feat(8.0): API simplification — remove neural()/Db.search, one storage path key, integration→0

8.0 RC cleanup toward "one place per thing, zero-config, no deprecation":

- Remove the `brain.neural()` clustering namespace (ImprovedNeuralAPI + the dead
  legacy NeuralAPI + the neural CLI + neural-only types). Similarity is `find({vector})`
  / `similar({to})`; attribute grouping is the aggregation `GROUP BY` engine. The separate
  entity-extraction / smart-import feature (NeuralImport, NeuralEntityExtractor, SmartExtractor,
  NaturalLanguageProcessor, `brain.extract()`/`brain.nlp()`) is kept.
- Remove `Db.search()`; `find()` is the one query verb (accepts a bare string or FindParams).
  Fix the bundled MCP client, which called a non-existent `brain.search(query, limit)` →
  now `find({ query, limit })`.
- Storage config: collapse to one canonical top-level `path` key. The pre-8.0 aliases
  (`rootDirectory`, `options.*`, `fileSystemStorage.*`) are removed and now THROW with the
  exact rename instead of silently defaulting to `./brainy-data` on upgrade. A single resolver
  feeds createStorage, the 7.x→8.0 migration probe, and the plugin-factory handoff, so a native
  storage provider resolves the identical root (no split-brain).
- Fix `similar({ threshold })`: the min-similarity filter was silently dropped; it is now
  applied as a post-filter on `result.score` (the documented way to bound semantic results).
- Fix `vfs.rename()` on a directory: child path updates spread the entity vector into `update()`
  and failed dimension validation; they are metadata-only updates now.
- Fix `vfs.move()`: copy+delete orphaned the content-addressed content blob (the destination
  shared the source hash, then unlink removed it). `move()` now delegates to `rename()` — an
  in-place path change that preserves the blob and the entity id, for files and directories.
- Fix streaming import: the bulk fast path never flushed mid-import nor signalled queryability.
  Entity writes are now chunked by a progressive flush interval (100 → 1000 → 5000); each chunk
  flushes and emits `progress.queryable`, so imported data is queryable during the import.
- Sweep all docs, comments, and JSDoc for the removed/changed APIs.

Integration suite: 49 files / 588 passed / 0 failed. Unit: 80 files / 1456 passed, no type errors.

src/vfs/VirtualFileSystem.ts

@@ -1482,18 +1482,17 @@ export class VirtualFileSystem implements IVirtualFileSystem {
       const relativePath = oldChildPath.substring(oldParentPath.length)
       const newChildPath = newParentPath + relativePath
 
-      // Update child entity
-      const updatedChild = {
-        ...child,
+      // Update child entity — metadata-only (mirrors rename() above). Spreading
+      // the whole child forwards its `vector` field into update(), which fails
+      // dimension validation when the child was fetched without vectors (and
+      // would needlessly touch the vector index when it wasn't).
+      await this.brain.update({
+        id: child.id,
         metadata: {
           ...child.metadata,
           path: newChildPath,
           modified: Date.now()
         }
-      }
-      await this.brain.update({
-        ...updatedChild,
-        id: child.id
       })
 
       // Update path cache
@@ -1923,18 +1922,14 @@ export class VirtualFileSystem implements IVirtualFileSystem {
   async move(src: string, dest: string): Promise<void> {
     await this.ensureInitialized()
 
-    // Move is just copy + delete
-    await this.copy(src, dest, { overwrite: false })
-
-    // Delete source after successful copy
-    const srcEntityId = await this.pathResolver.resolve(src)
-    const srcEntity = await this.brain.get(srcEntityId)
-
-    if (srcEntity!.metadata.vfsType === 'file') {
-      await this.unlink(src)
-    } else {
-      await this.rmdir(src, { recursive: true })
-    }
+    // A move is a RENAME (in-place path change), NOT copy + delete. The old
+    // copy+delete path was broken on the content-addressed blob store: copy()
+    // makes the destination reference the SAME content-hash as the source, then
+    // unlink(src) deletes that shared blob — orphaning the destination
+    // ("Blob metadata not found" on the next read). rename() updates the path
+    // in place (preserving the blob, keeping the same entity id) and already
+    // handles both files and directories, including child path updates.
+    await this.rename(src, dest)
   }
 
   async symlink(target: string, path: string): Promise<void> {