docs: expand tools section in HELP.md with per-tool descriptions

Replaces single flat table with category sections, each with a description
column. Footnotes moved to the top of the section for clarity. Covers all
30 tools including the new cortex_status, cortex_update, reminders_remove,
ae_journal_entry_read, ae_journal_entries_list, and email_send.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

cortex/static/HELP.md

@@ -61,22 +61,102 @@ The ⚡ toggle is **independent of the Role selector** — you can use any role
 
 **Available tools:**
 
-| Category | Tools |
+¹ Admin only — requires the `admin` role. Invisible to regular users.
-|---|---|
+² Confirmation required — the orchestrator pauses and shows Confirm / Deny buttons before executing.
-| Web | `web_search`, `http_fetch` |
-| Files | `file_read` ¹, `file_list` ¹, `file_write` ¹ ² |
-| Shell | `shell_exec` ¹ ², `claude_allow_dir` ¹ |
-| System | `cortex_restart` ¹ ², `cortex_logs` ¹, `cortex_status` ¹, `cortex_update` ¹ ² |
-| Tasks | `task_list`, `task_create`, `task_update`, `task_complete` |
-| Cron | `cron_list`, `cron_add`, `cron_remove` ², `cron_toggle` |
-| Reminders | `reminders_add`, `reminders_list`, `reminders_remove`, `reminders_clear` ² |
-| Scratchpad | `scratch_read`, `scratch_write`, `scratch_append`, `scratch_clear` |
-| Notifications | `email_send` ¹, `nc_talk_send` ¹ |
-| Aether Journals | `ae_journal_list`, `ae_journal_search`, `ae_journal_entries_list`, `ae_journal_entry_read`, `ae_journal_entry_create`, `ae_journal_entry_update`, `ae_journal_entry_disable`, `ae_journal_entry_append`, `ae_journal_entry_prepend` |
-| Aether Tasks | `ae_task_list` ¹ |
 
-¹ **Admin only** — requires the `admin` role. These tools are invisible to regular users.  
+**Web**
-² **Confirmation required** — the orchestrator pauses and asks you to confirm before executing. Reply to confirm and it will proceed.
+
+| Tool | What it does |
+|---|---|
+| `web_search` | DuckDuckGo search — returns titles, URLs, and snippets for the top results |
+| `http_fetch` | Fetch a specific URL and return the response body (8 192 char cap) |
+
+**Files** ¹
+
+| Tool | What it does |
+|---|---|
+| `file_read` ¹ | Read any file under the persona home directory |
+| `file_list` ¹ | List files and directories with sizes (200 entry cap) |
+| `file_write` ¹ ² | Write or append to a file under the persona home directory |
+
+**Shell** ¹
+
+| Tool | What it does |
+|---|---|
+| `shell_exec` ¹ ² | Run any shell command on the Cortex host; timeout 1–120 s |
+| `claude_allow_dir` ¹ | Add a directory to Claude Code's auto-allowed paths |
+
+**System** ¹
+
+| Tool | What it does |
+|---|---|
+| `cortex_restart` ¹ ² | Restart the Cortex service (5 s delay); connection drops — refresh the page |
+| `cortex_logs` ¹ | Recent lines from the systemd journal (default 50, max 200) |
+| `cortex_status` ¹ | Current git branch, commit, ahead/behind remote, and service state |
+| `cortex_update` ¹ ² | `git pull` + syntax check all `.py` files; reports what changed. Does **not** restart automatically — call `cortex_restart` after reviewing |
+
+**Tasks**
+
+| Tool | What it does |
+|---|---|
+| `task_list` | List personal tasks; pass `include_done=true` to include completed |
+| `task_create` | Create a task with title, optional notes and due date |
+| `task_update` | Update any fields on an existing task |
+| `task_complete` | Mark a task as complete |
+
+**Cron**
+
+| Tool | What it does |
+|---|---|
+| `cron_list` | List all scheduled jobs for this persona |
+| `cron_add` | Add a scheduled job — accepts cron syntax or plain-English interval |
+| `cron_remove` ² | Remove a scheduled job by ID |
+| `cron_toggle` | Enable or disable a job without removing it |
+
+**Reminders**
+
+| Tool | What it does |
+|---|---|
+| `reminders_add` | Add a reminder with optional label; surfaced in context at Tier 2+ |
+| `reminders_list` | List all pending reminders, numbered for easy removal |
+| `reminders_remove` | Remove a single reminder by number (call `reminders_list` first) |
+| `reminders_clear` ² | Clear all reminders at once |
+
+**Scratchpad**
+
+| Tool | What it does |
+|---|---|
+| `scratch_read` | Read the current scratchpad |
+| `scratch_write` | Overwrite the scratchpad with new content |
+| `scratch_append` | Append a timestamped section to the scratchpad |
+| `scratch_clear` | Erase the scratchpad |
+
+**Notifications** ¹
+
+| Tool | What it does |
+|---|---|
+| `email_send` ¹ | Send an email via SMTP; recipient must match your `email_allowlist.json` |
+| `nc_talk_send` ¹ | Send a message to a Nextcloud Talk conversation |
+
+**Aether Journals**
+
+| Tool | What it does |
+|---|---|
+| `ae_journal_list` | List all journals for the configured AE account (returns names + IDs) |
+| `ae_journal_search` | Search entries by keyword, tag, date range, type, status, or priority |
+| `ae_journal_entries_list` | Browse all entries in a specific journal, newest first; paginated |
+| `ae_journal_entry_read` | Read the full content of a single entry by ID |
+| `ae_journal_entry_create` | Create a new entry with title, content, tags, and summary |
+| `ae_journal_entry_update` | Patch any fields on an existing entry (title, content, tags, summary, enable) |
+| `ae_journal_entry_disable` | Soft-delete an entry (`enable=false`) without permanently removing it |
+| `ae_journal_entry_append` | Append a timestamped section to the bottom of an entry's content |
+| `ae_journal_entry_prepend` | Prepend a timestamped section to the top of an entry's content |
+
+**Aether Tasks** ¹
+
+| Tool | What it does |
+|---|---|
+| `ae_task_list` ¹ | List tasks from the agents_sync Kanban board (admin only) |
 
 Tools mode is best for tasks requiring research, multi-step reasoning, or side effects (e.g. "search for X", "add a task", "what's on my list?", "append this to my journal"). Regular chat is faster for conversational turns.