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.

pyproject.toml

@@ -90,7 +90,7 @@ hermes-agent = "run_agent:main"
 hermes-acp = "acp_adapter.entry:main"
 
 [tool.setuptools]
-py-modules = ["run_agent", "model_tools", "toolsets", "batch_runner", "trajectory_compressor", "toolset_distributions", "cli", "hermes_constants", "hermes_state", "hermes_time", "mini_swe_runner", "minisweagent_path", "rl_cli", "utils"]
+py-modules = ["run_agent", "model_tools", "toolsets", "batch_runner", "trajectory_compressor", "toolset_distributions", "cli", "hermes_constants", "hermes_state", "hermes_time", "mini_swe_runner", "rl_cli", "utils"]
 
 [tool.setuptools.packages.find]
 include = ["agent", "tools", "tools.*", "hermes_cli", "gateway", "gateway.*", "cron", "honcho_integration", "acp_adapter"]