[Phototonic]

Summary

Closes #494.

When capture updates leave several prompts pointing at one memory, the timeline can emit the memory twice and Svelte throws each_key_duplicate. Grouping now resolves explicit memory-to-prompt links first, then reverse links, using each unique item at most once. The current linked prompt takes priority; older prompts remain visible as standalone entries. One-sided links and page subsets remain supported.

Markdown add/update writes now serialize validated promptId, sessionID, and captureTimestamp fields. Reconciliation preserves surviving indexed metadata for legacy files, lets valid frontmatter capture fields override it, and retains the indexed session, pin state and user/project columns during replacement or shard moves. Capture updates also synchronize the indexed session column immediately.

Historical prompt backlinks remain supported. Blank or invalid capture fields do not explicitly clear surviving indexed values, and provenance already absent from both the file and index cannot be recovered. Existing scan/deletion policy and delete-before-insert behavior are unchanged.

This PR is independently based on main and contains no #495 deletion-safety changes. Its overlap with #496 is confined to reconcile.ts: a three-way application merged cleanly, and the combined regression suite passed. A rebase may be needed if #496 lands first.

Test plan

• Added 16 grouping tests, including all 1,944 two-memory/two-prompt link/order combinations, plus 6 real database integration scenarios and 2 document-validation tests.
• Real client/database integration: capture add/update, first/unchanged/edited reconciliation, legacy and malformed fields, empty-index rebuild, session queries, pin preservation, shard moves and row/count consistency. Embeddings are stubbed; no LLM or model download is required.
• Chromium 156 smoke test against the development UI and synthetic API responses: duplicate backlinks in both input orders, current-prompt priority, older standalone prompt, one-sided/page-boundary links, pinned-first ordering, select/deselect and pagination; no browser console or page errors.
• 网页 "Project Memories" 页面卡在 "Initializing…"(Svelte each_key_duplicate):同一条记忆被两句提问同时关 #494 focused suite: 43 passed, 0 failed across 8 files.
• Combined 网页 "Project Memories" 页面卡在 "Initializing…"(Svelte each_key_duplicate):同一条记忆被两句提问同时关 #494/fix(markdown): preserve index when vault inventory is unsafe #496 focused suite in a separate checkout: 63 passed, 0 failed across 9 files.
• All local tests used disposable storage/configuration with active data masked and a separate network namespace.
• Noted the compatibility and limitations above.

Checklist

• Branch is based on current main.
• bun test --timeout 30000: 1,186 passed, 4 platform-specific skips, 0 failed across 158 files (Bun 1.3.14, Linux).
• bun run typecheck passes (via bun run check).
• bun run check passes (formatting, lint and TypeScript).
• bun run build passes, with zero Svelte errors or warnings.
• Docs / README updated.