Fix critical reliability bugs across extension

[ashrielbrian]

Summary

Commit 1: Core reliability fixes

• Unified DB storage path: popup used idb://casper.db while background used idb://casper — two separate databases, so search always returned empty. Both now share DB_STORAGE constant.
• Fixed missing page inserts: added getOrCreatePage() so pages are inserted before embeddings, eliminating orphaned rows with page_id = null.
• Fixed race conditions: consolidated process_page handler into a single lock acquisition (was 3 separate lock/unlock cycles). sendResponse now called after the lock releases.
• Fixed hung message channels: added try/catch to all 3 background message handlers so sendResponse is always called, even on errors.
• Fixed silent filter failures: saveFilterSites and removeFilterSites used forEach(async ...) which doesn't await — transactions committed with zero queries. Replaced with for...of.
• Fixed SQL injection: parameterized embedding arrays, INTERVAL values, and added table name allowlist for countRows.
• Fixed React bugs: null guards on worker, try/catch/finally on search, corrected useEffect dependency arrays in Search and Settings, null-safe rendering in SearchResults.
• Hardened utilities: extractDomain wrapped in try/catch, zip handles mismatched array lengths.
• Operational fixes: getDB() error recovery, cached tokenizer singleton, content script error handling, worker cleanup on unmount.
• Cleanup: removed dead getDBName, unused PGliteWorker import, no-op saveModelType, console.logs.

Commit 2: Logging, HNSW index fix, PGliteWorker.create()

• Added [casper]-prefixed logging to all background.ts message handlers — processing decisions (skip/process/done) and errors are now visible in the service worker console. Previously there was zero logging, making it impossible to diagnose "embeddings not generated" reports.
• Content script checks background response and logs a warning on failure (errors were silently discarded).
• Fixed HNSW index DDL — CREATE INDEX ON embedding USING hnsw ... was missing IF NOT EXISTS, causing initSchema to fail on second invocation and breaking all subsequent DB operations in that process lifetime.
• Added initSchema idempotency test to prevent the HNSW index bug from regressing.
• Switched popup to PGliteWorker.create() — documented async API with proper TypeScript extension types.

Commit 3: Fix search result anchor navigation

• Fixed chunk ID tracking: chunk IDs were set to the last node in each chunk instead of the first, causing search result links to scroll to the wrong section of the page. Now curr_id is set once from the first node and reset correctly when a new chunk begins.
• Cleaned up empty fragment anchors: SearchResults.tsx no longer appends a bare # when chunk_tag_id is null/empty.

Commit 4: Fix Settings page reliability

• nukeDb: wrapped in transaction, removed redundant deletes already handled by ON DELETE CASCADE.
• onSettingsSave: moved setHasChanged(false) after the async updateSites() call so the Save button stays enabled if the save fails. Added try/catch with error logging.
• Auto-dismiss confirmation: "Database cleared!" message now disappears after 3 seconds instead of persisting for the entire popup session.
• Test crypto polyfill: added tests/setup.ts to polyfill globalThis.crypto for Node 18 — crypto.randomUUID() in initSchema was causing all tests to fail under the tsx loader.
• Added nukeDb test: verifies page/embedding/cache are cleared while filter sites are preserved.

Test plan

• pnpm test — all 9 tests pass (including nukeDb and idempotency tests)
• pnpm build — production build succeeds
• Load unpacked extension in Chrome (build/chrome-mv3-prod)
• Browse pages → service worker console shows [casper] Processing <url> / [casper] Done processing <url>
• Revisit same page → console shows [casper] Skipping <url> (already processed)
• Open popup → search returns results (validates unified DB + page inserts)
• Click search result → browser scrolls to the beginning of the matched content section, not the end
• Settings → Clear Database → confirmation appears and auto-dismisses after 3s; filter list unchanged
• Settings → add filter → Save → reopen popup → filter persists
• Settings → remove filter → Save → reopen popup → filter gone
• If errors occur, they're now visible in both the service worker and page consoles

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