refactor: split services/docker.py into docker/ package

Split monolithic docker.py into focused modules:
- docker/compose.py — compose generation, execute_compose_command, volume sorting
- docker/container.py — container status, IP, logs, network, port finding
- docker/config_staging.py — instance dir, env file, config file staging
- docker/tunnel.py — cloudflared tunnel lifecycle (moved from services/tunnel.py)
- docker/__init__.py — re-exports all public symbols for backward compatibility
- services/tunnel.py — thin re-export wrapper for backward compatibility

Also includes schema extraction files created in prior work:
- schemas/config/config_profile.py
- schemas/project/*.py
- schemas/system/health.py
- schemas/tool/*.py
- schemas/user/*.py

All existing imports like 'from src.services.docker import X' and
'from src.services.tunnel import X' continue to work unchanged.

Quality gates: py_compile passed, ruff passed, import test passed.

apps/api/src/services/docker/compose.py

@@ -0,0 +1,120 @@
+"""Docker Compose file generation and manipulation."""
+
+import logging
+import subprocess
+from collections import Counter
+from pathlib import Path
+from typing import Any
+
+logger = logging.getLogger(__name__)
+
+
+def sort_volumes_by_specificity(volumes: list[str]) -> list[str]:
+    """Sort volume strings so parent paths come before child paths.
+
+    Docker Compose mounts volumes in array order. A later mount at a parent
+    path hides earlier mounts at child paths. By sorting shallow paths first
+    and deep paths last, deeper (more specific) mounts overlay correctly.
+
+    Volume format: source:target or source:target:type
+
+    Args:
+        volumes: List of Docker volume mount strings.
+
+    Returns:
+        Sorted list with parent paths before child paths.
+    """
+
+    def _target_depth(vol: str) -> int:
+        parts = vol.split(":")
+        if len(parts) < 2:
+            return 0
+        target = parts[1].rstrip("/")
+        if not target or target == "/":
+            return 0
+        return target.count("/")
+
+    # Detect duplicate targets and warn
+    targets = []
+    for vol in volumes:
+        parts = vol.split(":")
+        targets.append(parts[1] if len(parts) > 1 else "")
+    dupes = [t for t, c in Counter(targets).items() if c > 1]
+    if dupes:
+        logger.warning("Duplicate mount targets detected: %s", dupes)
+
+    # Stable sort: parent paths first, child paths last
+    return sorted(volumes, key=_target_depth)
+
+
+def render_compose_template(template: str, variables: dict[str, Any]) -> str:
+    """Render a Docker Compose template with variable substitution.
+
+    Args:
+        template: The compose template string
+        variables: Dictionary of variable names to values
+
+    Returns:
+        Rendered compose file content
+    """
+    result = template
+    for key, value in variables.items():
+        placeholder = f"{{{{{key}}}}}"
+        result = result.replace(placeholder, str(value))
+    return result
+
+
+def write_compose_file(instance_dir: str, content: str) -> str:
+    """Write the rendered compose file to the instance directory.
+
+    Args:
+        instance_dir: Path to instance directory
+        content: Rendered compose content
+
+    Returns:
+        Path to the compose file
+    """
+    compose_path = Path(instance_dir) / "docker-compose.yml"
+    compose_path.write_text(content)
+    return str(compose_path)
+
+
+def execute_compose_command(
+    compose_path: str, action: str, timeout: int = 60, env_file: str | None = None
+) -> tuple[int, str, str]:
+    """Execute a docker compose command.
+
+    Args:
+        compose_path: Path to docker-compose.yml
+        action: The compose action (up, down, start, stop, restart)
+        timeout: Command timeout in seconds
+        env_file: Optional path to .env file for environment variables
+
+    Returns:
+        Tuple of (returncode, stdout, stderr)
+    """
+    instance_dir = Path(compose_path).parent
+
+    cmd = ["docker", "compose", "-f", compose_path]
+
+    if env_file:
+        cmd.extend(["--env-file", env_file])
+
+    if action == "up":
+        cmd.extend(["up", "-d", "--force-recreate"])
+    elif action == "down":
+        cmd.extend(["down", "-v"])
+    elif action in ("start", "stop", "restart"):
+        cmd.append(action)
+    else:
+        raise ValueError(f"Unknown compose action: {action}")
+
+    result = subprocess.run(
+        cmd,
+        cwd=str(instance_dir),
+        capture_output=True,
+        text=True,
+        timeout=timeout,
+    )
+
+    return result.returncode, result.stdout, result.stderr