feat(environments): unified spawn-per-call execution layer

Replace dual execution model (PersistentShellMixin + per-backend oneshot)
with spawn-per-call + session snapshot for all backends except ManagedModal.

Core changes:
- Every command spawns a fresh bash process; session snapshot (env vars,
  functions, aliases) captured at init and re-sourced before each command
- CWD persists via file-based read (local) or in-band stdout markers (remote)
- ProcessHandle protocol + _ThreadedProcessHandle adapter for SDK backends
- cancel_fn wired for Modal (sandbox.terminate) and Daytona (sandbox.stop)
- Shared utilities extracted: _pipe_stdin, _popen_bash, _load_json_store,
  _save_json_store, _file_mtime_key, _SYNC_INTERVAL_SECONDS
- Rate-limited file sync unified in base _before_execute() with _sync_files() hook
- execute_oneshot() removed; all 11 call sites in code_execution_tool.py
  migrated to execute()
- Daytona timeout wrapper replaced with SDK-native timeout parameter
- persistent_shell.py deleted (291 lines)

Backend-specific:
- Local: process-group kill via os.killpg, file-based CWD read
- Docker: -e env flags only on init_session, not per-command
- SSH: shlex.quote transport, ControlMaster connection reuse
- Singularity: apptainer exec with instance://, no forced --pwd
- Modal: _AsyncWorker + _ThreadedProcessHandle, cancel_fn -> sandbox.terminate
- Daytona: SDK-level timeout (not shell wrapper), cancel_fn -> sandbox.stop
- ManagedModal: unchanged (gateway owns execution); docstring added explaining why

tools/terminal_tool.py

@@ -611,9 +611,7 @@ def _create_environment(env_type: str, image: str, cwd: str, timeout: int,
     docker_env = cc.get("docker_env", {})
 
     if env_type == "local":
-        lc = local_config or {}
-        return _LocalEnvironment(cwd=cwd, timeout=timeout,
-                                 persistent=lc.get("persistent", False))
+        return _LocalEnvironment(cwd=cwd, timeout=timeout)
     
     elif env_type == "docker":
         return _DockerEnvironment(
@@ -705,7 +703,6 @@ def _create_environment(env_type: str, image: str, cwd: str, timeout: int,
             key_path=ssh_config.get("key", ""),
             cwd=cwd,
             timeout=timeout,
-            persistent=ssh_config.get("persistent", False),
         )
 
     else: