feat: add shell_exec tool and fix orchestrator model name resolution

- Add shell_exec to orchestrator tool suite (system.py + __init__.py)
  Runs arbitrary shell commands on the Cortex host with timeout (1–120s),
  combined stdout/stderr output, optional working_dir, and exit code reporting.
  Enables system diagnostics (df, ls, ps, journalctl, etc.) from Agent mode.

- Fix orchestrator_engine.run() to use model_name from resolved registry entry
  Previously used settings.orchestrator_model (.env hardcode) regardless of
  what model was assigned to the orchestrator role. Now accepts model_name param
  and falls back to settings value only when registry has no model_name.

- Update ARCH__FUTURE.md: date, running host, local orchestrator status,
  model registry V2 progress, added Cortex Mesh concept (section 9)

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

cortex/tools/__init__.py

@@ -20,7 +20,7 @@ from tools.ae_knowledge import journal_search as _ae_journal_search
 from tools.ae_knowledge import journal_entry_create as _ae_journal_entry_create
 from tools.ae_tasks import task_list as _ae_task_list
 from tools.files import file_read as _file_read
-from tools.system import claude_allow_dir as _claude_allow_dir
+from tools.system import claude_allow_dir as _claude_allow_dir, shell_exec as _shell_exec
 from tools.tasks import task_list as _task_list, task_create as _task_create
 from tools.tasks import task_update as _task_update, task_complete as _task_complete
 from tools.cron import (
@@ -192,6 +192,7 @@ _CALLABLES: dict[str, callable] = {
     "ae_task_list": _ae_task_list,
     "file_read": _file_read,
     "claude_allow_dir": _claude_allow_dir,
+    "shell_exec": _shell_exec,
     "task_list": _task_list,
     "task_create": _task_create,
     "task_update": _task_update,
@@ -236,6 +237,35 @@ _claude_allow_dir_declaration = types.FunctionDeclaration(
     ),
 )
 
+_shell_exec_declaration = 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"],
+    ),
+)
+
 _task_list_declaration = types.FunctionDeclaration(
     name="task_list",
     description=(
@@ -526,6 +556,7 @@ TOOL_DECLARATIONS = [
         _ae_task_list_declaration,
         _file_read_declaration,
         _claude_allow_dir_declaration,
+        _shell_exec_declaration,
         _task_list_declaration,
         _task_create_declaration,
         _task_update_declaration,