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

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))
-        pass
+            raise RuntimeError(str(exc)) from exc
+        # 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: