diff --git a/codemcp/main.py b/codemcp/main.py
index ec431ea..cf155e2 100644
--- a/codemcp/main.py
+++ b/codemcp/main.py
@@ -14,6 +14,7 @@
 from starlette.applications import Starlette
 from starlette.routing import Mount
 
+from .code_command import get_command_from_config
 from .common import normalize_file_path
 from .git_query import get_current_commit_hash
 from .tools.chmod import chmod
@@ -861,6 +862,149 @@ def run() -> None:
     mcp.run()
 
 
+@cli.command()
+@click.argument("command", type=str, required=True)
+@click.argument("args", nargs=-1, type=click.UNPROCESSED)
+@click.option(
+    "--path",
+    type=click.Path(exists=True),
+    default=".",
+    help="Path to the project directory (default: current directory)",
+)
+@click.option(
+    "--no-stream",
+    is_flag=True,
+    help="Don't stream output to the terminal in real-time",
+)
+def run(command: str, args: List[str], path: str, no_stream: bool) -> None:
+    """Run a command defined in codemcp.toml.
+
+    COMMAND: The name of the command to run as defined in codemcp.toml
+    ARGS: Optional arguments to pass to the command
+    """
+    import asyncio
+    import subprocess
+    from uuid import uuid4
+
+    # Configure logging
+    configure_logging()
+
+    # Convert args tuple to a space-separated string
+    args_str = " ".join(args) if args else None
+
+    # Generate a temporary chat ID for this command
+    chat_id = str(uuid4())
+
+    # Convert to absolute path if needed
+    project_dir = normalize_file_path(path)
+
+    try:
+        # Check if command exists in config
+        command_list = get_command_from_config(project_dir, command)
+        if not command_list:
+            click.echo(
+                f"Error: Command '{command}' not found in codemcp.toml", err=True
+            )
+            return
+
+        if no_stream:
+            # Use the standard non-streaming implementation
+            result = asyncio.run(run_command(project_dir, command, args_str, chat_id))
+            click.echo(result)
+        else:
+            # Check if directory is in a git repository and commit any pending changes
+            from .git import commit_changes, is_git_repository
+
+            is_git_repo = asyncio.run(is_git_repository(project_dir))
+            if is_git_repo:
+                logging.info(f"Committing any pending changes before {command}")
+                commit_result = asyncio.run(
+                    commit_changes(
+                        project_dir,
+                        f"Snapshot before auto-{command}",
+                        chat_id,
+                        commit_all=True,
+                    )
+                )
+                if not commit_result[0]:
+                    logging.warning(
+                        f"Failed to commit pending changes: {commit_result[1]}"
+                    )
+
+            # Extend the command with arguments if provided
+            full_command = command_list.copy()
+            if args_str:
+                import shlex
+
+                parsed_args = shlex.split(args_str)
+                full_command.extend(parsed_args)
+
+            # Stream output to the terminal in real-time
+            click.echo(f"Running command: {' '.join(str(c) for c in full_command)}")
+
+            # Run the command with live output streaming
+            try:
+                process = subprocess.Popen(
+                    full_command,
+                    cwd=project_dir,
+                    stdout=None,  # Use parent's stdout/stderr (the terminal)
+                    stderr=None,
+                    text=True,
+                    bufsize=0,  # Unbuffered
+                )
+
+                try:
+                    # Wait for the process to complete
+                    exit_code = process.wait()
+                except KeyboardInterrupt:
+                    # Handle Ctrl+C gracefully
+                    process.terminate()
+                    try:
+                        process.wait(timeout=1)
+                    except subprocess.TimeoutExpired:
+                        process.kill()
+                    click.echo("\nProcess terminated by user.")
+                    return
+
+                # Check if command succeeded
+                if exit_code == 0:
+                    # If it's a git repo, commit any changes made by the command
+                    if is_git_repo:
+                        from .code_command import check_for_changes
+
+                        has_changes = asyncio.run(check_for_changes(project_dir))
+                        if has_changes:
+                            logging.info(
+                                f"Changes detected after {command}, committing"
+                            )
+                            success, commit_result_message = asyncio.run(
+                                commit_changes(
+                                    project_dir,
+                                    f"Auto-commit {command} changes",
+                                    chat_id,
+                                    commit_all=True,
+                                )
+                            )
+
+                            if success:
+                                click.echo(
+                                    f"\nCode {command} successful and changes committed."
+                                )
+                            else:
+                                click.echo(
+                                    f"\nCode {command} successful but failed to commit changes."
+                                )
+                                click.echo(f"Commit error: {commit_result_message}")
+                    else:
+                        click.echo(f"\nCode {command} successful.")
+                else:
+                    click.echo(f"\nCommand failed with exit code {exit_code}.")
+            except Exception as cmd_error:
+                click.echo(f"Error during command execution: {cmd_error}", err=True)
+    except Exception as e:
+        click.echo(f"Error running command: {e}", err=True)
+
+
 @cli.command()
 @click.option(
     "--host",
diff --git a/e2e/test_run_command.py b/e2e/test_run_command.py
new file mode 100644
index 0000000..3d472c2
--- /dev/null
+++ b/e2e/test_run_command.py
@@ -0,0 +1,161 @@
+#!/usr/bin/env python3
+
+import subprocess
+import tempfile
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
+import pytest
+from click.testing import CliRunner
+
+import codemcp.git
+from codemcp.main import cli
+
+
+# Create non-async mock functions to replace async ones
+def mock_is_git_repository(*args, **kwargs):
+    return False
+
+
+def mock_check_for_changes(*args, **kwargs):
+    return False
+
+
+def mock_commit_changes(*args, **kwargs):
+    return (True, "Mock commit message")
+
+
+# Patch the modules directly
+codemcp.git.is_git_repository = mock_is_git_repository
+
+
+@pytest.fixture
+def test_project():
+    """Create a temporary directory with a codemcp.toml file for testing."""
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        # Create a codemcp.toml file with test commands
+        config_path = Path(tmp_dir) / "codemcp.toml"
+        with open(config_path, "w") as f:
+            f.write("""[commands]
+echo = ["echo", "Hello from codemcp run!"]
+echo_args = ["echo"]
+invalid = []
+""")
+
+        # Initialize a git repository
+        subprocess.run(["git", "init"], cwd=tmp_dir, check=True, capture_output=True)
+        subprocess.run(
+            ["git", "config", "user.name", "Test User"], cwd=tmp_dir, check=True
+        )
+        subprocess.run(
+            ["git", "config", "user.email", "test@example.com"], cwd=tmp_dir, check=True
+        )
+        subprocess.run(["git", "add", "codemcp.toml"], cwd=tmp_dir, check=True)
+        subprocess.run(
+            ["git", "commit", "-m", "Initial commit"], cwd=tmp_dir, check=True
+        )
+
+        yield tmp_dir
+
+
+def test_run_command_success(test_project):
+    """Test running a command successfully."""
+    runner = CliRunner()
+    result = runner.invoke(cli, ["run", "echo", "--path", test_project, "--no-stream"])
+
+    assert result.exit_code == 0
+    assert "Hello from codemcp run!" in result.output
+    assert "Code echo successful" in result.output
+
+
+def test_run_command_with_args(test_project):
+    """Test running a command with arguments."""
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "run",
+            "echo_args",
+            "Test",
+            "argument",
+            "string",
+            "--path",
+            test_project,
+            "--no-stream",
+        ],
+    )
+
+    assert result.exit_code == 0
+    assert "Test argument string" in result.output
+    assert "Code echo_args successful" in result.output
+
+
+def test_run_command_not_found(test_project):
+    """Test running a command that doesn't exist in config."""
+    runner = CliRunner()
+    result = runner.invoke(
+        cli, ["run", "nonexistent", "--path", test_project, "--no-stream"]
+    )
+
+    assert "Error: Command 'nonexistent' not found in codemcp.toml" in result.output
+
+
+def test_run_command_empty_definition(test_project):
+    """Test running a command with an empty definition."""
+    runner = CliRunner()
+    result = runner.invoke(
+        cli, ["run", "invalid", "--path", test_project, "--no-stream"]
+    )
+
+    assert "Error: Command 'invalid' not found in codemcp.toml" in result.output
+
+
+@patch("codemcp.git.is_git_repository", mock_is_git_repository)
+@patch("codemcp.code_command.check_for_changes", mock_check_for_changes)
+@patch("codemcp.git.commit_changes", mock_commit_changes)
+@patch(
+    "asyncio.run", lambda x: False
+)  # Mock asyncio.run to return False for all coroutines
+def test_run_command_stream_mode(test_project):
+    """Test running a command with streaming mode."""
+    import subprocess
+
+    # Create a mock for subprocess.Popen
+    mock_process = MagicMock()
+    mock_process.returncode = 0
+    mock_process.wait.return_value = 0
+
+    # Keep track of Popen calls
+    popen_calls = []
+
+    # Create a safe replacement for Popen that won't leave hanging processes
+    original_popen = subprocess.Popen
+
+    def mock_popen(cmd, **kwargs):
+        if (
+            isinstance(cmd, list)
+            and cmd[0] == "echo"
+            and "Hello from codemcp run!" in cmd
+        ):
+            popen_calls.append((cmd, kwargs))
+            return mock_process
+        # For any other command, create a safe echo process with proper cleanup
+        return original_popen(
+            ["echo", "Test"], stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        )
+
+    with patch("subprocess.Popen", mock_popen):
+        # Run the command with isolated stdin/stdout to prevent interference
+        runner = CliRunner(mix_stderr=False)
+        runner.invoke(cli, ["run", "echo", "--path", test_project])
+
+        # Check that our command was executed with the right parameters
+        assert any(cmd == ["echo", "Hello from codemcp run!"] for cmd, _ in popen_calls)
+
+        # Find the call for our echo command
+        for cmd, kwargs in popen_calls:
+            if cmd == ["echo", "Hello from codemcp run!"]:
+                # Verify streaming parameters
+                assert kwargs.get("stdout") is None
+                assert kwargs.get("stderr") is None
+                assert kwargs.get("bufsize") == 0