@torsday/omnifocus-mcp 1.2.2 → 1.5.3

package/README.md

@@ -17,19 +17,9 @@
 - [Why this exists](#why-this-exists)
 - [Quick start](#quick-start)
 - [Security & trust](#security--trust)
-- [Example interactions](#example-interactions)
-- [Prompts](#prompts)
-- [If you are an AI agent](#if-you-are-an-ai-agent)
-- [Tools](#tools)
-- [Resources](#resources)
-- [Transport text DSL](#transport-text-dsl)
 - [Architecture at a glance](#architecture-at-a-glance)
 - [Status and roadmap](#status-and-roadmap)
-- [Install](#install)
-- [Environment variables](#environment-variables)
-- [Troubleshooting](#troubleshooting)
-- [Client setup guides](#client-setup-guides)
-- [Design documents](#design-documents)
+- [Reference docs](#reference-docs)
 - [Contributing](#contributing)
 - [License](#license)
 
@@ -68,10 +58,14 @@ OmniFocus is a powerful GTD tool, but it's an island. Your tasks sit there while
 
 The server is built to a single-user local-first standard: no network surface, no cloud sync, typed errors with agent-readable remediation hints, safe by default.
 
+See [`docs/examples.md`](./docs/examples.md) for concrete prompt-to-tool-call sequences and [`docs/prompts.md`](./docs/prompts.md) for the bundled MCP prompt templates (`daily-review`, `weekly-review`, `capture-meeting`, `project-planning`).
+
 ---
 
 ## Quick start
 
+**Prerequisites:** macOS 13 (Ventura) or later · OmniFocus 3.x or 4.x (4.x recommended; some tools require 4.x — see [version compatibility](./docs/troubleshooting.md#omnifocus-version-compatibility)) · Node 24+ (not required for Homebrew install)
+
 1. **Install**
    ```bash
    # Homebrew (no Node required)
@@ -89,7 +83,7 @@ The server is built to a single-user local-first standard: no network surface, n
    env:     OMNIFOCUS_LOG_LEVEL=info   # optional; "debug" is verbose
    ```
 
-   Find your client below. Order is alphabetical; no client is recommended over another.
+   Two common cases inline; full per-client guides at [`docs/clients/`](./docs/clients/) (Claude Code, Claude Desktop, Codex, OpenCode, Pi, generic stdio).
 
    <details>
    <summary><strong>Claude Code</strong> (CLI; no file edit)</summary>
@@ -97,8 +91,7 @@ The server is built to a single-user local-first standard: no network surface, n
    ```bash
    claude mcp add omnifocus omnifocus-mcp
    ```
-
-   Detailed guide: [`docs/clients/claude-code.md`](./docs/clients/claude-code.md)
+   Detailed: [`docs/clients/claude-code.md`](./docs/clients/claude-code.md)
    </details>
 
    <details>
@@ -115,98 +108,14 @@ The server is built to a single-user local-first standard: no network surface, n
      }
    }
    ```
-
-   Detailed guide: [`docs/clients/claude-desktop.md`](./docs/clients/claude-desktop.md)
-   </details>
-
-   <details>
-   <summary><strong>Cline</strong> (VS Code extension) — extension settings (JSON)</summary>
-
-   In VS Code, open the Cline extension's MCP settings panel and add:
-
-   ```json
-   {
-     "mcpServers": {
-       "omnifocus": {
-         "command": "omnifocus-mcp",
-         "args": [],
-         "env": { "OMNIFOCUS_LOG_LEVEL": "info" }
-       }
-     }
-   }
-   ```
-
-   Cline's settings UI may surface the same fields as labelled inputs rather than raw JSON; the values are identical. Verify the panel location against the current Cline docs.
-   </details>
-
-   <details>
-   <summary><strong>OpenAI Codex CLI</strong> — <code>~/.codex/config.toml</code> (TOML)</summary>
-
-   ```toml
-   [mcp_servers.omnifocus]
-   command = "omnifocus-mcp"
-   args = []
-   env = { OMNIFOCUS_LOG_LEVEL = "info" }
-   ```
-
-   Detailed guide: [`docs/clients/codex.md`](./docs/clients/codex.md)
-   </details>
-
-   <details>
-   <summary><strong>Cursor</strong> — <code>~/.cursor/mcp.json</code> (JSON)</summary>
-
-   ```json
-   {
-     "mcpServers": {
-       "omnifocus": {
-         "command": "omnifocus-mcp",
-         "args": [],
-         "env": { "OMNIFOCUS_LOG_LEVEL": "info" }
-       }
-     }
-   }
-   ```
-
-   Verify the path against the current Cursor docs — recent versions also accept project-scoped `.cursor/mcp.json` at the repo root.
-   </details>
-
-   <details>
-   <summary><strong>Windsurf</strong> — <code>~/.codeium/windsurf/mcp_config.json</code> (JSON)</summary>
-
-   ```json
-   {
-     "mcpServers": {
-       "omnifocus": {
-         "command": "omnifocus-mcp",
-         "args": [],
-         "env": { "OMNIFOCUS_LOG_LEVEL": "info" }
-       }
-     }
-   }
-   ```
-
-   Verify the path against the current Windsurf docs — Codeium occasionally relocates config under `~/.codeium/`.
-   </details>
-
-   <details>
-   <summary><strong>Generic stdio client</strong> (anything else that speaks MCP/stdio)</summary>
-
-   Use your client's MCP config form. The shape is:
-
-   ```text
-   command: "omnifocus-mcp"
-   args:    []
-   env:     { "OMNIFOCUS_LOG_LEVEL": "info" }
-   ```
-
-   Detailed guide: [`docs/clients/generic-stdio.md`](./docs/clients/generic-stdio.md)
+   Detailed: [`docs/clients/claude-desktop.md`](./docs/clients/claude-desktop.md)
    </details>
 
 3. **Grant macOS Automation permission** on first use — the app running the MCP server will prompt to control OmniFocus; click **OK**. If denied by mistake: **System Settings → Privacy & Security → Automation → [app] → OmniFocus** ✓
 
 4. **Verify** — ask your assistant: *"Use the internal_status tool and tell me what it returns."*
 
-Detailed per-client guides: [`docs/clients/`](./docs/clients/)
+Stuck? See [`docs/troubleshooting.md`](./docs/troubleshooting.md).
 
 ---
 
@@ -214,8 +123,6 @@ Detailed per-client guides: [`docs/clients/`](./docs/clients/)
 
 `omnifocus-mcp` is a **local-only** Node.js process that drives a **local** OmniFocus app via Apple's `osascript` runtime. Installing this package does not introduce cloud connectivity, telemetry, or network egress that wasn't already on your machine.
 
-### Data flow
-
 ```
 OmniFocus DB (local) ─→ JXA / OmniJS via osascript (local) ─→ MCP server (local stdio)
                                                                     │
@@ -272,443 +179,7 @@ Three recipes that take seconds; you don't have to take this README's word for a
 
 The threat model deliberately excludes anything outside this codebase: vulnerabilities in OmniFocus itself, Apple's JXA / OmniJS / `osascript` runtimes, transitive npm-dependency CVEs (track and patch via `npm audit` / Dependabot, but not part of this project's guarantees), and any attacker with root-equivalent local access (who could replace `osascript`, the MCP server binary, or your shell). See [SECURITY.md § Scope](./SECURITY.md#scope).
 
-### Reference docs
-
-- [`SECURITY.md`](./SECURITY.md) — vulnerability reporting, scope
-- [`DESIGN.md` § 18 Security posture](./DESIGN.md#18-security-posture) — full threat model
-- [ADR-0004](./docs/adr/0004-raw-script-escape-hatch.md) — raw-script gating decision
-
----
-
-## Example interactions
-
-**"What's in my inbox right now?"**
-
-The assistant calls `task_list` with `{ "available": true, "limit": 20 }` and returns a formatted list of actionable inbox tasks with their IDs, due dates, and flags.
-
----
-
-**"Create a task to 'review Q2 budget' due Friday, flagged, in the Finance project."**
-
-1. Calls `project_list` to find the Finance project ID.
-2. Calls `task_create` with `{ "name": "review Q2 budget", "projectId": "<id>", "dueDate": "end-of-week", "flagged": true }`.
-3. Returns the created task with its persistent ID and confirms the due date resolved to the correct Friday.
-
----
-
-**"Mark all my overdue tasks as deferred to tomorrow."**
-
-1. Calls `task_list` with `{ "dueBefore": "today", "available": true }` to find overdue items.
-2. Calls `task_batch_update` with `{ "deferDate": "tomorrow" }` for all of them in one atomic call.
-3. Reports: *"Deferred 7 overdue tasks to tomorrow. Call sync_trigger if you want iCloud to update immediately."*
-
----
-
-**"Show me what's due this week in the Work perspective."**
-
-1. Calls `perspective_list` to find the "Work" perspective ID.
-2. Calls `perspective_evaluate` with `{ "perspectiveId": "<id>" }` to get tasks in that perspective.
-3. Filters and presents items with due dates within the current week.
-
----
-
-**"I just finished the sprint — complete all tasks in the Mobile App project."**
-
-1. Calls `project_get` to retrieve the project and its tasks.
-2. Calls `task_batch_complete` with the full list of task IDs in one call.
-3. Confirms the count and suggests calling `sync_trigger` for cross-device visibility.
-
----
-
-## Prompts
-
-`omnifocus-mcp` ships four **MCP prompt templates** — structured workflows you can invoke by name from any MCP client that surfaces `prompts/list` (most clients with a prompt picker UI).
-
-### `daily-review` — triage your day
-
-Loads your snapshot, overdue tasks, and today's forecast; reschedules or drops overdue items; confirms due-today tasks; processes the inbox. No parameters needed.
-
-```
-Use the daily-review prompt
-```
-
-### `weekly-review` — walk your projects
-
-Loads every project whose review date has arrived; checks each one for stale tasks; marks it reviewed or completes/drops it. No parameters needed.
-
-```
-Use the weekly-review prompt
-```
-
-### `capture-meeting` — extract action items
-
-Takes raw meeting notes and creates OmniFocus tasks for every commitment, follow-up, and decision point. Pass the notes as text and optionally a project ID.
-
-```
-Use the capture-meeting prompt with notes="Sync with Alice: she'll send the report by Thursday.
-Bob to review the contract. Need to schedule follow-up call."
-```
-
-Results in two inbox tasks: "Send report to [person]" and "Review contract" with the source sentences as notes.
-
-### `project-planning` — decompose a brief
-
-Creates a new project and populates it with a set of concrete, ordered, one-day tasks derived from a free-text brief.
-
-```
-Use the project-planning prompt with name="Q3 Marketing Site" brief="Redesign the marketing
-site landing page and pricing page. New brand colors, updated copy, responsive mobile layout.
-Launch by end of July."
-```
-
-Results in a new OmniFocus project with 8–12 tasks covering design, copy, development, and review phases, ready to schedule and assign.
-
----
-
-## If you are an AI agent
-
-This section is written for you. It covers the conventions you need to use this MCP effectively without trial and error.
-
-### IDs, not names
-
-Every OmniFocus resource — tasks, projects, tags, folders — is identified by a **persistent opaque ID** (e.g. `"hKx9vLmNp2"`). Names collide and change; IDs don't. Always resolve names to IDs with the corresponding `*_list` tool before calling any other tool.
-
-### Error codes and what to do next
-
-Every error carries a stable `code`, a human-readable `suggestion`, and a machine-readable `remediationClass`:
-
-| `remediationClass` | Meaning | Your action |
-|--------------------|---------|-------------|
-| `environment` | OmniFocus is not running, permissions denied, or a Pro/version feature is missing | Stop. Surface `suggestion` to the user; do not retry automatically |
-| `input` | Bad ID, invalid field value, schema violation, or loop detected | Fix the input using `details` for specifics; retry |
-| `transient` | Timeout, rate limit, queue full, or circuit open | Wait `details.retryAfterMs` ms, then retry once |
-| `infrastructure` | JXA or OmniJS script failed | Retry once; if still failing, surface to user |
-| `lifecycle` | Server is shutting down | Reconnect to a fresh server instance |
-
-`RateLimited` and `CircuitOpen` always include `details.retryAfterMs` (default `60000` ms). Do not poll faster than that.
-
-### Dates
-
-All date inputs accept either **ISO-8601 with UTC offset** (`"2026-04-22T09:00:00-07:00"`) or a **relative shortcut**:
-
-`today` · `tomorrow` · `yesterday` · `this-week` · `next-week` · `end-of-week` · `end-of-month`
-
-Shortcuts resolve to midnight in the server's local timezone.
-
-### Mutations and sync
-
-Every write tool returns the full updated domain object, not just an acknowledgement. The response `meta.syncPending` is `true` immediately after a write — OmniFocus has saved locally but not yet synced to iCloud. Call `sync_trigger` if cross-device visibility matters; otherwise sync happens automatically within a few minutes.
-
-### Null consistency
-
-All optional scalar fields are **always present** in responses, set to `null` when unset. You can safely destructure without null-checks on field presence.
-
-### Idempotency — safe retries
-
-`project_create`, `project_update`, and `project_delete` accept an optional `idempotency_key?: string`. If you supply one and the call succeeds, replaying the exact same key within 5 minutes returns the cached result with `meta.idempotentReplay: true` and skips the OmniFocus call. Use a deterministic key scoped to your session and intent (e.g. `"session-abc/create-project-finance"`).
-
-### Dry-run — validate before committing
-
-`task_update` and `project_update` accept `dry_run?: boolean`. When `true`, input is fully validated and the would-be result is returned, but nothing is written to OmniFocus. `meta.dryRun: true` is set on the response.
-
-### Additive tag edits — no read-modify-write needed
-
-`task_update` accepts `addTags`, `removeTags`, and `setFlagged` patch fields alongside the existing full-replacement `tagIds` field. Prefer these for incremental edits — they apply a diff atomically inside the write queue with no race against concurrent user edits.
-
-### Conflict detection — optimistic concurrency
-
-`task_update` accepts `expectedModifiedAt`. If the task was modified since your read, the server returns `OF_CONFLICT` (`remediationClass: "input"`). Re-read with `task_get`, merge your changes, and retry with the fresh `modifiedAt`.
-
-### Loop detection — don't get stuck
-
-If you call the same tool with identical arguments 5+ times in a 60-second window, the server appends `WARN_LOOP_DETECTED` to `meta.warnings`. At 10 repetitions it throws `OF_LOOP_DETECTED` (`remediationClass: "input"`). Act on the result of your previous call rather than repeating it.
-
-### Capabilities pre-flight
-
-Read `omnifocus://capabilities` once at session start. It returns OF version, edition (Standard/Pro), transport availability, and feature flags (`customPerspectives`, `forecastTag`, `rawScriptTools`). Use it to skip Pro-gated tools rather than discovering unavailability via error.
-
-### Rate limit state — self-throttle before hitting the wall
-
-Every response includes `meta.rateLimit?: { remaining: number; resetAt: string }`. Check this after each call. If `remaining < 10`, slow down. If `remaining === 0`, do not call before `meta.rateLimit.resetAt`. The default limit is 120 calls/min per tool.
-
-### Structured warnings — act on `meta.warnings[].code`
-
-Non-fatal issues appear in `meta.warnings` as `{ code, message, suggestion?, details? }`. Switch on `code`, not `message`:
-
-| `code` | Means | Action |
-|---|---|---|
-| `WARN_IDS_NOT_FOUND` | Some IDs in a bulk call were not found | Check `details.missing` |
-| `WARN_RESULT_TRUNCATED` | Response hit size limit; more items exist | Follow pagination cursor |
-| `WARN_SYNC_PENDING` | Write saved locally; iCloud sync not yet triggered | Call `sync_trigger` if needed |
-| `WARN_LOOP_DETECTED` | Same tool+args called ≥5 times in 60s | Act on previous result before repeating |
-
-### Incremental sync — `updatedSince`
-
-`task_list` accepts `updatedSince?: string` (ISO-8601 or relative shortcut). Use it to fetch only changed items after your initial load:
-
-```jsonc
-// First call: full load
-{ "available": true, "limit": 200 }
-
-// Subsequent calls: only changes
-{ "available": true, "updatedSince": "2026-04-21T10:00:00-07:00", "limit": 200 }
-```
-
-Note: deleted items cannot be surfaced via `updatedSince` — compare `meta.snapshot` counts if you need to detect deletions.
-
-### Navigation hints — follow `_links`
-
-Every `Task` response includes `_links` with resource URIs for related objects:
-
-```jsonc
-{
-  "id": "hKx9vLmNp2",
-  "_links": {
-    "self": "omnifocus://task/hKx9vLmNp2",
-    "project": "omnifocus://project/pXY3",
-    "tags": ["omnifocus://tag/tABC"]
-  }
-}
-```
-
-Pass the ID fragment to `task_get`, `project_get`, etc. You never need to construct a URI manually.
-
-### Response envelope
-
-All responses have this shape:
-
-```jsonc
-// success
-{ "data": { … }, "meta": { "correlationId": "…", "durationMs": 12, "cacheHit": false, "transport": "jxa", "syncPending": false } }
-
-// error
-{ "error": { "code": "OF_NOT_FOUND", "remediationClass": "input", "message": "…", "suggestion": "…", "details": { … } }, "meta": { … } }
-```
-
-### Where to start
-
-- **Daily work**: `task_list` (inbox or today filter) → `task_create` / `task_update` / `task_complete`
-- **Projects**: `project_list` → `project_create` / `project_update`
-- **Finding things**: `task_search` (keyword + optional tag/project/date filters); `tag_list` for available tags
-- **Bulk ops**: `task_batch_create` / `task_batch_update` / `task_batch_complete` for up to 50 items atomically
-- **Sync**: `sync_trigger` after bulk mutations; `internal_status` to check server health
-
----
-
-## Tools
-
-Tools are organized by domain — tasks, projects, tags, folders, perspectives, forecast, review, search, notes, attachments, sync, export, and observability. See [`docs/tools.md`](./docs/tools.md) for the full auto-generated reference with the live registered count, input schemas, example calls, and example responses.
-
-### App lifecycle
-| Tool | Description |
-|---|---|
-| `app_launch` | Explicitly launch OmniFocus (idempotent) |
-
-### Tasks
-| Tool | Description |
-|---|---|
-| `task_list` | List tasks with filters (available, flagged, due, project, tag, updatedSince) |
-| `task_get` | Get a single task by ID |
-| `task_get_many` | Get multiple tasks by ID in one call |
-| `task_create` | Create a task (project, tags, due, defer, flag, note, repeat) |
-| `task_update` | Update a task (addTags/removeTags, dry_run, expectedModifiedAt) |
-| `task_complete` | Mark a task complete |
-| `task_uncomplete` | Unmark a completed task |
-| `task_delete` | Delete a task |
-| `task_drop` | Drop (defer indefinitely) a task |
-| `task_undrop` | Restore a dropped task |
-| `task_move` | Reparent a task to a different project or parent task |
-| `task_reorder` | Reorder a task among its siblings |
-| `task_duplicate` | Duplicate a task (optionally recursive) |
-| `task_find_by_name` | Find tasks by exact or fuzzy name match |
-| `task_search` | Full-text search across task names and notes, with optional tag/project/date/availability filters |
-| `task_set_repetition` | Set a repeat rule on a task |
-| `task_clear_repetition` | Remove a repeat rule from a task |
-| `task_parse_transport_text` | Parse transport text DSL → structured tasks (no side effects) |
-| `task_batch_create` | Create up to 50 tasks atomically |
-| `task_batch_update` | Update up to 50 tasks atomically |
-| `task_batch_complete` | Complete up to 50 tasks atomically |
-
-### Projects
-| Tool | Description |
-|---|---|
-| `project_list` | List projects with filters (folder, status) |
-| `project_get` | Get a single project by ID |
-| `project_create` | Create a project (idempotency_key supported) |
-| `project_update` | Update a project (dry_run, idempotency_key, expectedModifiedAt) |
-| `project_complete` | Mark a project complete |
-| `project_delete` | Delete a project (idempotency_key supported) |
-| `project_drop` | Drop (defer indefinitely) a project |
-| `project_move` | Move a project to a different folder |
-| `project_mark_reviewed` | Mark a project as reviewed (alias for review_mark_reviewed) |
-
-### Folders
-| Tool | Description |
-|---|---|
-| `folder_list` | List folders |
-| `folder_get` | Get a single folder by ID |
-| `folder_create` | Create a folder |
-| `folder_update` | Rename a folder |
-| `folder_delete` | Delete a folder |
-| `folder_move` | Move a folder to a parent folder |
-
-### Tags
-| Tool | Description |
-|---|---|
-| `tag_list` | List tags |
-| `tag_get` | Get a single tag by ID |
-| `tag_create` | Create a tag |
-| `tag_update` | Rename a tag |
-| `tag_delete` | Delete a tag |
-| `tag_move` | Move a tag under a parent tag |
-| `tag_set_status` | Set tag status (active/on-hold/dropped) |
-| `tag_set_allows_next_action` | Toggle "allows next action" on a tag |
-| `tag_get_location` | Get a tag's location in the hierarchy |
-| `tag_set_location` | Set a tag's location in the hierarchy |
-
-### Notes
-| Tool | Description |
-|---|---|
-| `note_get` | Get a task or project note (plain text) |
-| `note_get_html` | Get a task or project note (HTML) |
-| `note_set` | Set a task or project note (plain text, replaces) |
-| `note_set_html` | Set a task or project note (HTML, replaces) |
-| `note_append` | Append text to a task or project note |
-
-### Attachments
-| Tool | Description |
-|---|---|
-| `attachment_list` | List attachments on a task or project |
-| `attachment_add` | Embed a local file as an attachment |
-| `attachment_remove` | Remove an attachment by ID |
-| `attachment_save_to_path` | Save an attachment's bytes to a local file |
-
-### Perspectives
-| Tool | Description |
-|---|---|
-| `perspective_list` | List all perspectives (built-in and custom) |
-| `perspective_evaluate` | Evaluate a perspective and return its tasks |
-
-### Forecast & search
-| Tool | Description |
-|---|---|
-| `forecast_get` | Get today's forecast grouped by overdue / due today / due later / inbox |
-| `search_query` | Full-text search across tasks and projects |
-
-### Review
-| Tool | Description |
-|---|---|
-| `review_list_due` | List projects whose next review date is today or past |
-| `review_mark_reviewed` | Mark a project as reviewed and set the next review date |
-| `review_set_interval` | Set the review interval (days) for a project |
-
-### Sync & app
-| Tool | Description |
-|---|---|
-| `sync_trigger` | Trigger an OmniFocus iCloud sync |
-| `sync_status` | Get the last sync timestamp and status |
-
-### Plug-ins
-| Tool | Description |
-|---|---|
-| `plugin_invoke` | Invoke an installed Omni Automation plug-in by bundle identifier |
-
-### Export & import
-| Tool | Description |
-|---|---|
-| `export_opml` | Export a project (or all projects) as OPML |
-| `export_taskpaper` | Export a project (or all projects) as TaskPaper |
-| `import_opml` | Import tasks from an OPML string into OmniFocus |
-| `import_taskpaper` | Import tasks from a TaskPaper string into OmniFocus |
-
-### Observability
-| Tool | Description |
-|---|---|
-| `internal_status` | Server health: transport status, queue depths, cache stats, rate limits |
-
-### Raw scripts _(opt-in, off by default)_
-| Tool | Description |
-|---|---|
-| `run_jxa_script` | Execute arbitrary JXA — requires `OMNIFOCUS_ALLOW_RAW_SCRIPT=1` |
-| `run_omnijs_script` | Execute arbitrary OmniJS — requires `OMNIFOCUS_ALLOW_RAW_SCRIPT=1` |
-
----
-
-## Resources
-
-The server registers resources under the `omnifocus://` scheme. Resources are read-only, URI-addressable, and enumerable via `resources/list`. Templated URIs follow [RFC 6570](https://www.rfc-editor.org/rfc/rfc6570) and accept the listed parameters as query strings or path segments.
-
-**Static URIs** — read with no parameters:
-
-| URI | Returns |
-|---|---|
-| `omnifocus://capabilities` | Server capabilities: OF version, edition, transport status, feature flags, calendar-bridge availability |
-| `omnifocus://snapshot` | Orientation counts: inbox, flagged, overdue, dueToday, reviewDue, syncStatus |
-| `omnifocus://inbox` | Inbox tasks as `Task[]` |
-| `omnifocus://tasks/inbox` | Inbox tasks (alias of `omnifocus://inbox`) |
-| `omnifocus://forecast/today` | Today's forecast grouped by overdue / dueToday / deferredToday / flagged |
-| `omnifocus://overdue` | All overdue tasks sorted by dueDate ASC |
-| `omnifocus://flagged` | All flagged available tasks |
-| `omnifocus://review-due` | Projects with nextReviewDate ≤ today |
-| `omnifocus://intents` | User-phrase → tool-sequence map: a small set of human-meaningful verbs that compose the full tool surface |
-| `omnifocus://stats` | Database-wide rollup: counts by project, tag, completion state |
-| `omnifocus://taxonomy-audit` | Structural audit — inconsistent tag/folder usage, orphans, drift signals |
-| `omnifocus://waiting-on` | Every task carrying a `waiting-on` fence, sorted by daysOverdue DESC |
-
-**Templated URIs** — accept parameters:
-
-| URI Template | Parameters | Returns |
-|---|---|---|
-| `omnifocus://project/{id}` | `id` | Single project + full task tree |
-| `omnifocus://tag/{id}` | `id` | Single tag + its active tasks |
-| `omnifocus://perspective/{id}` | `id` | Perspective evaluation result (same shape as `perspective_evaluate`); Pro only |
-| `omnifocus://tasks/project/{projectId}` | `projectId` | Active tasks under a project |
-| `omnifocus://tasks/tag/{tagId}` | `tagId` | Active tasks carrying a tag |
-| `omnifocus://recent-activity{?hours}` | `hours` (default: 24) | Tasks completed/dropped/created in the last N hours |
-| `omnifocus://retrospective{?from,to}` | `from`, `to` (ISO-8601) | Closed-task aggregation for a date range — weekly review fuel |
-| `omnifocus://velocity{?weeks}` | `weeks` (default: 4) | Per-week throughput: completed counts, completion rate trend |
-| `omnifocus://burndown/{projectId}` | `projectId` | Per-project burndown vs naive linear ideal; needs project dueDate |
-| `omnifocus://project-health{?staleDays}` | `staleDays` (default: 14) | Triage list: stalled projects, no-activity, review-overdue |
-| `omnifocus://calendar{?from,to}` | `from`, `to` (ISO-8601, defaults to today local) | macOS Calendar events from EventKit; needs Calendar TCC grant |
-| `omnifocus://agenda{?date}` | `date` (ISO-8601, defaults to today local) | Merged daily timeline: calendar events + OF forecast, kind-tagged |
-
----
-
-## Transport text DSL
-
-`task_parse_transport_text` parses a lightweight DSL inspired by OmniFocus Mail Drop into structured task objects. **No tasks are created** — pass the returned `tasks[]` to `task_create` or `task_batch_create` separately.
-
-### Token syntax
-
-| Token | Example | Meaning |
-|---|---|---|
-| `@tag` | `@work` | Assign a tag by name |
-| `#date` | `#2026-05-01` or `#today` | Due date |
-| `::date` | `::tomorrow` | Defer date |
-| `!!` | `!!` | Flag the task |
-| `//text` | `//Call back before noon` | Append as task note |
-| `Project: Name` | `Project: Finance` | Set project context for subsequent tasks |
-
-### Date shortcuts
-
-`today` · `tomorrow` · `yesterday` — resolved to midnight local time.
-
-Full ISO-8601 dates (`YYYY-MM-DD`) are also accepted. Unparseable dates emit a `warnings[]` entry.
-
-### Example
-
-```
-Project: Work
-Prepare Q2 report @work #end-of-week !!
-Send draft to Alice @work @email #tomorrow //attach spreadsheet
-Follow up with Bob ::next-week
-
-Project: Personal
-Buy groceries @errands #today
-Call dentist @phone ::tomorrow !! //ask about X-ray appointment
-```
-
-Tag names and project names are raw strings — resolve to IDs with `tag_list` and `project_list` before passing to `task_create`.
+Full threat model: [`SECURITY.md`](./SECURITY.md), [`docs/design/security.md`](./docs/design/security.md).
 
 ---
 
@@ -739,7 +210,7 @@ flowchart LR
 - **30s LRU read cache** — invalidated on every write. Mutations are never served stale.
 - **Middleware stack** — every registered tool runs through: `assertNotShuttingDown` → `circuitBreaker` → `rateLimitMeta` → `loopDetection`.
 
-The full layered diagram with queues, circuit breakers, and the test adapter lives in [`DESIGN.md §6`](./DESIGN.md#6-architecture).
+The full layered diagram with queues, circuit breakers, and the test adapter lives in [`docs/design/architecture.md`](./docs/design/architecture.md).
 
 ---
 
@@ -760,194 +231,26 @@ Track open issues and future enhancements on the [**GitHub Project board**](http
 
 ---
 
-## Install
-
-**Homebrew** (recommended for non-Node users):
-```bash
-brew install torsday/tap/omnifocus-mcp
-```
-
-**npm** (recommended if you already have Node 24+):
-```bash
-# Global install
-npm install -g @torsday/omnifocus-mcp
-
-# Or run without installing (npx)
-npx -y @torsday/omnifocus-mcp
-```
-
-**Any stdio MCP client** — add to your client's MCP server config (exact key name varies by client):
-```json
-{
-  "mcpServers": {
-    "omnifocus": {
-      "command": "omnifocus-mcp",
-      "args": [],
-      "env": { "OMNIFOCUS_LOG_LEVEL": "info" }
-    }
-  }
-}
-```
-
-**npx (no global install)**:
-```json
-{
-  "mcpServers": {
-    "omnifocus": {
-      "command": "npx",
-      "args": ["-y", "@torsday/omnifocus-mcp"],
-      "env": { "OMNIFOCUS_LOG_LEVEL": "info" }
-    }
-  }
-}
-```
-
-On first run, macOS asks the app running the server for permission to automate OmniFocus. Click **OK**. If you denied it by mistake: **System Settings → Privacy & Security → Automation → [app] → OmniFocus** ✓
-
-See the [troubleshooting guide](./docs/troubleshooting.md) and per-client guides in [`docs/clients/`](./docs/clients/) for detailed setup.
-
----
-
-## Environment variables
-
-| Variable | What | Default |
-|---|---|---|
-| `OMNIFOCUS_LOG_LEVEL` | `trace`\|`debug`\|`info`\|`warn`\|`error` — logs go to stderr | `info` |
-| `OMNIFOCUS_CACHE_TTL_MS` | Read-cache TTL in milliseconds | `30000` |
-| `OMNIFOCUS_READ_POOL_SIZE` | Concurrent `osascript` processes for reads | `2` |
-| `OMNIFOCUS_WRITE_QUEUE_CAP` | Max pending writes before `QueueFull` error | `50` |
-| `OMNIFOCUS_JXA_TIMEOUT_MS` | Per-call JXA hard timeout in milliseconds | `30000` |
-| `OMNIFOCUS_OMNIJS_TIMEOUT_MS` | Per-call OmniJS hard timeout in milliseconds | `45000` |
-| `OMNIFOCUS_ATTACHMENT_PATHS` | Colon-separated allowlist of absolute path prefixes for attachment ops | `$HOME` |
-| `OMNIFOCUS_MAX_ATTACHMENT_MB` | Maximum attachment file size in MB (0 = no cap) | `100` |
-| `OMNIFOCUS_TOOL_RATE_LIMIT` | Per-tool rate limit in `N/SECONDS` format | `120/60` |
-| `OMNIFOCUS_ALLOW_RAW_SCRIPT` | Set to `1` to register `run_jxa_script` / `run_omnijs_script` | unset |
-| `OMNIFOCUS_INTEGRATION` | Set to `1` to enable the integration test suite | unset |
-
-Full table with override semantics: [`DESIGN.md §22`](./DESIGN.md#22-configuration--environment).
-
-### Running integration tests
-
-Integration tests run against a live OmniFocus install:
-
-```bash
-# 1. Make sure OmniFocus is running and Automation permission is granted
-# 2. Seed fixture data (idempotent — safe to re-run):
-node scripts/seed-integration-db.js
-
-# Optional: wipe and re-create all fixtures from scratch:
-node scripts/seed-integration-db.js --clean
-
-# 3. Run the integration suite:
-OMNIFOCUS_INTEGRATION=1 pnpm test:integration
-```
-
-The seed script creates `mcp-fixture:` prefixed items (folders, projects, tasks, tags) that integration tests rely on.
-
----
-
-## Troubleshooting
-
-### OmniFocus is not running
-
-**Error:** `OF_NOT_RUNNING` — OmniFocus must be open for most operations.
-
-**Fix:** Launch OmniFocus manually, or call `app_launch` to open it via MCP.
-
----
-
-### macOS Automation permission denied
-
-**Symptom:** Every tool call returns `OF_PERMISSION_DENIED`.
-
-**Fix:**
-1. Open **System Settings → Privacy & Security → Automation**.
-2. Find the app running the MCP server (Terminal, your AI client app, or your CI runner's shell).
-3. Enable the **OmniFocus** checkbox.
-4. Restart omnifocus-mcp.
-
-```bash
-bash scripts/check-automation-permission.sh
-```
-
----
-
-### First-call timeout / slow startup
-
-JXA starts an `osascript` subprocess on each call. The first call after a system sleep or a fresh OmniFocus launch can take 5–15 seconds while the database loads. This is normal.
-
-If calls consistently time out:
-```bash
-OMNIFOCUS_JXA_TIMEOUT_MS=60000 omnifocus-mcp
-```
-
----
-
-### `run_jxa_script` / `run_omnijs_script` not available
-
-**Error:** `ValidationError: run_jxa_script is not available in this adapter configuration`
-
-**Fix:** The raw-script tools are opt-in. Start the server with:
-```bash
-OMNIFOCUS_ALLOW_RAW_SCRIPT=1 omnifocus-mcp
-```
-
-See [`docs/adr/0004-raw-script-escape-hatch.md`](./docs/adr/0004-raw-script-escape-hatch.md) for the security rationale.
-
----
-
-### Stale data after a write
-
-Writes are saved locally and show up immediately in subsequent tool calls. Changes don't reach other devices until iCloud sync runs. Call `sync_trigger` after bulk mutations or when cross-device visibility matters.
-
----
-
-### More help
-
-- [`docs/troubleshooting.md`](./docs/troubleshooting.md) — expanded troubleshooting guide
-- [`docs/clients/`](./docs/clients/) — per-client setup guides
-
----
-
-## Client setup guides
-
-| Client | Guide |
-|---|---|
-| Claude Code (CLI) | [`docs/clients/claude-code.md`](./docs/clients/claude-code.md) |
-| Claude Desktop | [`docs/clients/claude-desktop.md`](./docs/clients/claude-desktop.md) |
-| OpenAI Codex CLI | [`docs/clients/codex.md`](./docs/clients/codex.md) |
-| Generic stdio client | [`docs/clients/generic-stdio.md`](./docs/clients/generic-stdio.md) |
-
----
-
-## Design documents
-
-- **[`SPEC.md`](./SPEC.md)** — functional scope and non-functional requirements; resolved v1 decisions
-- **[`DESIGN.md`](./DESIGN.md)** — 28-section architecture; options evaluated; R/S/M assessment; example tool implementation
-- **[`docs/security.md`](./docs/security.md)** — attack surface, mitigations, and test coverage
-- **[`docs/domain-reference.md`](./docs/domain-reference.md)** — OmniFocus glossary, canonical schemas, lossiness matrix for export/import
-- **[`docs/adr/`](./docs/adr/)** — Architecture Decision Records covering every load-bearing choice:
+## Reference docs
 
-| # | Decision |
+| Doc | What |
 |---|---|
-| [0001](./docs/adr/0001-language-and-runtime.md) | TypeScript on Node.js 24 |
-| [0002](./docs/adr/0002-omnifocus-transport-dual.md) | JXA + OmniJS dual transport |
-| [0003](./docs/adr/0003-tool-surface-namespaced.md) | `<noun>_<verb>` tool namespacing |
-| [0004](./docs/adr/0004-raw-script-escape-hatch.md) | Opt-in raw-script tools |
-| [0005](./docs/adr/0005-script-assets-as-files.md) | Scripts as first-class files |
-| [0006](./docs/adr/0006-read-cache-strategy.md) | 30s LRU, invalidate-on-write |
-| [0007](./docs/adr/0007-dates-iso8601-with-offset.md) | ISO-8601 with offset at the boundary |
-| [0008](./docs/adr/0008-ids-branded-opaque-strings.md) | Branded opaque ID types |
-| [0009](./docs/adr/0009-concurrency-pool-and-queue.md) | Read pool + write queue + OmniJS queue |
-| [0010](./docs/adr/0010-mcp-transport-stdio.md) | stdio-only MCP transport (v1) |
-| [0011](./docs/adr/0011-versioning-and-stability.md) | Semver with explicit contract |
-| [0012](./docs/adr/0012-distribution-npx.md) | Distribution via `npx` / npm |
-| [0013](./docs/adr/0013-tool-response-envelope.md) | Uniform response envelope |
-| [0014](./docs/adr/0014-e2e-harness-strategy.md) | In-memory adapter switch for E2E |
-| [0015](./docs/adr/0015-nl-excellence-response-envelope.md) | NL-excellence envelope: clarification, hints, summary |
-| [0016](./docs/adr/0016-webhook-delivery.md) | Webhook delivery for OmniFocus state changes |
-| [0017](./docs/adr/0017-mutation-testing-release-gate.md) | Stryker mutation testing as release-time hard gate |
-| [0018](./docs/adr/0018-calendar-bridge-eventkit-only.md) | Calendar bridge — EventKit-only via Swift-binary subprocess |
+| [`docs/tools.md`](./docs/tools.md) | Auto-generated reference for every tool — input schemas, examples, responses |
+| [`src/tools/INDEX.md`](./src/tools/INDEX.md) | One-line-per-tool index grouped by domain (cheaper than grepping) |
+| [`docs/examples.md`](./docs/examples.md) | Concrete prompt → tool-call sequences |
+| [`docs/prompts.md`](./docs/prompts.md) | Bundled MCP prompt templates (`daily-review`, `weekly-review`, `capture-meeting`, `project-planning`) |
+| [`AGENTS.md`](./AGENTS.md) | Agent-facing guide — engineering conventions for contributors AND calling conventions for clients (IDs, error codes, dates, idempotency, `_links`, response envelope, `meta.warnings`, rate limits) |
+| [`docs/clients/`](./docs/clients/) | Per-client setup guides (Claude Code, Claude Desktop, Codex, OpenCode, Pi, generic stdio) |
+| [`docs/troubleshooting.md`](./docs/troubleshooting.md) | OmniFocus not running, Automation permission, slow startup, raw-script gating, sync staleness |
+| [`docs/domain-reference.md`](./docs/domain-reference.md) | OmniFocus glossary, canonical schemas, lossiness matrix for export/import |
+| [`docs/security.md`](./docs/security.md) | Attack surface, mitigations, test coverage |
+| [`SECURITY.md`](./SECURITY.md) | Vulnerability reporting, scope |
+| [`SPEC.md`](./SPEC.md) | Functional scope and resolved v1 decisions |
+| [`DESIGN.md`](./DESIGN.md) | Index of the per-area design files under [`docs/design/`](./docs/design/) — architecture, envelope, IDs/dates, security, testing, observability, configuration, distribution, example tool, resources |
+| [`docs/adr/`](./docs/adr/) | Architecture Decision Records — every load-bearing choice (TypeScript+Node 24, dual transport, namespacing, raw-script gating, scripts-as-files, LRU cache, ISO-8601 dates, branded IDs, pool+queue, stdio transport, semver, npx distribution, response envelope, E2E adapter switch, NL envelope, webhooks, Stryker mutation gate, EventKit calendar bridge, cross-transport ID interop, JXA helper inlining, reactive runtime spike, envelope text/structured split) |
+| [`CHANGELOG.md`](./CHANGELOG.md) | Release history per [Keep a Changelog](https://keepachangelog.com/) |
+
+For the **full environment-variable surface** with override semantics see [`docs/design/configuration.md`](./docs/design/configuration.md); the load-bearing knobs are `OMNIFOCUS_LOG_LEVEL`, `OMNIFOCUS_CACHE_TTL_MS`, `OMNIFOCUS_ALLOW_RAW_SCRIPT`, and `OMNIFOCUS_ATTACHMENT_PATHS`.
 
 ---
 
@@ -959,4 +262,4 @@ This is a single-developer project; external contributions are not currently sol
 
 ## License
 
-[MIT](./LICENSE) — see full text in `LICENSE`.
+MIT — see [`LICENSE`](./LICENSE).