Add background process management with process tool, wait, PTY, and stdin support

New process registry and tool for managing long-running background processes
across all terminal backends (local, Docker, Singularity, Modal, SSH).

Process Registry (tools/process_registry.py):
- ProcessSession tracking with rolling 200KB output buffer
- spawn_local() with optional PTY via ptyprocess for interactive CLIs
- spawn_via_env() for non-local backends (runs inside sandbox, never on host)
- Background reader threads per process (Popen stdout or PTY)
- wait() with timeout clamping, interrupt support, and transparent limit reporting
- JSON checkpoint to ~/.hermes/processes.json for gateway crash recovery
- Module-level singleton shared across agent loop, gateway, and RL

Process Tool (model_tools.py):
- 7 actions: list, poll, log, wait, kill, write, submit
- Paired with terminal in all toolsets (CLI, messaging, RL)
- Timeout clamping with transparent notes in response

Terminal Tool Updates (tools/terminal_tool.py):
- Replaced nohup background mode with registry spawn (returns session_id)
- Added workdir parameter for per-command working directory
- Added check_interval parameter for gateway auto-check watchers
- Added pty parameter for interactive CLI tools (Codex, Claude Code)
- Updated TERMINAL_TOOL_DESCRIPTION with full background workflow docs
- Cleanup thread now respects active background processes (won't reap sandbox)

Gateway Integration (gateway/run.py, session.py, config.py):
- Session reset protection: sessions with active processes exempt from reset
- Default idle timeout increased from 2 hours to 24 hours
- from_dict fallback aligned to match (was 120, now 1440)
- session_key env var propagated to process registry for session mapping
- Crash recovery on gateway startup via checkpoint probe
- check_interval watcher: asyncio task polls process, delivers updates to platform

RL Safety (environments/):
- tool_context.py cleanup() kills background processes on episode end
- hermes_base_env.py warns when enabled_toolsets is None (loads all tools)
- Process tool safe in RL via wait() blocking the agent loop

Also:
- Added ptyprocess as optional dependency (in pyproject.toml [pty] extra + [all])
- Fixed pre-existing bug: rl_test_inference missing from TOOL_TO_TOOLSET_MAP
- Updated AGENTS.md with process management docs and project structure
- Updated README.md terminal section with process management overview

gateway/session.py

@@ -270,11 +270,15 @@ class SessionStore:
     - {session_id}.jsonl: Conversation transcripts
     """
     
-    def __init__(self, sessions_dir: Path, config: GatewayConfig):
+    def __init__(self, sessions_dir: Path, config: GatewayConfig,
+                 has_active_processes_fn=None):
         self.sessions_dir = sessions_dir
         self.config = config
         self._entries: Dict[str, SessionEntry] = {}
         self._loaded = False
+        # Optional callback to check if a session has active background processes.
+        # When set, sessions with running processes are exempt from reset.
+        self._has_active_processes_fn = has_active_processes_fn
     
     def _ensure_loaded(self) -> None:
         """Load sessions from disk if not already loaded."""
@@ -320,7 +324,14 @@ class SessionStore:
         Check if a session should be reset based on policy.
         
         Returns True if the session is stale and should start fresh.
+        Sessions with active background processes are never reset.
         """
+        # Don't reset sessions that have active background processes
+        if self._has_active_processes_fn:
+            session_key = self._generate_session_key(source)
+            if self._has_active_processes_fn(session_key):
+                return False
+
         policy = self.config.get_reset_policy(
             platform=source.platform,
             session_type=source.chat_type