Reconcile cache with filesystem on get-projects so sessions stop going missing

[ymajoros]

Fixes #59.

Problem

Sessions and whole worktrees silently vanish from the sidebar while their transcripts are still on disk, and reopening/restarting doesn't bring them back.

get-projects only scans the filesystem on a cold start:

const needsPopulate = !isCachePopulated() || !isSearchIndexPopulated();
if (needsPopulate) { populateCacheViaWorker(); return []; }
return buildProjectsFromCache(showArchived);   // cache only, never reconciled

Once the cache is non-empty it's never reconciled again, so folders that changed while the app was closed — or that were never indexed by the current build (cache_meta.indexMtimeMs === 0) — never reappear. The live fs.watch only covers changes while the app is running.

Fix

Reconcile on get-projects before building from cache. The dead populateCacheFromFilesystem() (defined + exported, never called) is repurposed into reconcileCacheFromFilesystem(), now stat-gated: it re-indexes only folders that are new or whose newest .jsonl is newer than what was last indexed.

for (const folder of folders) {
  const meta = metaMap.get(folder);
  const folderPath = path.join(PROJECTS_DIR, folder);
  if (!meta || getFolderIndexMtimeMs(folderPath) > (meta.indexMtimeMs || 0)) {
    refreshFolder(folder);
  }
}

When nothing changed this is just a readdir + stat per folder — no transcript parsing, no DB writes — so the steady-state cost on get-projects is negligible; real work happens only for folders that actually need it. refreshFolder already does its own per-file mtime skip, so this composes cleanly.

Why here (vs. only at startup)

Reconciling on get-projects is self-healing for both the "changed while closed" and "old build never indexed it" cases, and naturally re-runs if folders drift later — without a separate watcher or timer. The mtime gate keeps it cheap. Happy to move it to a one-time startup pass instead if you'd prefer.

Testing

• node --test passes, including a new test/reconcile-cache.test.js that asserts the gate: a never-indexed folder and a stale folder (indexMtimeMs older than disk) get indexed, while an up-to-date folder is skipped.
• Verified live on Linux / 0.0.30: 27 worktree folders that were stuck empty (indexMtimeMs = 0) re-indexed and reappeared in the sidebar.

Notes

Pure cache/indexing change — no schema change, no change to session_meta (names/stars/archive) or settings.