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/comprehensive/public-api-complete.test.ts

@@ -524,102 +524,6 @@ describe('Brainy Public API - Complete Coverage', () => {
     })
   })
 
-  describe('Neural API', () => {
-    let entityIds: string[]
-
-    beforeEach(async () => {
-      brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
-      await brain.init()
-
-      const result = await brain.addMany({
-        items: [
-          { data: 'Cat', type: NounType.Concept, metadata: { category: 'animal' } },
-          { data: 'Dog', type: NounType.Concept, metadata: { category: 'animal' } },
-          { data: 'Tiger', type: NounType.Concept, metadata: { category: 'animal' } },
-          { data: 'Car', type: NounType.Thing, metadata: { category: 'vehicle' } },
-          { data: 'Truck', type: NounType.Thing, metadata: { category: 'vehicle' } },
-          { data: 'Python', type: NounType.Language, metadata: { category: 'programming' } },
-          { data: 'JavaScript', type: NounType.Language, metadata: { category: 'programming' } }
-        ]
-      })
-      entityIds = result.successful
-    }, 120000)
-
-    afterEach(async () => {
-      await brain.close()
-    })
-
-    describe('brain.neural().clusters()', () => {
-      it('should cluster entities by similarity', async () => {
-        const clusters = await brain.neural().clusters({
-          k: 3,
-          maxIterations: 10
-        })
-
-        expect(clusters).toBeDefined()
-        expect(clusters.length).toBeGreaterThan(0)
-        expect(clusters.every(c => c.members.length > 0)).toBe(true)
-      })
-    })
-
-    describe('brain.neural().hierarchy()', () => {
-      it('should build semantic hierarchy for an entity', async () => {
-        // hierarchy() requires an entity ID
-        const hierarchy = await brain.neural().hierarchy(entityIds[0])
-
-        expect(hierarchy).toBeDefined()
-        // Hierarchy structure includes optional root, levels, children, etc.
-        expect(typeof hierarchy).toBe('object')
-      })
-    })
-
-    describe('brain.neural().outliers()', () => {
-      it('should detect anomalous entities', async () => {
-        await brain.add({
-          data: 'Quantum physics equations and string theory',
-          type: NounType.Document,
-          metadata: { category: 'science' }
-        })
-
-        const outliers = await brain.neural().outliers({
-          threshold: 0.8
-        })
-
-        expect(outliers).toBeDefined()
-        expect(Array.isArray(outliers)).toBe(true)
-      })
-    })
-
-    describe('brain.neural().visualize()', () => {
-      it('should generate visualization data', async () => {
-        const vizData = await brain.neural().visualize({
-          dimensions: 2,
-          algorithm: 'force'
-        })
-
-        expect(vizData).toBeDefined()
-        expect(vizData.nodes).toBeDefined()
-        expect(Array.isArray(vizData.nodes)).toBe(true)
-      })
-    })
-
-    describe('brain.neural().neighbors()', () => {
-      it('should find nearest neighbors', async () => {
-        if (entityIds.length > 0) {
-          const result = await brain.neural().neighbors(entityIds[0], {
-            limit: 3
-          })
-
-          // NeighborsResult has a neighbors array
-          expect(result).toBeDefined()
-          expect(result.neighbors).toBeDefined()
-          // Small datasets may not produce nearest neighbors
-          expect(result.neighbors.length).toBeGreaterThanOrEqual(0)
-        }
-      })
-    })
-  })
-
   describe('Statistics', () => {
     beforeEach(async () => {
       brain = new Brainy({ requireSubtype: false, storage: { type: 'memory' } })
@@ -659,7 +563,7 @@ describe('Brainy Public API - Complete Coverage', () => {
       const fsBrain = new Brainy({ requireSubtype: false,
         storage: {
           type: 'filesystem',
-          options: { path: fsTestDir }
+          path: fsTestDir
         }
       })
 
@@ -693,7 +597,7 @@ describe('Brainy Public API - Complete Coverage', () => {
       const fsBrain = new Brainy({ requireSubtype: false,
         storage: {
           type: 'filesystem',
-          options: { path: fsTestDir }
+          path: fsTestDir
         }
       })