chore: remove all remaining mini-swe-agent references

Complete cleanup after dropping the mini-swe-agent submodule (PR #2804):

- Remove MSWEA_SILENT_STARTUP and MSWEA_GLOBAL_CONFIG_DIR env var
  settings from cli.py, run_agent.py, hermes_cli/main.py, doctor.py
- Remove mini-swe-agent health check from hermes doctor
- Remove 'minisweagent' from logger suppression lists
- Remove litellm/typer/platformdirs from requirements.txt
- Remove mini-swe-agent install steps from install.ps1 (Windows)
- Remove mini-swe-agent install steps from website docs
- Update all stale comments/docstrings referencing mini-swe-agent
  in terminal_tool.py, tools/__init__.py, code_execution_tool.py,
  environments/README.md, environments/agent_loop.py
- Remove mini_swe_runner from pyproject.toml py-modules
  (still exists as standalone script for RL training use)
- Shrink test_minisweagent_path.py to empty stub

The orphaned mini-swe-agent/ directory on disk needs manual removal:
  rm -rf mini-swe-agent/

website/docs/getting-started/installation.md

@@ -132,13 +132,10 @@ You can combine extras: `uv pip install -e ".[messaging,cron]"`
 
 </details>
 
-### Step 4: Install Submodule Packages
+### Step 4: Install Optional Submodules (if needed)
 
 ```bash
-# Terminal tool backend (required for terminal/command-execution)
-uv pip install -e "./mini-swe-agent"
-
-# RL training backend
+# RL training backend (optional)
 uv pip install -e "./tinker-atropos"
 ```
 
@@ -238,7 +235,6 @@ export VIRTUAL_ENV="$(pwd)/venv"
 
 # Install everything
 uv pip install -e ".[all]"
-uv pip install -e "./mini-swe-agent"
 uv pip install -e "./tinker-atropos"
 npm install  # optional, for browser tools and WhatsApp