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/cli/index.ts

@@ -8,7 +8,6 @@
 
 import { Command } from 'commander'
 import chalk from 'chalk'
-import { neuralCommands } from './commands/neural.js'
 import { coreCommands } from './commands/core.js'
 import { utilityCommands } from './commands/utility.js'
 import { vfsCommands } from './commands/vfs.js'
@@ -194,65 +193,6 @@ program
   .option('--json', 'Output as JSON')
   .action(validateCommand)
 
-// ===== Neural Commands =====
-
-program
-  .command('similar [a] [b]')
-  .alias('sim')
-  .description('Calculate similarity between two items (interactive if parameters missing)')
-  .option('--explain', 'Show detailed explanation')
-  .option('--breakdown', 'Show similarity breakdown')
-  .action(neuralCommands.similar)
-
-program
-  .command('cluster')
-  .alias('clusters')
-  .description('Find semantic clusters in the data (interactive mode available)')
-  .option('--algorithm <type>', 'Clustering algorithm (hierarchical|kmeans|dbscan)', 'hierarchical')
-  .option('--threshold <number>', 'Similarity threshold', '0.7')
-  .option('--min-size <number>', 'Minimum cluster size', '2')
-  .option('--max-clusters <number>', 'Maximum number of clusters')
-  .option('--near <query>', 'Find clusters near a query')
-  .option('--show', 'Show visual representation')
-  .action(neuralCommands.cluster)
-
-program
-  .command('related [id]')
-  .alias('neighbors')
-  .description('Find semantically related items (interactive if no ID)')
-  .option('-l, --limit <number>', 'Number of results', '10')
-  .option('-r, --radius <number>', 'Semantic radius', '0.3')
-  .option('--with-scores', 'Include similarity scores')
-  .option('--with-edges', 'Include connections')
-  .action(neuralCommands.related)
-
-program
-  .command('hierarchy [id]')
-  .alias('tree')
-  .description('Show semantic hierarchy for an item (interactive if no ID)')
-  .option('-d, --depth <number>', 'Hierarchy depth', '3')
-  .option('--parents-only', 'Show only parent hierarchy')
-  .option('--children-only', 'Show only child hierarchy')
-  .action(neuralCommands.hierarchy)
-
-program
-  .command('outliers')
-  .alias('anomalies')
-  .description('Detect semantic outliers')
-  .option('-t, --threshold <number>', 'Outlier threshold', '0.3')
-  .option('--explain', 'Explain why items are outliers')
-  .action(neuralCommands.outliers)
-
-program
-  .command('visualize')
-  .alias('viz')
-  .description('Generate visualization data')
-  .option('-f, --format <format>', 'Output format (json|d3|graphml)', 'json')
-  .option('--max-nodes <number>', 'Maximum nodes', '500')
-  .option('--dimensions <number>', '2D or 3D', '2')
-  .option('-o, --output <file>', 'Output file')
-  .action(neuralCommands.visualize)
-
 // ===== VFS Commands (Subcommand Group) =====
 
 program