feat(mcp): per-file staleness banner + tunable watcher debounce (#403) (#428)

Two coupled changes addressing the issue's underlying ask — "how does the
agent know when the index lags" — without resorting to a static wait.

Per-file staleness banner
-------------------------
FileWatcher now tracks per-path `pendingFiles` (path, firstSeenMs,
lastSeenMs, indexing) — events since the last successful sync, cleared
only after a sync whose `syncStartedMs >= lastSeenMs` commits. Chokidar
initial-scan events are gated behind a `ready` flag (with `waitUntilReady()`
exposed so tests can deterministically wait through it) so a fresh startup
doesn't falsely flag every existing file as pending.

ToolHandler now wraps every code-returning response (search, context,
callers, callees, impact, trace, explore, node, files) with
`withStalenessNotice`: intersects "files referenced in the response" with
`getPendingFiles()` and emits a hybrid signal —

  * banner at the top for files referenced AND pending (with edit age +
    indexing/pending-sync state, telling the agent to Read those specific
    files directly; the rest of the response stays fresh and codegraph
    stays authoritative for it),
  * compact footer for pending files elsewhere in the project not
    referenced above (capped at 5).

Cost is one boolean check + N substring matches when pending; zero
allocation when idle. `codegraph_status` surfaces the same data as a
first-class `### Pending sync:` section so the agent can ask "is the index
caught up?" in one call.

Cross-project quirk: when an agent passes `projectPath` matching the
default session's project, the staleness wrapper switches from the cached
cross-project CodeGraph (no watcher) to the default one (with watcher) so
the signal still fires. Same fix applied to `handleStatus`.

CODEGRAPH_WATCH_DEBOUNCE_MS
---------------------------
MCP `serve --mcp` now reads `CODEGRAPH_WATCH_DEBOUNCE_MS` and forwards it
to `cg.watch({ debounceMs })`. Clamped to [100ms, 60s]; out-of-range or
non-numeric values fall back to the FileWatcher default (2000ms). Active
value is logged to stderr on watcher startup so it's discoverable. The
docs in `server-instructions.ts`, `installer/instructions-template.ts`,
and `.cursor/rules/codegraph.mdc` no longer claim "~500ms"; they now
describe the banner mechanism instead — since per-file staleness replaces
the "wait N ms" guidance entirely, the docs become accurate at any
debounce value.

Validation
----------
* 847 unit/integration tests pass (added 15 new ones — pending-file
  tracking, banner/footer routing, status section, env-var parsing).
* Direct MCP probe through a real `codegraph serve --mcp` process: edit a
  file, query within the debounce window, banner fires naming the
  edited file with edit-age.
* Real Claude TUI session via `scripts/agent-eval/itrun.sh` with
  `CODEGRAPH_WATCH_DEBOUNCE_MS=10000`: agent edits `math.ts`, calls
  `codegraph_explore`, reads the banner, **and discloses it unprompted in
  its final reply**: "note: symbol index is mid-sync for the new `divide`,
  but the source it returned is verbatim from disk."

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/mcp/server-instructions.ts

@@ -59,7 +59,7 @@ of calls; a grep/read exploration is dozens.
 - **Don't grep first** when looking up a symbol by name — \`codegraph_search\` is faster and returns kind + location + signature.
 - **Don't chain \`codegraph_search\` + \`codegraph_node\`** when you just want context — \`codegraph_context\` is one round-trip.
 - **Don't loop \`codegraph_node\` over many symbols** — one \`codegraph_explore\` call returns them all grouped by file, while each separate call re-reads the whole context and costs far more. Use \`codegraph_node\` for a single symbol.
-- **Don't query the index immediately after editing a file** — the watcher needs ~500ms to debounce + sync. Wait for the next turn.
+- **After editing, check the staleness banner.** When a tool response starts with "⚠️ Some files referenced below were edited since the last index sync…", the listed files are pending re-index — Read those specific files for accurate content. Every file NOT in that banner is fresh, so still trust codegraph. \`codegraph_status\` also lists pending files under "Pending sync".
 
 ## Limitations