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.js

@@ -12,7 +12,8 @@ const normalizePolicy = (value) => {
   for (const [sessionId, enabled] of entries) {
     if (sessionId && typeof enabled === 'boolean') sessions[sessionId] = enabled;
   }
-  return { sessions };
+  const revision = Number.isSafeInteger(source.revision) && source.revision >= 0 ? source.revision : 0;
+  return { sessions, revision };
 };
 
 const wait = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
@@ -38,6 +39,7 @@ export function createPermissionAutoAcceptRuntime({
 
   const snapshot = () => ({
     sessions: { ...policy.sessions },
+    revision: policy.revision,
   });
 
   const load = async () => {
@@ -76,6 +78,7 @@ export function createPermissionAutoAcceptRuntime({
     const result = await persistUpdate((current) => ({
       ...current,
       sessions: { ...current.sessions, [sessionId.trim()]: enabled },
+      revision: current.revision + 1,
     }));
     if (enabled) await reconcilePending({ directories: [directory] });
     return result;