perf: overhaul session loading, caching, and runtime isolation (#2360)

Improve OpenChamber responsiveness under large session workloads while fixing
cache, synchronization, and persistence correctness across runtimes, projects,
directories, and worktrees.

- prioritize selected and visible sessions during bootstrap and defer
  non-critical enrichment work
- reduce redundant message loading, event processing, store publication, and
  hidden sidebar work
- prevent stale session and message requests from overwriting newer
  authoritative state
- preserve existing data when authoritative fetches fail instead of treating
  failures as successful empty responses
- scope session materialization, messages, drafts, queues, todos, pins,
  permissions, folders, tabs, Git state, and pull request data by runtime and
  directory identity
- harden runtime switching, reconnect, cleanup, mutation reconciliation, and
  persisted-state ordering
- preserve live subagent Task linkage when metadata arrives after an older
  message request or while streaming parts are suspended
- coalesce overlapping tail refreshes without losing newer refresh demand
- improve cold-session loading by moving deferrable work out of the critical
  bootstrap path
- isolate URL authentication, mobile credentials, native secrets, and other
  runtime-owned state across endpoint changes
- bound long-lived caches and remove avoidable allocations from event and
  rendering hot paths
- limit virtualization to archive collections where it improves rendering
  without disrupting active sidebar layout
- stabilize session folders, pin ordering, expanded state, and persisted
  sidebar behavior
- open skill files through the same secure editor and outside-workspace grant
  flow used by file navigation, including worktree sessions
- expand regression coverage for stale completions, runtime collisions,
  reconnect behavior, persistence races, authoritative empty results, and
  subagent refresh ordering
- document the updated synchronization, cache ownership, performance, and
  runtime-isolation invariants

packages/electron/main.mjs

@@ -490,12 +490,16 @@ const readJsonFile = (filePath) => {
 };
 
 const writeJsonFile = async (filePath, data) => {
-  await fsp.mkdir(path.dirname(filePath), { recursive: true });
+  const directory = path.dirname(filePath);
+  await fsp.mkdir(directory, { recursive: true, mode: 0o700 });
+  if (process.platform !== 'win32') await fsp.chmod(directory, 0o700);
   // Atomic: write to a temp file then rename. Readers never see a partial
   // JSON file that could parse-error and get coerced to {}.
   const tmp = `${filePath}.tmp-${process.pid}-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
-  await fsp.writeFile(tmp, JSON.stringify(data, null, 2));
+  await fsp.writeFile(tmp, JSON.stringify(data, null, 2), { encoding: 'utf8', mode: 0o600 });
+  if (process.platform !== 'win32') await fsp.chmod(tmp, 0o600);
   await fsp.rename(tmp, filePath);
+  if (process.platform !== 'win32') await fsp.chmod(filePath, 0o600);
 };
 
 const readSettingsRoot = () => {