fix: resolve stale MCP runtime EOF follow-ups (#531)

- fail closed when runtime diagnostics fail unexpectedly
- move MCP connection healthcheck under scripts/
- document #543 as the remaining IDE namespace proof
- keep namespace binding test isolated from mocked git metadata

docs/wiki/Open-Decisions.md

@@ -9,3 +9,4 @@ Pending architectural and workflow decisions:
 - **Operation-scoped role selection (#228)** — Move from launcher-profile-dependent routing to per-operation profile resolution.
 - **Gitea-Tools wiki for dadeschools remote** — This bootstrap covers `prgs`; dadeschools instance wiki parity is undecided.
 - **Server-side self-merge block** — Complement tool gates with Gitea branch protection where available.
+- **IDE-namespace callable-tool proof (#543)** — Remaining follow-up. PR #545 (stale MCP runtime race-control) adds runtime staleness guards before mutations and improves diagnostics, but does not include a full cross-namespace callable tool proof for IDE-spawned MCP sessions. Track completion of direct "callable from IDE namespace" verification under #543.

gitea_mcp_server.py

@@ -694,8 +694,13 @@ def _verify_role_mutation_workspace(
                 raise RuntimeError("; ".join(runtime_reasons))
     except Exception as exc:
         if "stale-runtime:" in str(exc):
-            raise RuntimeError(str(exc))
+            raise RuntimeError(str(exc)) from exc
-        pass
+        # Fail-closed: unexpected error while performing stale-runtime guard must not be swallowed.
+        # Surface an actionable diagnostic instead of allowing a mutation under unknown runtime state.
+        raise RuntimeError(
+            f"stale-runtime: runtime diagnostic check failed unexpectedly ({type(exc).__name__}: {exc}). "
+            "Failing closed. Verify MCP server processes, profile configuration, and OS process visibility; retry after full MCP server restart."
+        ) from exc
 
     role = _effective_workspace_role()
     git_state = issue_lock_worktree.read_worktree_git_state(
@@ -8338,7 +8343,12 @@ def gitea_route_task_session(
 
 
 def _check_mcp_runtimes_diagnostics(task: str, matching_profiles: list[str]) -> list[str]:
-    """Check running runtimes and return errors if they are missing or stale."""
+    """Check running runtimes and return errors if they are missing or stale.
+
+    NOTE: IDE-namespace callable-tool proof for #543 is a documented follow-up
+    if this change does not fully close the gap for tools invoked from
+    IDE-launched MCP client namespaces. See docs/wiki/Open-Decisions.md.
+    """
     import subprocess
     import re
     from datetime import datetime
@@ -8407,7 +8417,7 @@ def _check_mcp_runtimes_diagnostics(task: str, matching_profiles: list[str]) ->
     if self_stale:
         reasons.append(
             "stale-runtime: The active Gitea MCP server process is stale (running code from before changes were merged). "
-            "Please fully restart the Gitea MCP server (e.g. touch /Users/jasonwalker/.gemini/config/mcp_config.json) and retry."
+            "Please fully restart the Gitea MCP server (for the affected profile) and retry."
         )
 
     if matching_profiles:

scripts/test_mcp_conn.py

@@ -1,10 +1,20 @@
 #!/usr/bin/env python3
 """Live health-check script to verify Gitea MCP namespace connections.
 
-Spawns the MCP server processes as defined in the IDE's global config,
+Spawns the MCP server processes as defined in a config file,
 performs the JSON-RPC handshake, and queries the tools list to verify
 that the connection is fully operational and doesn't return EOF.
+
+Usage:
+  python scripts/test_mcp_conn.py [config.json]
+
+Env:
+  GITEA_MCP_HEALTHCHECK_CONFIG  Path to mcpServers JSON config (e.g. ~/.gemini/config/mcp_config.json)
+
+The config file must contain an object with "mcpServers": { "gitea-author": {...}, ... }
+Each server entry has "command", optional "args", optional "env".
 """
+import argparse
 import json
 import os
 import subprocess
@@ -103,12 +113,26 @@ def test_connection(name, config):
         return False
 
 def main():
-    config_path = "/Users/jasonwalker/.gemini/config/mcp_config.json"
+    parser = argparse.ArgumentParser(description="Gitea MCP connection health check")
+    parser.add_argument(
+        "config",
+        nargs="?",
+        default=os.environ.get("GITEA_MCP_HEALTHCHECK_CONFIG"),
+        help="Path to MCP config JSON with mcpServers (or set GITEA_MCP_HEALTHCHECK_CONFIG)"
+    )
+    args = parser.parse_args()
+
+    config_path = args.config
+    if not config_path:
+        print("ERROR: No config path provided. Pass as argument or set GITEA_MCP_HEALTHCHECK_CONFIG.")
+        print("Example: GITEA_MCP_HEALTHCHECK_CONFIG=/path/to/mcp_config.json python scripts/test_mcp_conn.py")
+        sys.exit(2)
+
     try:
         with open(config_path) as f:
             mcp_config = json.load(f)
     except Exception as e:
-        print(f"Failed to load mcp_config.json: {e}")
+        print(f"Failed to load config {config_path}: {e}")
         sys.exit(1)
 
     servers = mcp_config.get("mcpServers", {})
@@ -118,7 +142,7 @@ def main():
             if not test_connection(name, servers[name]):
                 failed = True
         else:
-            print(f"Server '{name}' not found in mcp_config.json")
+            print(f"Server '{name}' not found in config")
 
     if failed:
         sys.exit(1)
@@ -127,3 +151,4 @@ def main():
 
 if __name__ == "__main__":
     main()
+

tests/test_namespace_workspace_binding.py

@@ -234,7 +234,20 @@ class TestNamespaceWorkspaceIntegration(unittest.TestCase):
         mock_run.return_value = MagicMock(returncode=0, stdout=f"{CONTROL_ROOT}/.git\n")
         os.environ[nwb.AUTHOR_WORKTREE_ENV] = AUTHOR_DIRTY
         srv._preflight_resolved_role = "reviewer"
+        clean_git_state = {
+            "current_branch": "master",
+            "porcelain_status": "",
+            "head_sha": "abc123",
+        }
         with mock.patch.object(srv, "PROJECT_ROOT", MCP_PROCESS_ROOT):
             with mock.patch("gitea_mcp_server.get_profile", return_value=self._merger_profile()):
-                resolved = srv._verify_role_mutation_workspace("prgs")
+                with mock.patch(
+                    "gitea_mcp_server.issue_lock_worktree.read_worktree_git_state",
+                    return_value=clean_git_state,
+                ):
+                    with mock.patch(
+                        "gitea_mcp_server.root_checkout_guard.resolve_remote_master_sha",
+                        return_value="abc123",
+                    ):
+                        resolved = srv._verify_role_mutation_workspace("prgs")
         self.assertEqual(resolved, os.path.realpath(MCP_PROCESS_ROOT))