fix(flush): clear() and repairIndex() set the dirty witness themselves

Both mutate durable state outside the two commit paths, so neither was seen by
the flush witness added with the idle-flush law. A clear() followed by a
flush() would have found the brain "clean" and skipped the entity-tree stamp,
leaving a stamp describing the population the clear had just removed — a false
divergence warning at the next open. Closing the gap where it is, rather than
widening the witness to guess.

src/brainy.ts

@@ -8523,6 +8523,11 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    */
   async clear(): Promise<void> {
     await this.ensureInitialized()
+    // A clear mutates durable state without going through a commit path, so
+    // it must set the dirty witness itself — otherwise a `clear()` followed by
+    // `flush()` would find the brain "clean" and skip the entity-tree stamp,
+    // leaving a stamp that describes the population this call just removed.
+    this._dirtySinceLastFlush = true
 
     // Clear storage
     await this.storage.clear()
@@ -18394,6 +18399,10 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    */
   async repairIndex(options?: { rebuild?: Array<'metadata' | 'graph' | 'vector'> | 'all' }): Promise<RepairReport> {
     await this.ensureInitialized()
+    // A repair recounts, prunes and rebuilds outside the commit paths; the
+    // dirty witness is set so a caller's flush after a repair does its normal
+    // work rather than finding the brain "clean".
+    this._dirtySinceLastFlush = true
     const startedAt = Date.now()
     const families: RepairFamilyReport[] = []