refactor: remove deprecated settings-based local search engines (#2344)

* refactor: remove deprecated settings-based local search engines

The old settings-based local engines (research_papers, project_docs,
personal_notes, local_all) are fully superseded by the database-backed
Collection system with CollectionSearchEngine and LibraryRAGSearchEngine.

- Delete LocalAllSearchEngine and LocalSearchEngine classes
- Remove 58 settings entries from default_settings.json
- Remove local engine registration from search_engines_config.py
- Remove local_search_engines() function
- Clean up LocalEmbeddingManager: remove 14 dead methods and unused attrs
- Remove Docker volume mounts for local_collections
- Update security whitelist, rate limiter, bearer config
- Remove dead force_reindex code path in research_functions.py
- Update docs to reference Collections UI
- Remove/update all associated tests
- Regenerate golden master settings

* fix: address review comments from djpetti

- Revert unintentional formatting change in theme options (keep compact inline format)
- Restore unicode arrow character (→) that was escaped to \u2192 by JSON serializer
- Rename search_engine_local.py → local_embedding_manager.py since it only contains
  LocalEmbeddingManager now (no search engines)
- Remove unused chunk_size, chunk_overlap, cache_dir params from LocalEmbeddingManager
- Update all imports and references across codebase

.github/scripts/check-file-writes.sh

@@ -181,7 +181,7 @@ if [ -n "$ALL_MATCHES" ]; then
 
     # Filter system config files (not user data)
     if [ "$skip_line" -eq 0 ]; then
-      if echo "$line" | grep -qE "web/app_factory\.py|web/server_config\.py|web_search_engines/engines/search_engine_local\.py|document_loaders/bytes_loader\.py"; then
+      if echo "$line" | grep -qE "web/app_factory\.py|web/server_config\.py|document_loaders/bytes_loader\.py"; then
         skip_line=1
       fi
     fi