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>

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