fix(mcp,extraction): exit a daemon whose install changed; never store a grammar-load failure (#2335, #2336) (#2346)

* fix(mcp,extraction): a daemon whose install changed exits; grammar-load failures are never stored (#2335, #2336)

A daemon that outlived an upgrade loaded grammars lazily from an install
that no longer existed, and stored every file its watcher re-indexed as a
zero-node row under the file's new content hash: no hash-based sync ever
revisited those rows, and `codegraph status` called the index up to date.

- The daemon checks its own package.json every 30 s
  (CODEGRAPH_DAEMON_INSTALL_CHECK_MS, 0 turns it off) and exits once the
  file is gone or carries another version, so the next session starts a
  daemon from the current install.
- A result whose grammar failed to load (`parser_error`) is never stored:
  the file keeps its previous data and the next sync or index retries it,
  and a row an older engine stored that way is re-indexed even though its
  hash matches. The tag-based CFML path reports a missing grammar with the
  same code.
- A launcher whose own install was deleted no longer crashes on the spawn
  error of the daemon it tried to start.
- `codegraph status` and `status --json` (filesNeedingReindex,
  filesWithParseErrors) report indexed files whose symbols are missing
  although their content is current (#2336), and `files --json` carries
  each file's recorded errors.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix(mcp): a session whose own install changed never claims the writer lock (#2335)

A daemon now exits once its install is upgraded or removed, and nobody
holds the writer slot for a successor at that point. Its sessions run the
same replaced code and serve themselves in-process the moment it goes; one
that found the slot free claimed it as its writer even though its engine
could not load (a real npm upgrade: "Cannot find module
'./sqlite-adapter'"), and so kept a daemon from the current install from
starting. Such a session now falls back read-only and says to restart it.

Also adds the CHANGELOG entries for the install check and grammar-load
failures (#2335) and for the status report (#2336).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

src/index.ts

@@ -25,6 +25,7 @@ import {
   BuildContextOptions,
   FindRelevantContextOptions,
   UnresolvedReference,
+  IndexHealth,
 } from './types';
 import { DatabaseConnection, getDatabasePath, removeDatabaseFiles } from './db';
 import { WalCheckpointValve, resolveWalValveMb } from './db/wal-valve';
@@ -43,6 +44,7 @@ import {
   extractFromSource,
   initGrammars,
 } from './extraction';
+import { hasGrammarLoadFailure, isFileLevelOnlyLanguage } from './extraction/grammars';
 import {
   ReferenceResolver,
   createResolver,
@@ -2065,6 +2067,34 @@ export class CodeGraph {
     return this.queries.countGeneratedFiles();
   }
 
+  /**
+   * Indexed files whose symbols are missing although their content is current
+   * — rows a content-hash comparison calls up to date (#2336). Reported by
+   * `status`; `sync` repairs the `needsReindex` group.
+   */
+  getIndexHealth(): IndexHealth {
+    const needsReindex: string[] = [];
+    const parseErrors: string[] = [];
+    for (const file of this.queries.getFilesWithoutNodesOrWithErrors()) {
+      const errors = file.errors ?? [];
+      if (hasGrammarLoadFailure(errors)) {
+        // Stored without being parsed — its grammar could not load (#2335).
+        needsReindex.push(file.path);
+      } else if (file.nodeCount === 0) {
+        // Every parse stores at least the file node, so zero nodes means a
+        // wiped row (#1541) or a recorded failure — except file-level-only
+        // languages and files over the size limit, which are empty on purpose.
+        if (isFileLevelOnlyLanguage(file.language)) continue;
+        if (errors.length === 0) needsReindex.push(file.path);
+        else if (errors.some((e) => e.severity === 'error' || e.code === 'parse_error')) parseErrors.push(file.path);
+      } else if (errors.some((e) => e.code === 'parse_error')) {
+        // Parsed, but the tree had errors and no symbols survived.
+        parseErrors.push(file.path);
+      }
+    }
+    return { needsReindex, parseErrors };
+  }
+
   // ===========================================================================
   // Graph Query Methods
   // ===========================================================================