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@@ -24,7 +24,69 @@ codegraph sync # incremental — only changed files
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## Stay fresh automatically
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-When the MCP server is running, CodeGraph watches your project with native OS file events and syncs in the background — debounced, and filtered to source files only. You don't need to run `sync` by hand during an agent session.
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+**You don't need to run `codegraph sync` by hand during an agent session.** When your agent (Claude Code, Cursor, Codex, opencode) launches `codegraph serve --mcp`, three layers cooperate to keep the index in step with your code — and to never give the agent a quiet wrong answer in the small window between an edit and the next sync.
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+
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+### 1. File watcher with debounced auto-sync (always on)
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+
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+`serve --mcp` spins up a native file watcher (FSEvents on macOS, inotify on Linux, ReadDirectoryChangesW on Windows) over the project root. Every source-file create / modify / delete is captured. A debounce timer collapses bursts of edits into a single sync.
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+
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+```
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+agent writes src/Widget.ts
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+ → watcher fires (event delivery: typically <100ms)
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+ → 2000ms debounce
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+ → sync runs; Widget.ts's nodes + edges are in the index
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+ → next agent query sees it
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+```
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+
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+**Tunable**: `CODEGRAPH_WATCH_DEBOUNCE_MS` overrides the default 2000ms, clamped to `[100ms, 60s]`. Useful when a build step or formatter writes many files in a tight burst — bump it to `5000` or `10000` so the watcher coalesces them into one sync.
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+
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+### 2. Per-file staleness banner — covers the debounce window
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+
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+The watcher debounce introduces a small window (typically 2s) where a freshly-edited file is on disk but not yet in the index. CodeGraph closes that window with a per-file staleness banner: if any MCP tool response would reference a file that's currently pending re-index, the response prepends a `⚠️` banner naming the stale file:
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+
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+```
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+⚠️ Some files referenced below were edited since the last index sync —
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+their codegraph entries may be stale:
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+ - src/Widget.ts (edited 800ms ago, pending sync)
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+For accurate content of those specific files, Read them directly.
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+The rest of this response is fresh.
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+
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+## Code Context
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+…
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+```
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+
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+Agents read this and follow up with a direct `Read` on the named file — validated end-to-end with Claude Code, where the agent literally says "Reading the file directly for the live content" before opening it. So even during the 2-second debounce window, the agent never gets a silent wrong answer.
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+
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+Pending files **not** referenced by the response surface as a small footer instead (`(Note: N file(s) elsewhere in this project are pending index sync but were not referenced above: …)`). Either way, the signal is explicit.
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+
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+### 3. Connect-time catch-up — covers gaps when the MCP server wasn't running
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+
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+When your editor / agent (re)connects to the MCP server, codegraph runs a fast filesystem-based reconciliation (a `(size, mtime)` stat pre-filter, then a content hash on the rest) before answering the first query. So files changed while no MCP server was running — a `git pull` from the terminal, an edit from another editor, an agent that finished and exited — are caught up automatically on the next session's first tool call.
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+
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+### Verify what the watcher sees
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+
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+`codegraph_status` exposes the pending set first-class — useful for an agent asking "is the index caught up?" in one call:
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+
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+```
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+codegraph_status →
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+ ## CodeGraph Status
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+ …
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+ ### Pending sync:
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+ - src/Widget.ts (edited 1200ms ago)
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+```
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+
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+If `### Pending sync:` isn't in the response, nothing is in flight.
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+
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+### When manual `codegraph sync` makes sense
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+
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+Almost never. The edge cases:
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+
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+- **The watcher is disabled.** Sandboxes that block local fs watchers, or you've set `CODEGRAPH_NO_DAEMON=1` to opt out of the shared daemon. In those cases `codegraph sync` is the manual fallback.
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+- **Pre-flight before a CI run.** If you're scripting against the index outside an agent session, a single `codegraph sync` at the start of the script guarantees the index reflects the current working tree.
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+
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+Otherwise: just use it. The watcher + banner + connect-sync covers the AI-assisted workflow end-to-end. If you're seeing files genuinely missed after the debounce window has passed, that's a bug — please file an issue with a reproduction.
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+
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+> See the v0.9.5 release notes for the [staleness banner (#403)](https://github.com/colbymchenry/codegraph/releases/tag/v0.9.5) and the connect-time catch-up (#414); both shipped together.
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## Check status
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@@ -32,7 +94,7 @@ When the MCP server is running, CodeGraph watches your project with native OS fi
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codegraph status
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```
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-Reports node/edge/file counts, the active SQLite backend, and the journal mode.
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+Reports node/edge/file counts, the active SQLite backend, and the journal mode. In an agent session, the MCP-side `codegraph_status` additionally surfaces the `### Pending sync:` block described above.
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## What gets indexed
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