docs: sync all documentation to current state (2026-04-28)

HELP.md:
- Replace stale "Agent Mode" section with accurate "Tools (⚡)" section
  including full tool table (27 tools across 9 categories)
- Fix header controls table: distinguish Context & Memory panel (sliders)
  from Settings dropdown (☰)
- Update Settings panel section: "Backend" → "Role", add S/M/L and ⌃↵
  to Display controls list
- Update Backends section to match Role toggle terminology

TODO__Agents.md:
- Mark 5 new journal tools as complete (ae_journal_list, entry_update,
  entry_disable, entry_append, entry_prepend)
- Add completed sections for: shell_exec tool, Tools toggle decoupling,
  UI input area polish (2026-04-28)

MASTER.md:
- Date: 2026-04-27 → 2026-04-28
- Orchestrator row: "Agent mode in UI" → "⚡ Tools toggle in UI (27 tools)"

CLAUDE.md:
- Date: 2026-04-03 → 2026-04-28
- Add orchestrator row to Current State table
- Add full 27-tool list for quick reference

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

CLAUDE.md

@@ -212,9 +212,9 @@ clearly asked for a directory to be unblocked.
 
 ---
 
-## Current State (2026-04-03)
+## Current State (2026-04-28)
 
-Cortex is running and stable. All three primary channels are live:
+Cortex is running and stable. All channels are live:
 
 | Channel | Status | Notes |
 |---|---|---|
@@ -222,9 +222,16 @@ Cortex is running and stable. All three primary channels are live:
 | Nextcloud Talk | ✅ Live | HMAC-signed webhook, async reply |
 | Google Chat | ✅ Live | Workspace Add-on, `hostAppDataAction` response format |
 | Local backend | ✅ Live | Open WebUI/Ollama, per-user multi-model config |
+| Orchestrator | ✅ Live | Gemini API tool loop → Claude response; ⚡ toggle in UI |
 
 Active users: scott (inara, developer), holly (tina), brian (wintermute)
 
+**27 orchestrator tools:** web_search, file_read, shell_exec, claude_allow_dir,
+task_list/create/update/complete, cron_list/add/remove/toggle,
+reminders_add/list/clear, scratch_read/write/append/clear,
+ae_journal_list/search/entry_create/entry_update/entry_disable/entry_append/entry_prepend,
+ae_task_list.
+
 See `documentation/TODO__Agents.md` for the active task list.
 See `documentation/ROADMAP.md` for phases and what's next.
 

cortex/static/HELP.md

@@ -6,7 +6,7 @@
      and are appended automatically by help.html when present.
 -->
 
-*Last updated: 2026-04-27*
+*Last updated: 2026-04-28*
 
 ---
 
@@ -15,21 +15,21 @@
 | Button | What it does |
 |---|---|
 | **Sessions** | Open the sessions panel — list, resume, or start sessions |
-| **Files** | Open the identity file editor (SOUL, MEMORY, etc.) |
+| **N** (sliders icon) | Open the Context & Memory panel (N = current context tier) |
-| **⚙ N** | Open the Settings panel (N = current context tier) |
+| **☰** | Settings menu — Files, Account, Sign Out |
 | **?** | Open this help panel |
 
-The **⚙ Settings** panel contains all configuration options:
+The **Context & Memory** panel (sliders icon with tier number) contains all configuration options:
 
 | Section | Controls |
 |---|---|
 | **Context Tier** | T1 – T4 context depth |
 | **Memory Layers** | Toggle Long / Mid / Short memory on/off |
-| **Distill Memory** | Manually trigger short / mid / long / all distillation |
+| **Distill Memory** | Manually trigger Short / Mid / Long / All distillation |
-| **Backend** | Active LLM backend — click to cycle: claude → gemini → local → auto |
+| **Role** | Active LLM role — click to cycle through configured role assignments |
-| **Display** | Aa/A+/A− font size cycle · ☾/☀ theme toggle |
+| **Display** | **Aa** cycles font size · **☾** toggles theme · **S/M/L** cycles input area height · **⌃↵** toggles send shortcut |
 
-All header settings (theme, font size, tier, memory layers) persist in `localStorage` across page refreshes.
+All settings persist in `localStorage` across page refreshes.
 
 ---
 
@@ -46,22 +46,36 @@ Each assistant response shows a small **model tag** in the bottom-right corner i
 
 ---
 
-## Agent Mode
+## Tools (⚡)
 
-Click the **Agent** button in the input row to enable Agent mode. The button highlights and Send changes to **Run**.
+Click the **⚡** button in the input row to enable the Tools toggle. When lit (amber), **Send** changes to **Run** and messages are routed through the **orchestrator** instead of directly to the chat model.
 
-In Agent mode, messages are routed through the **orchestrator** instead of directly to the chat model:
+The orchestrator runs a multi-step tool loop:
 
-1. The **orchestrator model** runs a tool loop — searches the web, reads files, checks tasks, calls APIs as needed
+1. The **orchestrator model** reasons about the request and calls tools as needed — web search, file reads, task management, shell commands, Aether Journals, and more
 2. It produces an enriched summary of what it found
-3. The **responder model** receives that context and writes the final user-facing reply
+3. The **responder model** (set by the active Role) receives that context and writes the final user-facing reply
 4. A `⚡ N tool calls: …` note appears below the response listing what was used
 
-Which model acts as orchestrator is set in **Settings → Models → Role Assignments → Orchestrator**. By default this is Gemini API; a capable local model can be assigned instead.
+The ⚡ toggle is **independent of the Role selector** — you can use any role (chat, coder, research, etc.) with or without tools. The orchestrator model is configured in **Account → Model Registry → Role Assignments → Orchestrator**. By default this is Gemini API.
 
-Agent mode is best for tasks that require research, multi-step reasoning, or tool use (e.g. "search for X", "add a task", "what's on my list?"). Regular chat is faster for conversational turns.
+**Available tools:**
 
-Agent mode sessions persist to history exactly like regular chat.
+| Category | Tools |
+|---|---|
+| Web | `web_search` |
+| Files | `file_read` |
+| Shell | `shell_exec`, `claude_allow_dir` |
+| Tasks | `task_list`, `task_create`, `task_update`, `task_complete` |
+| Cron | `cron_list`, `cron_add`, `cron_remove`, `cron_toggle` |
+| Reminders | `reminders_add`, `reminders_list`, `reminders_clear` |
+| Scratchpad | `scratch_read`, `scratch_write`, `scratch_append`, `scratch_clear` |
+| Aether Journals | `ae_journal_list`, `ae_journal_search`, `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` |
+
+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.
+
+Orchestrated sessions persist to history exactly like regular chat.
 
 ---
 
@@ -97,11 +111,11 @@ Three backends are available:
 | **Gemini** | Google Gemini via the Gemini CLI |
 | **Local** | Any OpenAI-compatible endpoint (Open WebUI, Ollama, OpenRouter, etc.) |
 
-The **⚙ Backend** toggle cycles: **auto → claude → gemini → local → auto**
+The **Role** toggle in the Context & Memory panel cycles through configured role assignments. Each role maps to a Primary / Backup 1 / Backup 2 model chain set in the Model Registry.
 
-- **auto** uses the model assigned to the `chat` role in your Model Registry (recommended)
+- The active model label appears below the toggle button
-- Selecting a specific backend forces that backend for all messages, regardless of role assignments
+- `auto` (default) uses the model assigned to the `chat` role in your Model Registry
-- The active model label appears below the toggle button when a specific backend is active
+- Forcing a specific backend overrides the role assignment for that session
 
 If the active backend fails, a fallback is tried automatically. A **⚡** badge appears on the response when this happens.
 

documentation/MASTER.md

@@ -1,7 +1,7 @@
 # Cortex / Inara — Master Index
 
 > Start here. This document is a map, not a manual.
-> Last updated: 2026-04-27
+> Last updated: 2026-04-28
 
 ---
 
@@ -23,7 +23,7 @@ Cortex is a self-hosted personal AI platform. It routes messages from any input
 | Claude backend | ✅ Live | Primary — via Claude Code CLI |
 | Gemini backend | ✅ Live | Fallback — via Gemini CLI |
 | Local backend | ✅ Live | Third option — Open WebUI/Ollama on scott_gaming |
-| Gemini orchestrator | ✅ Live | Tool loop → Claude response, Agent mode in UI |
+| Gemini orchestrator | ✅ Live | Tool loop → Claude response, ⚡ Tools toggle in UI (27 tools) |
 | Model registry V2 | ✅ Live | Providers (Anthropic/Google/Local), multi-account Gemini |
 | Memory distillation | ✅ Live | Short (daily) / Mid (weekly) / Long (monthly) |
 | Multi-user | ✅ Live | Scott, Holly, Brian — each with own personas |

documentation/TODO__Agents.md

@@ -36,8 +36,13 @@ See `DESIGN__Model_Registry_V2.md` for full design.
 
 ### [Intelligence] Knowledge consolidation — Phase 1
 See `ARCH__Intelligence_Layer.md` for full design.
+- [x] Tool: `ae_journal_list` — list all journals for the account — 2026-04-28
 - [x] Tool: `ae_journal_search` — search before creating to avoid duplicates
 - [x] Tool: `ae_journal_entry_create` — write a new entry with source metadata
+- [x] Tool: `ae_journal_entry_update` — PATCH any fields on an existing entry — 2026-04-28
+- [x] Tool: `ae_journal_entry_disable` — soft-delete via enable=false — 2026-04-28
+- [x] Tool: `ae_journal_entry_append` — read→append timestamped section→write (running logs) — 2026-04-28
+- [x] Tool: `ae_journal_entry_prepend` — read→prepend timestamped section→write (newest-first logs) — 2026-04-28
 - [ ] Import script: walk a markdown directory, chunk by H2 section, create entries
 - [ ] Target: markdown files from `~/DgrZone_Nextcloud/` and `~/OSIT_Nextcloud/`
 - [ ] Tag strategy: source path, date, topic tags from frontmatter or filename
@@ -99,6 +104,32 @@ base accessible to local models. Endpoints documented in `docs/OPEN_WEBUI_API.md
 
 ## ✅ Completed
 
+### [UI] Input area polish — 2026-04-28
+- Single cycling S/M/L button replaces 3 separate height buttons (same UX as font size)
+- S size collapses mode-select to a row (compact); M/L keep vertical column layout
+- Input height minimum derived from setting so empty textarea reflects selected size
+- Context & Memory panel and Settings dropdown are mutually exclusive (closeAllPanels fix)
+- Both panels now use consistent shadow (var(--shadow)) and z-index (200)
+
+### [Tools] Tools toggle — decoupled from Role/Backend — 2026-04-28
+- Removed "Agent" mode from the mode selector; replaced with independent ⚡ toggle
+- `toolsEnabled` persists in localStorage; routes to orchestrator regardless of active mode
+- Layout: column (M/L) or row (S) driven by `data-size` attribute set by JS
+- chat_role flows from UI → OrchestrateRequest → orchestrator_engine.run(response_role=...)
+
+### [Tools] shell_exec tool — 2026-04-28
+- `shell_exec(command, working_dir, timeout)` in `cortex/tools/system.py`
+- Runs any shell command on the Cortex host; timeout clamped 1–120s
+- Use for system diagnostics: `df -h`, `ps aux`, `journalctl`, `free -h`, etc.
+
+### [Tools] Aether Journals full toolkit — 2026-04-28
+- `ae_journal_list` — list all journals + ids for the account
+- `ae_journal_entry_update` — PATCH any fields (title, content, summary, tags, enable)
+- `ae_journal_entry_disable` — soft-delete via enable=false
+- `ae_journal_entry_append` — read→append timestamped section→write (running/data logs)
+- `ae_journal_entry_prepend` — read→prepend timestamped section→write (newest-first)
+- Shared `_get_entry` / `_patch_entry` helpers; OpenAI JSON Schema auto-derived from Gemini declarations
+
 ### [Local] Per-user multi-model local LLM settings — 2026-04-01
 - `home/{username}/local_llm.json` — `hosts[]` + `models[]` + `active_model_id` structure
 - `cortex/user_settings.py` — CRUD functions: save_host, add_model, remove_model, set_active_model, get_active_local_model