Merge origin/main into atropos-integrations

Merged main's latest changes including:
- New hermes_cli/ unified CLI commands
- File operations tools, fuzzy match, patch parser
- RL training tools and tinker-atropos submodule
- Enhanced batch_runner and run_agent
- Gateway improvements (Telegram, Discord)
- Cron job management
- Installation scripts

Preserved our branch-specific features:
- Modal backend (atropos/backends/modal_backend.py)
- Modal terminal tool integration (ModalProfile, _ModalSandboxPool, etc.)
- Singularity/Apptainer support
- Atropos AgentEnv Modal config fields
- Combined pyproject.toml extras (atropos + messaging + cron + cli)

Conflict resolution:
- cli.py, model_tools.py, README.md: accepted main (newer features)
- pyproject.toml: combined both extras and package lists
- tools/terminal_tool.py: accepted main's base + re-inserted Modal integration

.gitignore

@@ -39,6 +39,10 @@ agent-browser/
 *.pem
 privvy*
 images/
+__pycache__/
+hermes_agent.egg-info/
+wandb/
+testlogs
 
 # CLI config (may contain sensitive SSH paths)
 cli-config.yaml