refactor(8.0): remove dead, unreachable, and unwired modules

Pre-GA dead-code sweep. A deterministic import-reachability walk from the
package's real entry points (the exports map, the CLI bin, the conversation
surface) found 34 source modules that nothing reachable imports — they
compile and ship as dist output that no consumer or internal path can ever
reach. All were superseded duplicates, abandoned parallel implementations,
or built-but-never-wired features:

  - superseded duplicates of live modules: an older "unified" entry, a
    standalone neural-import variant, a static NLP processor + its matcher,
    a parallel API-types module, a duplicate progress-types module
  - an abandoned import path (orchestrator + entity deduplicator + barrels)
    left behind when ingestion moved to the coordinator
  - unwired feature modules (instance pool, import presets, cached
    embeddings, relationship-confidence scorer) reachable only from tests
  - dead leaf utilities (write buffer, deleted-items index, bounded
    registry, two crypto shims, a cache manager, a structured logger, a
    stale v5 type-migration helper, a browser-only FS type shim) and
    several dead re-export barrels
  - a CLI catalog command wired into no command

Also removed two tests that only exercised deleted modules, repointed two
VFS tests off a deleted barrel onto the implementation module, and deleted
one example that demoed removed features.

Verified: clean build (both tsc passes), unit 1505 + integration 607 green,
and a re-run of the reachability walk reports zero remaining orphans.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

src/transaction/index.ts

@@ -1,34 +0,0 @@
-/**
- * Transaction System
- *
- * Provides atomicity for Brainy operations.
- * All operations succeed or all rollback - no partial failures.
- *
- * @module transaction
- */
-
-export * from './types.js'
-export * from './errors.js'
-export { Transaction } from './Transaction.js'
-export { TransactionManager, type TransactionStats } from './TransactionManager.js'
-
-// Re-export for convenience
-export type {
-  Operation,
-  RollbackAction,
-  TransactionState,
-  TransactionContext,
-  TransactionFunction,
-  TransactionResult,
-  TransactionOptions
-} from './types.js'
-
-export {
-  TransactionError,
-  TransactionExecutionError,
-  TransactionRollbackError,
-  InvalidTransactionStateError,
-  TransactionTimeoutError
-} from './errors.js'
-
-export { RevisionConflictError } from './RevisionConflictError.js'