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/db/queries.ts

@@ -3253,6 +3253,18 @@ export class QueryBuilder {
     return rows.map(rowToFileRecord);
   }
 
+  /**
+   * Files stored with no nodes or with recorded extraction errors — the only
+   * rows that can be missing their symbols (`CodeGraph.getIndexHealth`). A
+   * healthy index returns few or none, so this stays cheap on a large one.
+   */
+  getFilesWithoutNodesOrWithErrors(): FileRecord[] {
+    const rows = this.db
+      .prepare('SELECT * FROM files WHERE node_count = 0 OR errors IS NOT NULL ORDER BY path')
+      .all() as FileRow[];
+    return rows.map(rowToFileRecord);
+  }
+
   /**
    * Most recent index timestamp (ms since epoch) across all tracked files, or
    * null when nothing is indexed yet. One indexed aggregate, no per-row scan. (#329)