agent-toolkit-mcp-server

A user-facing MCP server that augments Claude Code's built-in harness with four capability areas the harness does not have natively:

• Notes — persistent, named markdown notes with SQLite FTS5 full-text search
• Todos — persistent todos, cross-session, optionally project-scoped
• Timers — durable scheduled wake-ups (SQLite-backed; poll fired events)
• Projects — a cross-project registry of repos/folders by name, with optional member sub-paths and per-project markdown docs

Install / run

uvx agent-toolkit-mcp-server

Or register it as an MCP server in your Claude Code config.

Storage layout

All state lives under a single directory, configurable via AGENT_TOOLKIT_HOME (default ~/.agent-toolkit/):

~/.agent-toolkit/
├── data.db                       # SQLite: todos, timers, projects, FTS index
├── notes/
│   ├── _global/
│   └── <project>/                # markdown files with YAML frontmatter
└── projects/
    └── <project>/docs/           # per-project markdown docs

Notes and project docs are markdown files with YAML frontmatter — canonical, human-editable, greppable on disk. The FTS5 index is rebuilt from disk on startup and kept fresh by note/doc mutating tools. Mutating tools bump revision; pass expected_revision to detect concurrent writes.

The first time you start v0.3.0 against an existing ~/.agent-toolkit/ from v0.2.x, the server migrates projects.json, todos/, and timers/ into data.db, then renames the source paths with a .migrated suffix as backup. Migration is idempotent.

Project scope: omit project (or pass an empty string) for the global scope. Otherwise the value must match a name registered via project_register.

Tool index

Notes (16)

note_list, note_tags_list, note_read, note_find, note_tail, note_write, note_rename, note_add_tags, note_remove_tags, note_append, note_append_section, note_edit, note_clear, note_delete, note_archive, note_search

note_search runs an FTS5 MATCH query across notes and (optionally) project docs. Empty project = search all scopes; named project = restrict to that scope. Returns {kind, project, name, title, snippet}.

Todos (11)

todo_create, todo_list, todo_get, todo_update, todo_complete, todo_delete, todo_add_tag, todo_remove_tag, todo_tags_list, todo_add_blocker, todo_remove_blocker

todo_list status values: open|in_progress|done|cancelled|active|all where active = open + in_progress.

Timers (7)

timer_set, timer_list, timer_cancel, timer_pause, timer_resume, timer_fired, timer_ack

A daemon thread inside the server wakes every 5 seconds, moves due timers from timers into fired_timers, and re-arms recurring ones.

Projects (10)

project_register, project_list, project_get, project_update, project_remove, project_resolve, project_doc_list, project_doc_read, project_doc_write, project_doc_delete

A project may include optional members — a JSON array of {path, label, description} entries describing related folders/repos that make up the logical project (e.g. frontend + backend in a polyrepo). project_get returns members plus the list of attached doc names. Project docs live at <home>/projects/<project>/docs/<slug>.md and are indexed by FTS together with notes; surface them with note_search (or list with project_doc_list).

Errors

All tool errors are returned as JSON, never raised:

{ "error": true, "code": "not_found", "message": "..." }

Revision conflicts return code: "revision_mismatch" along with the current revision so agents can re-read and retry.