feat: add update_note and append_to_note MCP tools

[nguyenngothuong]

Closes #895. The Tolaria MCP server previously only let agents create new notes (create_note with O_EXCL). This PR adds write-back to existing notes so agents can maintain living documents (Agent notes, evolving Project notes, frontmatter status / schedule / related_to updates) instead of fragmenting them into supplementary notes.

What was implemented

Two new writable, non-destructive MCP tools operating on existing notes, layered exactly like create_note (vault.js primitive → tool-service method → stdio + WebSocket registration):

• update_note — replace full content (frontmatter + body). Atomic temp-file + rename so a crashed write never truncates a note. Optional expectedMtime (the mtimeMs from get_note) fails fast on concurrent edits, leaving the on-disk note untouched.
• append_to_note — append markdown verbatim to the body. No conflict guard because append cannot lose data on its own. Lower-risk path for logs/journals.

Both reuse the existing realpath traversal guard, resolve via the same writableVaultPath / writableNotePath helpers, emit vault_changed so the UI refreshes, and use the existing writable annotation profile (readOnlyHint: false, destructiveHint: false, openWorldHint: false) — i.e. MCP clients treat them like create_note (non-destructive local write, no extra approval).

Design follows the spec in #895 exactly. The optional expectedMtime conflict guard is opt-in (issue suggestion), so the common single-editor agent flow stays a single update_note call without a mandatory read.

QA

Verified via MCP stdio integration tests:

• update_note / append_to_note are listed with correct annotations and required ['path', 'content'] schema.
• Round-trip update_note then read-back matches the new content.
• append_to_note appends verbatim (no auto-newline — agents control formatting).
• update_note rejects path-traversal outside the vault; fails on expectedMtime mismatch without touching the note.
• append_to_note rejects path-traversal; throws ENOENT for missing notes.

No native UI QA needed — no UI change (these are MCP-only tools).

Tests / coverage

cd mcp-server && node --test test.js tool-service.test.js → 53 pass / 0 fail (8 new cases across vault primitives, service layer, and stdio MCP integration). pnpm lint clean. Pre-push gate: 25/25 Playwright smoke pass.

CodeScene

PAT / project not set in this environment, so the gate skipped. Boy Scout rule applied manually — vault.js helpers (writeExistingUtf8File, appendUtf8File, assertNoteMatchesExpectedMtime) are focused single-purpose functions, and the atomic write cleans up its temp file on a failed rename so it never leaks.

Codacy

No Critical / High findings introduced — all writes go through the existing resolveVaultNotePath traversal guard (no new path handling); expectedMtime is opt-in and never silently overwrites.

Localization

No UI copy changes.

PostHog

No event needed — MCP tool calls are agent-driven, not user-driven UI actions; instrumenting them would create noise.

Refactoring

Extracted resolveWritableNote and noteContent helpers in tool-service.js to keep the two new methods parallel with createNote without duplication.

ADRs

ADR-0142 records the design and the alternatives considered (mandatory expectedMtime, frontmatter-patch tool, in-place write, append-only shipping).

Docs

mcp-server/index.js tool banner updated to list the new tools. Bundle regenerated (pnpm bundle-mcp) — bundle is gitignored, rebuilt at release time.

Demo vault dirt

git status --short -- demo-vault demo-vault-v2 clean.