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/run.py

@@ -72,7 +72,13 @@ class GatewayRunner:
     def __init__(self, config: Optional[GatewayConfig] = None):
         self.config = config or load_gateway_config()
         self.adapters: Dict[Platform, BasePlatformAdapter] = {}
-        self.session_store = SessionStore(self.config.sessions_dir, self.config)
+
+        # Wire process registry into session store for reset protection
+        from tools.process_registry import process_registry
+        self.session_store = SessionStore(
+            self.config.sessions_dir, self.config,
+            has_active_processes_fn=lambda key: process_registry.has_active_for_session(key),
+        )
         self.delivery_router = DeliveryRouter(self.config)
         self._running = False
         self._shutdown_event = asyncio.Event()
@@ -106,6 +112,15 @@ class GatewayRunner:
         # Discover and load event hooks
         self.hooks.discover_and_load()
         
+        # Recover background processes from checkpoint (crash recovery)
+        try:
+            from tools.process_registry import process_registry
+            recovered = process_registry.recover_from_checkpoint()
+            if recovered:
+                print(f"[gateway] Recovered {recovered} background process(es) from previous run")
+        except Exception as e:
+            print(f"[gateway] Process checkpoint recovery: {e}")
+        
         connected_count = 0
         
         # Initialize and connect each configured platform
@@ -429,6 +444,15 @@ class GatewayRunner:
                 "response": (response or "")[:500],
             })
             
+            # Check for pending process watchers (check_interval on background processes)
+            try:
+                from tools.process_registry import process_registry
+                while process_registry.pending_watchers:
+                    watcher = process_registry.pending_watchers.pop(0)
+                    asyncio.create_task(self._run_process_watcher(watcher))
+            except Exception as e:
+                print(f"[gateway] Process watcher setup error: {e}", flush=True)
+
             # Check if the agent encountered a dangerous command needing approval
             # The terminal tool stores the last pending approval globally
             try:
@@ -701,6 +725,75 @@ class GatewayRunner:
             return prefix
         return user_text
 
+    async def _run_process_watcher(self, watcher: dict) -> None:
+        """
+        Periodically check a background process and push updates to the user.
+
+        Runs as an asyncio task. Stays silent when nothing changed.
+        Auto-removes when the process exits or is killed.
+        """
+        from tools.process_registry import process_registry
+
+        session_id = watcher["session_id"]
+        interval = watcher["check_interval"]
+        session_key = watcher.get("session_key", "")
+        platform_name = watcher.get("platform", "")
+        chat_id = watcher.get("chat_id", "")
+
+        print(f"[gateway] Process watcher started: {session_id} (every {interval}s)", flush=True)
+
+        last_output_len = 0
+        while True:
+            await asyncio.sleep(interval)
+
+            session = process_registry.get(session_id)
+            if session is None:
+                break
+
+            current_output_len = len(session.output_buffer)
+            has_new_output = current_output_len > last_output_len
+            last_output_len = current_output_len
+
+            if session.exited:
+                # Process finished -- deliver final update
+                new_output = session.output_buffer[-1000:] if session.output_buffer else ""
+                message_text = (
+                    f"[Background process {session_id} finished with exit code {session.exit_code}~ "
+                    f"Here's the final output:\n{new_output}]"
+                )
+                # Try to deliver to the originating platform
+                adapter = None
+                for p, a in self.adapters.items():
+                    if p.value == platform_name:
+                        adapter = a
+                        break
+                if adapter and chat_id:
+                    try:
+                        await adapter.send(chat_id, message_text)
+                    except Exception as e:
+                        print(f"[gateway] Watcher delivery error: {e}", flush=True)
+                break
+
+            elif has_new_output:
+                # New output available -- deliver status update
+                new_output = session.output_buffer[-500:] if session.output_buffer else ""
+                message_text = (
+                    f"[Background process {session_id} is still running~ "
+                    f"New output:\n{new_output}]"
+                )
+                adapter = None
+                for p, a in self.adapters.items():
+                    if p.value == platform_name:
+                        adapter = a
+                        break
+                if adapter and chat_id:
+                    try:
+                        await adapter.send(chat_id, message_text)
+                    except Exception as e:
+                        print(f"[gateway] Watcher delivery error: {e}", flush=True)
+
+        print(f"[gateway] Process watcher ended: {session_id}", flush=True)
+
     async def _run_agent(
         self,
         message: str,
@@ -824,6 +917,10 @@ class GatewayRunner:
         tools_holder = [None]   # Mutable container for the tool definitions
         
         def run_sync():
+            # Pass session_key to process registry via env var so background
+            # processes can be mapped back to this gateway session
+            os.environ["HERMES_SESSION_KEY"] = session_key or ""
+
             # Read from env var or use default (same as CLI)
             max_iterations = int(os.getenv("HERMES_MAX_ITERATIONS", "60"))