripts/mcp_server.py

@@ -79,6 +79,9 @@ async def call_tool(name: str, arguments: dict) -> list[TextContent]:
 
 
 async def main() -> None:
+    # Configure mcp_client with the project root so py_* tools are not ACCESS DENIED
+    project_root = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+    mcp_client.configure([], extra_base_dirs=[project_root])
     async with stdio_server() as (read_stream, write_stream):
         await server.run(
             read_stream,