fix(sync): invalidate bootstrap context when a newer same-directory run starts

## Problem
Review on #3151: with isCurrent reduced to store liveness, a completed
run's context stays current while a forced same-directory rerun starts,
so a late deferred response could commit over the newer run's state.

## Fix
Track a per-directory run sequence. isCurrent captures the sequence at
run start and stays true across settle (deferred recovery pulls still
commit — the original bug) but flips false the moment a newer run for
the same directory begins. Entries are cleared on directory disposal.

## Validation
- New test: after a forced rerun the first context is retired and the
  second is current. 20 pass in child-store.test.ts.
- bun test src/sync/: 540 pass / 15 fail — same 15 pre-existing on main.
- type-check and oxlint clean on authored lines.

packages/ui/src/sync/child-store.test.ts

@@ -584,4 +584,29 @@ describe('ChildStoreManager bootstrap context liveness', () => {
     expect(captured?.isCurrent()).toBe(false);
     manager.disposeAll();
   });
+
+  test('a newer same-directory run invalidates the previous context', async () => {
+    const manager = new ChildStoreManager();
+    const contexts: DirectoryBootstrapContext[] = [];
+    const cleanup = manager.configure({
+      onBootstrap: (context) => {
+        contexts.push(context);
+      },
+    });
+    manager.requestBootstrap({ directory: '/workspace', priority: 'selected', reason: 'current-directory' });
+    await settle();
+    expect(contexts[0]?.isCurrent()).toBe(true);
+
+    // A forced rerun for the same directory must retire the previous
+    // context: its in-flight deferred responses may no longer commit over
+    // whatever the newer run synchronizes.
+    manager.requestBootstrap({ directory: '/workspace', priority: 'selected', reason: 'server-connected', force: true });
+    await settle();
+    expect(contexts).toHaveLength(2);
+    expect(contexts[0]?.isCurrent()).toBe(false);
+    expect(contexts[1]?.isCurrent()).toBe(true);
+
+    cleanup();
+    manager.disposeAll();
+  });
 });

packages/ui/src/sync/child-store.ts

@@ -307,6 +307,8 @@ export class ChildStoreManager {
   private bootstrapConcurrency = 2
   private bootstrapGeneration = 0
   private bootstrapSequence = 0
+  private bootstrapRunSequence = 0
+  private readonly directoryBootstrapRuns = new Map<string, number>()
   private manualBootstrapDemandRevision = 0
   private disposed = false
 
@@ -600,14 +602,18 @@ export class ChildStoreManager {
       // token in `.finally()` as soon as onBootstrap settles, while
       // bootstrapDirectory schedules deferred recovery pulls (permission.list
       // and friends) from a `setTimeout(0)` that always runs after that
-      // cleanup — gating those on the token made them dead code. The pump
-      // never replaces a running entry for the same directory (queueBootstrap
-      // defers via rerunRequested), so during the run itself this is
-      // equivalent. Mirrors the isCurrent contract in session-message-loader.
+      // cleanup — gating those on the token made them dead code. A per-
+      // directory run sequence keeps the context current across settle (so
+      // deferred pulls commit) while invalidating it as soon as a newer run
+      // starts, so a late deferred response cannot overwrite a newer run's
+      // state. Mirrors the isCurrent contract in session-message-loader.
+      const runSequence = ++this.bootstrapRunSequence
+      this.directoryBootstrapRuns.set(next.directory, runSequence)
       const store = this.children.get(next.directory)
       const isCurrent = () => (
         !this.disposed
         && this.bootstrapGeneration === running.generation
+        && this.directoryBootstrapRuns.get(next.directory) === runSequence
         && this.children.get(next.directory) === store
       )
       let bootstrapPromise: Promise<void>
@@ -681,6 +687,7 @@ export class ChildStoreManager {
     this.manualBootstrapDemands.delete(directory)
     this.bootstrapStates.delete(directory)
     this.bootstrapFailures.delete(directory)
+    this.directoryBootstrapRuns.delete(directory)
     for (const demands of this.bootstrapDemandsByOwner.values()) demands.delete(directory)
     this.children.delete(directory)
     this.notifyRegistrySubscribers()