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.

tests/integration/all-apis-comprehensive.test.ts

@@ -35,7 +35,7 @@ describe('Comprehensive All-APIs Test', () => {
     brain = new Brainy({ requireSubtype: false,
       storage: {
         type: 'filesystem',
-        options: { path: testDir }
+        path: testDir
       }
     })
     await brain.init()
@@ -309,44 +309,6 @@ describe('Comprehensive All-APIs Test', () => {
     })
   })
 
-  describe('Neural APIs', () => {
-    it('neural.similar() - should calculate similarity', async () => {
-      const neural = brain.neural()
-
-      const similarity = await neural.similar('test text 1', 'test text 2')
-
-      expect(typeof similarity).toBe('number')
-      expect(similarity).toBeGreaterThan(0)
-      expect(similarity).toBeLessThanOrEqual(1)
-      console.log(`✅ neural.similar() computed similarity: ${similarity.toFixed(4)}`)
-    })
-
-    it('neural.neighbors() - should find neighbors', async () => {
-      const neural = brain.neural()
-
-      // Create test entity
-      const entityId = await brain.add({
-        data: 'Neighbor test',
-        type: NounType.Document
-      })
-
-      const neighbors = await neural.neighbors(entityId)
-
-      expect(neighbors).toBeDefined()
-      expect(Array.isArray(neighbors.neighbors)).toBe(true)
-      console.log(`✅ neural.neighbors() found ${neighbors.neighbors.length} neighbors`)
-    })
-
-    it('neural.outliers() - should detect outliers', async () => {
-      const neural = brain.neural()
-
-      const outliers = await neural.outliers({ limit: 10 })
-
-      expect(Array.isArray(outliers)).toBe(true)
-      console.log(`✅ neural.outliers() detected ${outliers.length} outliers`)
-    })
-  })
-
   describe('Production Quality Checks', () => {
     it('should handle large batch operations', async () => {
       const start = Date.now()