feat(8.0): brain.fillSubtypes migration helper + pre-RC1 gap closure

- brain.fillSubtypes(rules): idempotent subtype back-fill for pre-8.0 data.
  One rule per NounType/VerbType (literal default or per-entry function);
  fills only entries still missing a subtype through the public update()/
  updateRelation() paths; returns { scanned, filled, skipped, errors, byType }.
  Full unit suite in tests/unit/brainy/fill-subtypes.test.ts.
- Fix getNouns/getVerbs pagination hasMore (peek one past the window) —
  was permanently false, silently truncating every multi-page walk.
- find({ near }) without near.id now throws a teaching error instead of an
  opaque storage sharding failure; CLI --threshold without --near applies a
  plain score floor.
- CLI init/close audit: every one-shot command init()s, close()s, and exits
  explicitly; delete the unmaintained interactive REPL; replace the cloud-era
  storage subcommands with status/batch-delete; new types/validate commands.
- requireSubtype JSDoc now documents the 8.0 default-on contract; audit()
  recommendation points at fillSubtypes.
- Docs: data-storage-architecture rewritten to the real 8.0 on-disk layout;
  README storage section reflects filesystem+memory and snapshots; eli5 and
  SEMANTIC_VFS /as-of/ semantics corrected; internal tracker IDs and
  .strategy references scrubbed from published files.

docs/vfs/SEMANTIC_VFS.md

@@ -47,16 +47,18 @@ const authFiles = await vfs.readdir('/by-concept/authentication')
 const aliceFiles = await vfs.readdir('/by-author/alice')
 ```
 
-### 2. **Time Travel**
-See your codebase as it existed at any point:
+### 2. **Change Tracking by Date**
+List the files that were modified on any given day:
 ```typescript
-// Code from March 15th
-const snapshot = await vfs.readdir('/as-of/2024-03-15')
+// Files that changed on March 15th
+const changed = await vfs.readdir('/as-of/2024-03-15')
 
-// Compare with today
+// Everything under /src right now
 const current = await vfs.readdir('/src')
 ```
 
+`/as-of/<date>` selects by *modification date* — it reads the files' current content, not historical versions. For true point-in-time queries over entity state, use the Db API (`brain.asOf(generation)`).
+
 ### 3. **Knowledge Graph Navigation**
 Navigate by semantic relationships:
 ```typescript
@@ -118,13 +120,14 @@ await vfs.stat('/by-author/alice/config.ts')
 ### 4. By Time (Temporal) ✅ **Production**
 ```typescript
 await vfs.readdir('/as-of/2024-03-15')
-// Files modified on March 15, 2024
+// Files modified on March 15, 2024 (24-hour window)
 
-await vfs.readFile('/as-of/2024-03-15/src/auth.ts')
-// Read auth.ts as it existed that day
+await vfs.readFile('/as-of/2024-03-15/auth.ts')
+// Current content of auth.ts, addressed by modification date —
+// the path only resolves if auth.ts was modified that day
 ```
 
-**How it works:** Tracks `modified` timestamp. Uses B-tree range queries (`greaterEqual`/`lessEqual`) for O(log n) performance.
+**How it works:** Tracks the `modified` timestamp on every file and runs a range query (`greaterEqual`/`lessEqual`) over one 24-hour window for O(log n) performance. The VFS does not store historical file contents — `/as-of/` filters by *when a file last changed*; reads return the current bytes. For point-in-time state, use the Db API (`brain.asOf(generation)`).
 
 **Status:** ✅ Fully implemented and tested at 10K file scale
 
@@ -222,7 +225,7 @@ console.log(authFiles)
 // ['login.ts', 'signup.ts', 'oauth.ts']
 ```
 
-### Example 2: Time Travel
+### Example 2: Changes by Day
 ```typescript
 // See what changed today
 const today = new Date().toISOString().split('T')[0]
@@ -232,8 +235,8 @@ const todaysFiles = await vfs.readdir(`/as-of/${today}`)
 const yesterday = new Date(Date.now() - 86400000).toISOString().split('T')[0]
 const yesterdaysFiles = await vfs.readdir(`/as-of/${yesterday}`)
 
-const newFiles = todaysFiles.filter(f => !yesterdaysFiles.includes(f))
-console.log('New files today:', newFiles)
+const onlyToday = todaysFiles.filter(f => !yesterdaysFiles.includes(f))
+console.log('Changed today (untouched yesterday):', onlyToday)
 ```
 
 ### Example 3: Graph Navigation
@@ -432,25 +435,17 @@ await vfs.writeFile(path, code, {
 })
 ```
 
-### 3. Optimize for Your Scale
+### 3. Combine Dimensions
 ```typescript
-// For < 100K files: Post-filtering is fine
-// For > 100K files: Use flattened indexes
-
-// Force index refresh after bulk operations
-await brain.storage.rebuildIndexes()
-```
-
-### 4. Combine Dimensions
-```typescript
-// Find security files Alice worked on this week
+// Find security files Alice changed on a given day
+// (each /as-of/<date> path covers exactly that one day)
 const aliceFiles = await vfs.readdir('/by-author/alice')
 const securityFiles = await vfs.readdir('/by-tag/security')
-const thisWeek = await vfs.readdir(`/as-of/${weekAgo}`)
+const changedThatDay = await vfs.readdir('/as-of/2024-03-15')
 
 const intersection = aliceFiles
   .filter(f => securityFiles.includes(f))
-  .filter(f => thisWeek.includes(f))
+  .filter(f => changedThatDay.includes(f))
 ```
 
 ---
@@ -469,14 +464,14 @@ console.log(entity.metadata.concepts)
 
 ### Slow Queries on Large Datasets
 ```typescript
-// Check if indexes are built
-const stats = await brain.storage.getIndexStats()
+// Check if indexes are built and populated
+const stats = await brain.getIndexStats()
 console.log(stats)
-
-// Rebuild if needed
-await brain.storage.rebuildIndexes()
 ```
 
+If an index looks empty or inconsistent, rebuild from raw storage with the CLI
+(stop the live writer first): `brainy inspect repair <data-dir>`.
+
 ### Semantic Path Returns Empty
 ```typescript
 // Check if metadata exists