refactor(8.0): remove dead/deprecated code (legacy sweep)

- Deleted getIdsForFilterOld() — a 74-line "DEPRECATED old implementation"
  private method in the metadata index with no callers.
- Deleted getEdgesBySource/ByTarget/ByType from FileSystemStorage — three
  deprecated methods that only `console.warn` + `return []` (stub returns the
  repo forbids); not called anywhere and not required by any interface.
- Removed dead commented-out code fragments (an aspirational find() block in the
  NLP processor; a stale duplicate `const groups` line in the VFS generator).

Build + unit gate green.

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

src/importers/VFSStructureGenerator.ts

@@ -189,8 +189,7 @@ export class VFSStructureGenerator {
       reportProgress('metadata', `Preserved source file: ${options.sourceFilename}`)
     }
 
-    // Note: groups already calculated above for progress tracking
-    // const groups = this.groupEntities(importResult, options)
+    // `groups` was already computed above (for progress tracking) and is reused here.
 
     // Create directories and files for each group
     for (const [groupName, entities] of groups.entries()) {