fix: run manifest containers as root and drop privileges in entrypoint

The compose file was forcing the container to run as uid 1001, so the
entrypoint could not create /workspace even with sudo configured.

- Remove Dockerfile USER directive so containers start as root
- Make compile_compose use user: 0:0 when the manifest declares a user
- Make the entrypoint drop to the container user via  after setup,
  preserving environment variables and command arguments
- Update unit tests to assert root startup and privilege drop

Quality gates:
- pytest tests/unit: 210 passed
- ruff: clean on changed files
- mypy: clean on changed files

apps/api/tests/unit/test_manifest_compiler.py

@@ -237,6 +237,47 @@ def test_compile_dockerfile_uses_user_npm_prefix() -> None:
     assert "ENV PATH=/home/custom/.npm-global/bin:$PATH" in dockerfile
 
 
+@pytest.mark.unit
+def test_compile_dockerfile_starts_as_root_and_drops_privileges() -> None:
+    """The Dockerfile must not set USER so the entrypoint starts as root.
+
+    The entrypoint itself drops privileges to the container user before
+    exec-ing the real command.
+    """
+    manifest = {
+        "base_image": "ubuntu:24.04",
+        "interface_type": "terminal",
+        "user": {"name": "dev", "uid": 1000, "gid": 1000},
+    }
+    dockerfile = compile_dockerfile(manifest)
+    entrypoint = compile_entrypoint(manifest)
+
+    assert "USER dev" not in dockerfile
+    assert 'exec su -s /bin/bash -c "exec \\"$@\\"" dev -- "$@"' in entrypoint
+
+
+@pytest.mark.unit
+def test_compile_compose_runs_as_root() -> None:
+    """The compose service must start as root so the entrypoint can fix /workspace."""
+    manifest = {
+        "base_image": "ubuntu:24.04",
+        "interface_type": "terminal",
+        "user": {"name": "dev", "uid": 1000, "gid": 1000},
+    }
+    variables = {
+        "IMAGE_TAG": "test:latest",
+        "INSTANCE_NAME": "test-instance",
+        "REPO_PATH": "/host/repos/my-app",
+        "WORKSPACE_NAME": "my-app",
+        "TOOL_PORT": 0,
+        "EXTRA_ENV": {},
+        "EXTRA_VOLUMES": [],
+    }
+    compose = compile_compose(manifest, variables)
+
+    assert "user: 0:0" in compose
+
+
 @pytest.mark.unit
 class TestCompileEntrypoint:
     """Tests for the generated permission-fixing entrypoint."""