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

environments/hermes_base_env.py

@@ -258,6 +258,11 @@ class HermesAgentBaseEnv(BaseEnv):
             logger.info("Sampled toolsets from '%s': %s", config.distribution, group_toolsets)
         else:
             group_toolsets = config.enabled_toolsets  # None means "all available"
+            if group_toolsets is None:
+                logger.warning(
+                    "enabled_toolsets is None -- loading ALL tools including messaging. "
+                    "Set explicit enabled_toolsets for RL training."
+                )
 
         tools = get_tool_definitions(
             enabled_toolsets=group_toolsets,

environments/tool_context.py

@@ -438,11 +438,21 @@ class ToolContext:
 
     def cleanup(self):
         """
-        Release all resources (terminal VMs, browser sessions) for this rollout.
+        Release all resources (terminal VMs, browser sessions, background processes)
+        for this rollout.
 
         Called automatically by the base environment via try/finally after
         compute_reward() completes. You generally don't need to call this yourself.
         """
+        # Kill any background processes from this rollout (safety net)
+        try:
+            from tools.process_registry import process_registry
+            killed = process_registry.kill_all(task_id=self.task_id)
+            if killed:
+                logger.debug("Process cleanup for task %s: killed %d process(es)", self.task_id, killed)
+        except Exception as e:
+            logger.debug("Process cleanup for task %s: %s", self.task_id, e)
+
         try:
             cleanup_vm(self.task_id)
         except Exception as e: