refactor: split tool declarations into domain files + role config UI

tools/__init__.py shrinks from 1,137 → 250 lines. Each domain file now
owns both its callables and its FunctionDeclarations (DECLARATIONS list),
so adding a new tool only touches one file.

New TOOL_CATEGORIES dict exported from __init__ — used by the UI for
grouped tool checkboxes.

Role config UI (Settings → Model Registry → Role Assignments):
- ⚙ button per role expands an inline configure panel
- Textarea for system_append (injected into system prompt for this role)
- Grouped checkboxes for tool allow-list (all checked = no restriction)
- POST /api/models/role-config saves both fields; updates ROLE_CONFIG_DATA
  in-page so re-open reflects current state without a page reload

Backend:
- model_registry.set_role_config() writes system_append + tools to registry
- TOOL_CATEGORIES exported from tools/__init__ for UI rendering
- TOOLS.md header updated: 30 → 39 tools (ae_journal_* and cortex_* additions)

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

cortex/tools/system.py

@@ -11,6 +11,8 @@ import os
 import subprocess
 from pathlib import Path
 
+from google.genai import types
+
 logger = logging.getLogger(__name__)
 
 # Absolute paths — resolved relative to this file so they work regardless of cwd
@@ -246,3 +248,87 @@ async def cortex_update() -> str:
         lines.append("Call `cortex_restart` to apply the update.")
 
     return "\n".join(lines)
+
+
+DECLARATIONS = [
+    types.FunctionDeclaration(
+        name="shell_exec",
+        description=(
+            "Execute a shell command on the Cortex host machine and return its output. "
+            "Use for system diagnostics: disk usage (df -h), process status (ps aux), "
+            "directory listings (ls), memory (free -h), uptime, network info, log tails, etc. "
+            "Commands run as the Cortex service user. Timeout enforced (default 30s, max 120s). "
+            "Avoid destructive commands — prefer read-only system queries."
+        ),
+        parameters=types.Schema(
+            type=types.Type.OBJECT,
+            properties={
+                "command": types.Schema(type=types.Type.STRING, description="Shell command to run (e.g. 'df -h', 'ls ~/agents_sync/', 'journalctl --user -u cortex -n 50')"),
+                "working_dir": types.Schema(type=types.Type.STRING, description="Optional working directory (e.g. '~/agents_sync/projects'). Defaults to home directory."),
+                "timeout": types.Schema(type=types.Type.INTEGER, description="Timeout in seconds (default 30, max 120)"),
+            },
+            required=["command"],
+        ),
+    ),
+    types.FunctionDeclaration(
+        name="claude_allow_dir",
+        description=(
+            "Add a directory to Claude Code's auto-allow list so Claude can read or write "
+            "files there without prompting. Edits ~/.claude/settings.json on the local machine. "
+            "Use this when Claude is silently hanging or being blocked from accessing a directory. "
+            "Changes take effect in the next Claude Code session."
+        ),
+        parameters=types.Schema(
+            type=types.Type.OBJECT,
+            properties={
+                "path": types.Schema(type=types.Type.STRING, description="Absolute or home-relative path to the directory (e.g. ~/OSIT_dev/aether_api_fastapi or /home/scott/agents_sync)"),
+                "mode": types.Schema(type=types.Type.STRING, description="Permission mode: 'r' (read-only), 'w' (write-only), or 'rw' (both). Default: rw"),
+            },
+            required=["path"],
+        ),
+    ),
+    types.FunctionDeclaration(
+        name="cortex_restart",
+        description=(
+            "Restart the Cortex service via systemd. Schedules a restart 5 seconds from now. "
+            "The current connection will drop — inform the user to refresh the page. "
+            "Use after config changes, memory edits, or when the service needs a fresh start. "
+            "ADMIN ONLY."
+        ),
+        parameters=types.Schema(type=types.Type.OBJECT, properties={}),
+    ),
+    types.FunctionDeclaration(
+        name="cortex_logs",
+        description=(
+            "Fetch recent lines from the Cortex systemd service journal. "
+            "Use for debugging errors, checking startup status, or reviewing recent activity. "
+            "ADMIN ONLY."
+        ),
+        parameters=types.Schema(
+            type=types.Type.OBJECT,
+            properties={
+                "lines": types.Schema(type=types.Type.INTEGER, description="Number of log lines to return (default 50, max 200)"),
+            },
+        ),
+    ),
+    types.FunctionDeclaration(
+        name="cortex_status",
+        description=(
+            "Return Cortex service status: current git branch and commit, how many commits "
+            "ahead/behind the remote, and the systemctl service state. "
+            "Use to check what version is running or whether the service is healthy. "
+            "ADMIN ONLY."
+        ),
+        parameters=types.Schema(type=types.Type.OBJECT, properties={}),
+    ),
+    types.FunctionDeclaration(
+        name="cortex_update",
+        description=(
+            "Pull the latest code from git, run a syntax check on all Python files, and report "
+            "what changed. Does NOT restart automatically — call cortex_restart separately after "
+            "reviewing the output. Will report syntax errors if the pull introduces broken code. "
+            "ADMIN ONLY. Requires confirmation."
+        ),
+        parameters=types.Schema(type=types.Type.OBJECT, properties={}),
+    ),
+]