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/

scripts/install.ps1

@@ -505,7 +505,7 @@ function Install-Repository {
     git -c windows.appendAtomically=false config windows.appendAtomically false 2>$null
 
     # Ensure submodules are initialized and updated
-    Write-Info "Initializing submodules (mini-swe-agent, tinker-atropos)..."
+    Write-Info "Initializing submodules..."
     git -c windows.appendAtomically=false submodule update --init --recursive 2>$null
     if ($LASTEXITCODE -ne 0) {
         Write-Warn "Submodule init failed (terminal/RL tools may need manual setup)"
@@ -559,19 +559,7 @@ function Install-Dependencies {
     
     Write-Success "Main package installed"
     
-    # Install submodules
-    Write-Info "Installing mini-swe-agent (terminal tool backend)..."
-    if (Test-Path "mini-swe-agent\pyproject.toml") {
-        try {
-            & $UvCmd pip install -e ".\mini-swe-agent" 2>&1 | Out-Null
-            Write-Success "mini-swe-agent installed"
-        } catch {
-            Write-Warn "mini-swe-agent install failed (terminal tools may not work)"
-        }
-    } else {
-        Write-Warn "mini-swe-agent not found (run: git submodule update --init)"
-    }
-    
+    # Install optional submodules
     Write-Info "Installing tinker-atropos (RL training backend)..."
     if (Test-Path "tinker-atropos\pyproject.toml") {
         try {