refactor: remove mini-swe-agent dependency — inline Docker/Modal backends (#2804)

Drop the mini-swe-agent git submodule. All terminal backends now use
hermes-agent's own environment implementations directly.

Docker backend:
- Inline the `docker run -d` container startup (was 15 lines in
  minisweagent's DockerEnvironment). Our wrapper already handled
  execute(), cleanup(), security hardening, volumes, and resource limits.

Modal backend:
- Import swe-rex's ModalDeployment directly instead of going through
  minisweagent's 90-line passthrough wrapper.
- Bake the _AsyncWorker pattern (from environments/patches.py) directly
  into ModalEnvironment for Atropos compatibility without monkey-patching.

Cleanup:
- Remove minisweagent_path.py (submodule path resolution helper)
- Remove submodule init/install from install.sh and setup-hermes.sh
- Remove mini-swe-agent from .gitmodules
- environments/patches.py is now a no-op (kept for backward compat)
- terminal_tool.py no longer does sys.path hacking for minisweagent
- mini_swe_runner.py guards imports (optional, for RL training only)
- Update all affected tests to mock the new direct subprocess calls
- Update README.md, CONTRIBUTING.md

No functionality change — all Docker, Modal, local, SSH, Singularity,
and Daytona backends behave identically. 6093 tests pass.

cli.py

@@ -31,7 +31,7 @@ from typing import List, Dict, Any, Optional
 logger = logging.getLogger(__name__)
 
 # Suppress startup messages for clean CLI experience
-os.environ["MSWEA_SILENT_STARTUP"] = "1"  # mini-swe-agent
+os.environ["MSWEA_SILENT_STARTUP"] = "1"  # suppress mini-swe-agent startup noise if installed
 os.environ["HERMES_QUIET"] = "1"  # Our own modules
 
 import yaml
@@ -78,7 +78,7 @@ _hermes_home = Path(os.getenv("HERMES_HOME", Path.home() / ".hermes"))
 _project_env = Path(__file__).parent / '.env'
 load_hermes_dotenv(hermes_home=_hermes_home, project_env=_project_env)
 
-# Point mini-swe-agent at ~/.hermes/ so it shares our config
+# Point mini-swe-agent at ~/.hermes/ if installed (RL training use)
 os.environ.setdefault("MSWEA_GLOBAL_CONFIG_DIR", str(_hermes_home))
 
 # =============================================================================