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Colby McHenry
f48b3129f9
`MCPEngine.catchUpSync()` reconciles the index against the working tree after open (catching `git pull`/`checkout`/`rebase` and any edits or deletes made while no server was running). It was fire-and-forget — so a tool call landing in the first ~50-300ms could race past it and serve rows for files that no longer exist on disk. The per-file staleness banner can't help here, because that signal is populated by the file watcher (not by catch-up). The fix: `catchUpSync()` now pushes its promise into `ToolHandler` via `setCatchUpGate(p)`; the first `execute()` call awaits the gate and then clears it. Subsequent calls pay nothing. Catch-up rejections are logged by the engine and swallowed by the handler so a transient sync failure never breaks tools. Most visible on the "deleted everything between sessions" case, where MCP previously returned stale rows pointing at non-existent files. Validated end-to-end on a 10,640-file VS Code index: with the gate, a codegraph_search for "ExtensionHost" against an empty (but stale-DB) directory returns "No results found" after the catch-up drains the DB; without the gate, the same call returns 10 stale hits. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>