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.

mini_swe_runner.py

@@ -42,11 +42,13 @@ from dotenv import load_dotenv
 # Load environment variables
 load_dotenv()
 
-# Add mini-swe-agent to path if not installed. In git worktrees the populated
-# submodule may live in the main checkout rather than the worktree itself.
-from minisweagent_path import ensure_minisweagent_on_path
-
-ensure_minisweagent_on_path(Path(__file__).resolve().parent)
+# mini-swe-agent is an optional dependency for this runner.
+# Install separately: git submodule update --init mini-swe-agent && pip install -e ./mini-swe-agent
+try:
+    import minisweagent  # noqa: F401
+    _HAS_MINISWEAGENT = True
+except ImportError:
+    _HAS_MINISWEAGENT = False
 
 
 # ============================================================================
@@ -110,7 +112,10 @@ def create_environment(
     **kwargs
 ):
     """
-    Create an execution environment from mini-swe-agent.
+    Create an execution environment.
+
+    Uses mini-swe-agent environments when available, which requires the
+    mini-swe-agent submodule to be installed separately.
     
     Args:
         env_type: One of "local", "docker", "modal"
@@ -122,6 +127,12 @@ def create_environment(
     Returns:
         Environment instance with execute() method
     """
+    if not _HAS_MINISWEAGENT:
+        raise ImportError(
+            "mini-swe-agent is required for mini_swe_runner.py. "
+            "Install it: git submodule update --init mini-swe-agent && pip install -e ./mini-swe-agent"
+        )
+
     if env_type == "local":
         from minisweagent.environments.local import LocalEnvironment
         return LocalEnvironment(cwd=cwd, timeout=timeout)