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/web/server/lib/permission-auto-accept/runtime.test.js

@@ -38,9 +38,18 @@ describe('permission auto-accept runtime', () => {
     const second = createRuntime({ stored: first.getSettings() });
     await expect(second.runtime.load()).resolves.toEqual({
       sessions: { root: true },
+      revision: 1,
     });
   });
 
+  it('increments the authoritative policy revision', async () => {
+    const { runtime, getSettings } = createRuntime();
+
+    await expect(runtime.setSessionPolicy('root', true)).resolves.toMatchObject({ revision: 1 });
+    await expect(runtime.setSessionPolicy('child', false)).resolves.toMatchObject({ revision: 2 });
+    expect(getSettings().permissionAutoAccept.revision).toBe(2);
+  });
+
   it('uses nearest explicit ancestor policy for subagents', async () => {
     const { runtime, emit } = createRuntime({
       stored: { permissionAutoAccept: { sessions: { root: true, child: false } } },
@@ -132,6 +141,6 @@ describe('permission auto-accept runtime', () => {
       .map(([url]) => new URL(url).pathname);
     expect(replyPaths).toEqual(['/permission/root-pending/reply']);
     expect(fetchImpl.mock.calls.some(([url]) => new URL(url).searchParams.get('directory') === '/project')).toBe(true);
-    expect(await runtime.load()).toEqual({ sessions: { root: true } });
+    expect(await runtime.load()).toEqual({ sessions: { root: true }, revision: 1 });
   });
 });