diff --git a/.gitignore b/.gitignore
index 36dbfc2..fd59029 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,5 +17,4 @@ docs/
 __pycache__/
 poetry.lock
 .pytest_cache/
-tests/
 botpy.log
diff --git a/nanobot/cli/commands.py b/nanobot/cli/commands.py
index 3ced25e..4e61deb 100644
--- a/nanobot/cli/commands.py
+++ b/nanobot/cli/commands.py
@@ -177,18 +177,12 @@ def onboard():
     # Create workspace
     workspace = get_workspace_path()
     
-    create_templates = True
-    if workspace.exists():
-        console.print(f"[yellow]Workspace already exists at {workspace}[/yellow]")
-        if not typer.confirm("Create missing default templates? (will not overwrite existing files)"):
-            create_templates = False
-    else:
+    if not workspace.exists():
         workspace.mkdir(parents=True, exist_ok=True)
         console.print(f"[green]✓[/green] Created workspace at {workspace}")
     
     # Create default bootstrap files
-    if create_templates:
-        _create_workspace_templates(workspace)
+    _create_workspace_templates(workspace)
     
     console.print(f"\n{__logo__} nanobot is ready!")
     console.print("\nNext steps:")
diff --git a/tests/test_commands.py b/tests/test_commands.py
new file mode 100644
index 0000000..462973f
--- /dev/null
+++ b/tests/test_commands.py
@@ -0,0 +1,134 @@
+import os
+import shutil
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
+import pytest
+from typer.testing import CliRunner
+
+from nanobot.cli.commands import app
+
+runner = CliRunner()
+
+
+@pytest.fixture
+def mock_paths():
+    """Mock configuration and workspace paths for isolation."""
+    with patch("nanobot.config.loader.get_config_path") as mock_config_path, \
+         patch("nanobot.config.loader.save_config") as mock_save_config, \
+         patch("nanobot.utils.helpers.get_workspace_path") as mock_ws_path:
+        
+        # Create temporary paths
+        base_dir = Path("./test_onboard_data")
+        if base_dir.exists():
+            shutil.rmtree(base_dir)
+        base_dir.mkdir()
+        
+        config_file = base_dir / "config.json"
+        workspace_dir = base_dir / "workspace"
+        
+        mock_config_path.return_value = config_file
+        mock_ws_path.return_value = workspace_dir
+        
+        # We need save_config to actually write the file for existence checks to work
+        def side_effect_save_config(config):
+            with open(config_file, "w") as f:
+                f.write("{}")
+
+        mock_save_config.side_effect = side_effect_save_config
+        
+        yield config_file, workspace_dir
+        
+        # Cleanup
+        if base_dir.exists():
+            shutil.rmtree(base_dir)
+
+
+def test_onboard_fresh_install(mock_paths):
+    """Test onboarding with no existing files."""
+    config_file, workspace_dir = mock_paths
+    
+    result = runner.invoke(app, ["onboard"])
+    
+    assert result.exit_code == 0
+    assert "Created config" in result.stdout
+    assert "Created workspace" in result.stdout
+    assert "nanobot is ready" in result.stdout
+    
+    assert config_file.exists()
+    assert workspace_dir.exists()
+    assert (workspace_dir / "AGENTS.md").exists()
+    assert (workspace_dir / "memory" / "MEMORY.md").exists()
+
+
+def test_onboard_existing_config_no_overwrite(mock_paths):
+    """Test onboarding with existing config, user declines overwrite."""
+    config_file, workspace_dir = mock_paths
+    
+    # Pre-create config
+    config_file.write_text('{"existing": true}')
+    
+    # Input "n" for overwrite prompt
+    result = runner.invoke(app, ["onboard"], input="n\n")
+    
+    assert result.exit_code == 0
+    assert "Config already exists" in result.stdout
+    
+    # Verify config was NOT changed
+    assert '{"existing": true}' in config_file.read_text()
+    
+    # Verify workspace was still created
+    assert "Created workspace" in result.stdout
+    assert workspace_dir.exists()
+    assert (workspace_dir / "AGENTS.md").exists()
+
+
+def test_onboard_existing_config_overwrite(mock_paths):
+    """Test onboarding with existing config, user checks overwrite."""
+    config_file, workspace_dir = mock_paths
+    
+    # Pre-create config
+    config_file.write_text('{"existing": true}')
+    
+    # Input "y" for overwrite prompt
+    result = runner.invoke(app, ["onboard"], input="y\n")
+    
+    assert result.exit_code == 0
+    assert "Config already exists" in result.stdout
+    assert "Created config" in result.stdout
+    
+    # Verify config WAS changed (our mock writes "{}")
+    test_content = config_file.read_text()
+    assert test_content == "{}" or test_content == "" 
+
+    assert workspace_dir.exists()
+
+
+def test_onboard_existing_workspace_safe_create(mock_paths):
+    """Test onboarding with existing workspace safely creates templates without prompting."""
+    config_file, workspace_dir = mock_paths
+    
+    # Pre-create workspace
+    workspace_dir.mkdir(parents=True)
+    
+    # Scenario: Config exists (keep it), Workspace exists (add templates automatically)
+    config_file.write_text("{}")
+    
+    inputs = "n\n"  # No overwrite config
+    result = runner.invoke(app, ["onboard"], input=inputs)
+    
+    assert result.exit_code == 0
+    # Workspace exists message
+    # Depending on implementation, it might say "Workspace already exists" or just proceed.
+    # Code in commands.py Line 180: if not workspace.exists(): ...
+    # It does NOT print "Workspace already exists" if it exists.
+    # It only prints "Created workspace" if it created it.
+    
+    assert "Created workspace" not in result.stdout
+    
+    # Should NOT prompt for templates
+    assert "Create missing default templates?" not in result.stdout
+    
+    # But SHOULD create them (since _create_workspace_templates is called unconditionally)
+    assert "Created AGENTS.md" in result.stdout
+    assert (workspace_dir / "AGENTS.md").exists()