perf(vfs): repairContainment's reconcile is one paged edge walk, not one graph call per file

Pass 2 issued one awaited related({ to }) per VFS entity — O(entities)
serialized graph calls, measured in whole minutes on large brains. Now a
single paged walk over every Contains edge (type-only, 1,000 per page)
feeds an in-memory group-by-target, and only actual defects mutate. The
verdicts are unchanged: a stale parent's edge is removed, a missing edge
is restored, duplicates cannot survive, and user knowledge edges are
never touched.

Pinned in tests/integration/vfs-containment-batched.test.ts: exact
removed/restored counts on a seeded defect tree, tree correctness after
the repair, user edges untouched, and the cost shape — related() call
count independent of the entity count.

src/vfs/VirtualFileSystem.ts

@@ -2295,6 +2295,31 @@ export class VirtualFileSystem implements IVirtualFileSystem {
       cursor = page.nextCursor
     }
 
+    // Pass 2: ONE paged walk over every Contains edge, grouped by target in
+    // memory. The earlier shape issued one awaited related({ to }) per VFS
+    // entity — O(entities) serialized graph calls, measured in whole minutes
+    // on large brains. This shape is O(edges / page) calls regardless of how
+    // many entities exist; mutations alone stay per-defect.
+    const incomingByTarget = new Map<string, Relation<any>[]>()
+    {
+      const pageSize = 1000
+      let pageOffset = 0
+      for (;;) {
+        const page = await this.brain.related({
+          type: VerbType.Contains,
+          limit: pageSize,
+          offset: pageOffset
+        })
+        for (const edge of page) {
+          const bucket = incomingByTarget.get(edge.to)
+          if (bucket) bucket.push(edge)
+          else incomingByTarget.set(edge.to, [edge])
+        }
+        if (page.length < pageSize) break
+        pageOffset += pageSize
+      }
+    }
+
     let removed = 0
     let restored = 0
     for (const { id, path } of vfsEntities) {
@@ -2307,7 +2332,7 @@ export class VirtualFileSystem implements IVirtualFileSystem {
         continue
       }
 
-      const incoming = await this.brain.related({ to: id, type: VerbType.Contains })
+      const incoming = incomingByTarget.get(id) ?? []
       let expectedSeen = false
       for (const edge of incoming) {
         const isVfsEdge = edge.subtype === 'vfs-contains' || (edge.metadata as any)?.isVFS === true