fix(containers): compose profile and Git mounts safely

Stage profile sources per instance and compose overlapping bind mounts so Docker cannot mask Git content or leave writable files root-owned.\n\n- preserve shared Git clones while applying profile overlays\n- add mount composition and ownership regression coverage\n- update OpenSpec tracking

apps/api/src/api/config/config_profiles.py

@@ -34,7 +34,6 @@ from src.services.config.crud_service import (
     update_profile,
     validate_default_profiles,
 )
-from src.services.tool.instance_service import resolve_git_mounts
 from src.services.config.resolver_service import (
     resolve_default_profile,
     validate_git_url,
@@ -193,6 +192,10 @@ async def refresh_profile_git_mounts(
             status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
         )
 
+    # Import lazily: instance_service imports tool schemas that transitively
+    # load API routers, so importing it during router initialization cycles.
+    from src.services.tool.instance_service import resolve_git_mounts
+
     outcomes = await _running_profile_outcomes(session, profile.id)
     for outcome in outcomes:
         instance = await session.get(ToolInstance, uuid.UUID(outcome["instance_id"]))

apps/api/src/services/tool/instance_service.py

@@ -127,11 +127,11 @@ def _chown_staged_mounts(
     uid: int,
     gid: int,
 ) -> None:
-    """Recursively chown staged mount sources to the container user.
+    """Recursively chown instance-local mount sources to the container user.
 
-    Config-profile mounts, git mounts, and SSH key mounts are staged under
-    instance_dir by the API process (root). Without this, the container
-    user cannot write into bind-mounted directories such as ~/.config.
+    Profile copies, profile/Git composites, and SSH key mounts are created by
+    the API process. Their sources must be owned by the target container user
+    before Docker bind-mounts them into writable paths.
     """
     for vol in extra_volumes:
         source = vol.get("source", "")
@@ -156,27 +156,180 @@ def _relative_under(parent: str, child: str) -> str | None:
     return None
 
 
+def _stage_profile_mounts(profile_mounts: list[dict], instance_dir: str) -> list[dict]:
+    """Copy profile bind sources into an instance-local, writable staging area."""
+    staged_mounts: list[dict] = []
+    staging_root = os.path.join(instance_dir, "mounts", "profiles")
+
+    for mount in profile_mounts:
+        source = mount.get("source", "")
+        target = mount.get("target", "")
+        if not source or not target:
+            continue
+        if not os.path.exists(source):
+            logger.warning("Skipping missing config profile mount source: %s", source)
+            continue
+
+        digest = hashlib.sha256(f"{source}\0{target}".encode()).hexdigest()[:16]
+        staged_source = os.path.join(staging_root, digest)
+        try:
+            if os.path.lexists(staged_source):
+                if os.path.isdir(staged_source):
+                    shutil.rmtree(staged_source)
+                else:
+                    os.unlink(staged_source)
+            os.makedirs(os.path.dirname(staged_source), exist_ok=True)
+
+            if os.path.isdir(source):
+                shutil.copytree(source, staged_source, symlinks=True)
+            else:
+                shutil.copy2(source, staged_source, follow_symlinks=False)
+        except OSError as exc:
+            logger.error("Failed to stage config profile mount %s: %s", source, exc)
+            continue
+
+        staged_mount = dict(mount)
+        staged_mount["source"] = staged_source
+        staged_mounts.append(staged_mount)
+
+    return staged_mounts
+
+
+def _mounts_overlap(first_target: str, second_target: str) -> bool:
+    """Return whether two normalized container mount targets intersect."""
+    return (
+        _relative_under(first_target, second_target) is not None
+        or _relative_under(second_target, first_target) is not None
+    )
+
+
+def _copy_mount_source(source: str, destination: str) -> None:
+    """Copy a bind-mount source into its destination in a composite tree."""
+    try:
+        if os.path.isdir(source):
+            os.makedirs(destination, exist_ok=True)
+            for entry in os.listdir(source):
+                source_entry = os.path.join(source, entry)
+                destination_entry = os.path.join(destination, entry)
+                if os.path.isdir(source_entry):
+                    shutil.copytree(
+                        source_entry,
+                        destination_entry,
+                        dirs_exist_ok=True,
+                        symlinks=True,
+                    )
+                else:
+                    os.makedirs(os.path.dirname(destination_entry), exist_ok=True)
+                    shutil.copy2(source_entry, destination_entry, follow_symlinks=False)
+            return
+
+        os.makedirs(os.path.dirname(destination), exist_ok=True)
+        shutil.copy2(source, destination, follow_symlinks=False)
+    except OSError as exc:
+        raise RuntimeError(f"Unable to compose mount source {source}: {exc}") from exc
+
+
 def _stack_profile_mounts_with_git_mounts(
     profile_mounts: list[dict],
     git_mount_volumes: list[dict],
+    instance_dir: str,
 ) -> list[dict]:
-    """Leave profile and Git sources isolated.
+    """Build instance-local composite mounts for overlapping profile and Git paths.
 
-    Git mount sources are shared, read-only canonical checkouts. Profile
-    content must never be copied into one because doing so dirties the
-    checkout and leaks one profile's content to every instance using it.
+    Docker applies one bind mount per target; it never merges their contents.
+    A composite therefore copies shared Git content first and profile content
+    second, so profile files extend (and intentionally override) the Git tree
+    without dirtying the shared clone.
     """
-    for profile_mount in profile_mounts:
-        profile_target = profile_mount.get("target", "")
-        for git_mount in git_mount_volumes:
-            if _relative_under(git_mount.get("target", ""), profile_target) is not None:
-                logger.warning(
-                    "Config profile mount %s overlaps Git mount %s; keeping sources isolated",
-                    profile_target,
-                    git_mount.get("target"),
+    records: list[tuple[str, dict]] = [
+        ("profile", mount) for mount in profile_mounts
+    ] + [("git", mount) for mount in git_mount_volumes]
+    components: list[list[int]] = []
+    remaining: set[int] = set(range(len(records)))
+
+    while remaining:
+        component_indices: set[int] = {min(remaining)}
+        remaining.difference_update(component_indices)
+        pending = list(component_indices)
+        while pending:
+            current_index = pending.pop()
+            current_target = records[current_index][1].get("target", "")
+            for candidate_index in list(remaining):
+                candidate_target = records[candidate_index][1].get("target", "")
+                if _mounts_overlap(current_target, candidate_target):
+                    remaining.remove(candidate_index)
+                    component_indices.add(candidate_index)
+                    pending.append(candidate_index)
+        components.append(sorted(component_indices))
+
+    result: list[dict] = []
+    for component_indexes in components:
+        component_records = [records[index] for index in component_indexes]
+        kinds = {kind for kind, _mount in component_records}
+        if kinds != {"profile", "git"}:
+            result.extend(mount for _kind, mount in component_records)
+            continue
+
+        targets = [
+            os.path.normpath(mount["target"]) for _kind, mount in component_records
+        ]
+        composite_target = os.path.commonpath(targets)
+        if any(
+            not os.path.isdir(mount["source"])
+            and os.path.normpath(mount["target"]) == composite_target
+            for _kind, mount in component_records
+        ):
+            composite_target = os.path.dirname(composite_target)
+
+        digest_input = "\0".join(
+            f"{kind}:{mount['source']}:{mount['target']}"
+            for kind, mount in component_records
+        )
+        composite_source = os.path.join(
+            instance_dir,
+            "mounts",
+            "composites",
+            hashlib.sha256(digest_input.encode()).hexdigest()[:16],
+        )
+        try:
+            if os.path.lexists(composite_source):
+                shutil.rmtree(composite_source)
+            os.makedirs(composite_source, exist_ok=True)
+        except OSError as exc:
+            raise RuntimeError(
+                f"Unable to prepare composite mount directory {composite_source}: {exc}"
+            ) from exc
+
+        for kind in ("git", "profile"):
+            for record_kind, mount in component_records:
+                if record_kind != kind:
+                    continue
+                relative_target = _relative_under(composite_target, mount["target"])
+                destination = (
+                    composite_source
+                    if relative_target == ""
+                    else os.path.join(composite_source, relative_target or "")
                 )
-                break
-    return profile_mounts
+                _copy_mount_source(mount["source"], destination)
+
+        result.append(
+            {
+                "source": composite_source,
+                "target": composite_target,
+                "type": "bind",
+                "readonly": all(
+                    mount.get("readonly", False) for _kind, mount in component_records
+                ),
+            }
+        )
+        logger.info(
+            "Composed %d profile/Git mounts at %s into %s",
+            len(component_records),
+            composite_target,
+            composite_source,
+        )
+
+    return result
 
 
 async def resolve_git_mounts(
@@ -1435,22 +1588,22 @@ async def start_tool_instance(
             git_mount_volumes = await resolve_git_mounts(
                 session, resolved, instance_dir, working_directory, home_dir
             )
-            # Stack static file mounts on top of git repo mounts so they do
-            # not mask each other when they target the same directory.
-            stacked_profile_mounts = _stack_profile_mounts_with_git_mounts(
-                profile_mounts, git_mount_volumes
+            staged_profile_mounts = _stage_profile_mounts(profile_mounts, instance_dir)
+            composed_mounts = _stack_profile_mounts_with_git_mounts(
+                staged_profile_mounts,
+                git_mount_volumes,
+                instance_dir,
             )
-            extra_volumes.extend(stacked_profile_mounts)
-            extra_volumes.extend(git_mount_volumes)
+            extra_volumes.extend(composed_mounts)
             logger.debug(
-                "Applied config profile %s to instance %s (env=%d, files=%d, mounts=%d, git_mounts=%d, stacked=%d)",
+                "Applied config profile %s to instance %s (env=%d, files=%d, profile_mounts=%d, git_mounts=%d, composed_mounts=%d)",
                 resolved.profile_name,
                 instance.id,
                 len(profile_env),
                 len(profile_files),
-                len(profile_mounts),
+                len(staged_profile_mounts),
                 len(git_mount_volumes),
-                len(profile_mounts) - len(stacked_profile_mounts),
+                len(composed_mounts),
             )
         except ConfigProfileCycleError as exc:
             logger.error(

apps/api/tests/unit/test_instance_service.py

@@ -2,13 +2,16 @@
 
 import hashlib
 import uuid
+from pathlib import Path
 from unittest.mock import MagicMock, AsyncMock
 
 import pytest
 
 from src.services.tool.instance_service import (
+    _chown_staged_mounts,
     _get_repository_mount_name,
     _stack_profile_mounts_with_git_mounts,
+    _stage_profile_mounts,
     clone_git_repo,
     modify_compose_file,
     prepare_manifest_instance,
@@ -123,151 +126,185 @@ class TestCloneGitRepo:
 
 @pytest.mark.unit
 class TestStackProfileMountsWithGitMounts:
-    """Tests for _stack_profile_mounts_with_git_mounts."""
+    """Tests for composing profile and Git mounts without Docker masking."""
 
-    def test_exact_overlap_keeps_profile_files_out_of_git_source(
-        self, tmp_path
+    def test_stages_profile_source_under_instance_directory(self, tmp_path) -> None:
+        """Profile sources must be instance-local before ownership is fixed."""
+        instance_dir = tmp_path / "instance"
+        profile_source = tmp_path / "profile" / "settings.json"
+        profile_source.parent.mkdir(parents=True)
+        profile_source.write_text("{}")
+
+        staged = _stage_profile_mounts(
+            [{"source": str(profile_source), "target": "/home/user/.pi/settings.json"}],
+            str(instance_dir),
+        )
+
+        assert staged[0]["source"].startswith(str(instance_dir))
+        assert staged[0]["source"] != str(profile_source)
+        assert Path(staged[0]["source"]).read_text() == "{}"
+
+    def test_staged_profile_source_is_chowned_for_container_user(
+        self, monkeypatch, tmp_path
     ) -> None:
-        """Overlaps must not dirty the shared Git checkout."""
+        """The ownership pass must include the instance-local profile copy."""
+        from src.services.tool import instance_service
+
+        instance_dir = tmp_path / "instance"
+        profile_source = tmp_path / "profile"
+        profile_source.mkdir()
+        (profile_source / "settings.json").write_text("{}")
+        staged = _stage_profile_mounts(
+            [{"source": str(profile_source), "target": "/home/user/.pi"}],
+            str(instance_dir),
+        )
+        chown = MagicMock()
+        monkeypatch.setattr(instance_service, "_chown_path", chown)
+
+        _chown_staged_mounts(staged, str(instance_dir), 1000, 1000)
+
+        chown.assert_called_once_with(staged[0]["source"], 1000, 1000)
+
+    def test_exact_overlap_creates_instance_local_composite(self, tmp_path) -> None:
+        """Profile files extend a Git root without mutating its shared clone."""
+        instance_dir = tmp_path / "instance"
         git_source = tmp_path / "git" / "repo-clone"
         git_source.mkdir(parents=True)
         (git_source / "existing.txt").write_text("from git")
-
-        profile_source = tmp_path / "profile" / "home_user_.pi"
-        profile_source.mkdir(parents=True)
+        profile_source = tmp_path / "profile"
+        profile_source.mkdir()
         (profile_source / "settings.json").write_text("{}")
 
-        profile_mounts = [
-            {
-                "source": str(profile_source),
-                "target": "/home/user/.pi",
-                "type": "bind",
-                "readonly": False,
-            }
-        ]
-        git_mount_volumes = [
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
-        ]
-
+        profile_mounts = _stage_profile_mounts(
+            [
+                {
+                    "source": str(profile_source),
+                    "target": "/home/user/.pi",
+                    "type": "bind",
+                }
+            ],
+            str(instance_dir),
+        )
         result = _stack_profile_mounts_with_git_mounts(
-            profile_mounts, git_mount_volumes
+            profile_mounts,
+            [{"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}],
+            str(instance_dir),
         )
 
-        assert result == profile_mounts
-        assert (git_source / "existing.txt").read_text() == "from git"
-        assert not (git_source / "settings.json").exists()
+        assert len(result) == 1
+        composite = result[0]
+        assert composite["target"] == "/home/user/.pi"
+        assert composite["source"].startswith(str(instance_dir))
+        assert not (tmp_path / "git" / "repo-clone" / "settings.json").exists()
+        assert (
+            tmp_path / "git" / "repo-clone" / "existing.txt"
+        ).read_text() == "from git"
+        assert (tmp_path / "instance" / "mounts" / "composites").exists()
+        assert (Path(composite["source"]) / "existing.txt").read_text() == "from git"
+        assert (Path(composite["source"]) / "settings.json").read_text() == "{}"
 
-    def test_descendant_overlap_keeps_sources_isolated(self, tmp_path) -> None:
-        """A child profile mount must not mutate the shared Git checkout."""
+    def test_descendant_profile_mount_extends_git_root(self, tmp_path) -> None:
+        """Nested targets are composed at the Git root, preserving siblings."""
+        instance_dir = tmp_path / "instance"
         git_source = tmp_path / "git"
         git_source.mkdir()
         (git_source / "README").write_text("repo")
-
-        profile_source = tmp_path / "profile" / "agent"
-        profile_source.mkdir(parents=True)
+        profile_source = tmp_path / "profile"
+        profile_source.mkdir()
         (profile_source / "settings.json").write_text("x")
 
-        profile_mounts = [
-            {
-                "source": str(profile_source),
-                "target": "/home/user/.pi/agent",
-                "type": "bind",
-            }
-        ]
-        git_mount_volumes = [
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
-        ]
-
+        profile_mounts = _stage_profile_mounts(
+            [{"source": str(profile_source), "target": "/home/user/.pi/agent"}],
+            str(instance_dir),
+        )
         result = _stack_profile_mounts_with_git_mounts(
-            profile_mounts, git_mount_volumes
+            profile_mounts,
+            [{"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}],
+            str(instance_dir),
         )
 
-        assert result == profile_mounts
+        assert len(result) == 1
+        composite = Path(result[0]["source"])
+        assert result[0]["target"] == "/home/user/.pi"
+        assert (composite / "README").read_text() == "repo"
+        assert (composite / "agent" / "settings.json").read_text() == "x"
         assert not (git_source / "agent").exists()
-        assert (git_source / "README").read_text() == "repo"
 
-    def test_non_overlapping_mounts_left_untouched(self, tmp_path) -> None:
-        """Profile mounts that do not overlap a git mount are returned as-is."""
+    def test_file_profile_mount_extends_git_root(self, tmp_path) -> None:
+        """A file bind mount is composed into the Git directory, not masked."""
+        instance_dir = tmp_path / "instance"
         git_source = tmp_path / "git"
         git_source.mkdir()
-
-        profile_source = tmp_path / "profile"
-        profile_source.mkdir()
-        (profile_source / "config").write_text("c")
-
-        profile_mounts = [
-            {
-                "source": str(profile_source),
-                "target": "/home/user/.config",
-                "type": "bind",
-            }
-        ]
-        git_mount_volumes = [
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
-        ]
-
-        result = _stack_profile_mounts_with_git_mounts(
-            profile_mounts, git_mount_volumes
-        )
-
-        assert result == profile_mounts
-
-    def test_git_source_file_does_not_consume_profile_mount(self, tmp_path) -> None:
-        """If the overlapping git-mount source is a file, the profile mount
-        cannot be merged and must be kept."""
-        git_source = tmp_path / "file.txt"
-        git_source.write_text("file")
-
-        profile_source = tmp_path / "profile"
-        profile_source.mkdir()
-        (profile_source / "settings.json").write_text("{}")
-
-        profile_mounts = [
-            {
-                "source": str(profile_source),
-                "target": "/home/user/.pi",
-                "type": "bind",
-            }
-        ]
-        git_mount_volumes = [
-            {
-                "source": str(git_source),
-                "target": "/home/user/.pi/file.txt",
-                "type": "bind",
-            }
-        ]
-
-        result = _stack_profile_mounts_with_git_mounts(
-            profile_mounts, git_mount_volumes
-        )
-
-        assert result == profile_mounts
-
-    def test_profile_source_file_does_not_mutate_git_source(self, tmp_path) -> None:
-        """A profile file must not be copied into a shared Git checkout."""
-        git_source = tmp_path / "git"
-        git_source.mkdir()
-
+        (git_source / "README").write_text("repo")
         profile_source = tmp_path / "settings.json"
         profile_source.write_text("{}")
 
-        profile_mounts = [
-            {
-                "source": str(profile_source),
-                "target": "/home/user/.pi/settings.json",
-                "type": "bind",
-            }
-        ]
-        git_mount_volumes = [
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
-        ]
-
+        profile_mounts = _stage_profile_mounts(
+            [
+                {
+                    "source": str(profile_source),
+                    "target": "/home/user/.pi/settings.json",
+                }
+            ],
+            str(instance_dir),
+        )
         result = _stack_profile_mounts_with_git_mounts(
-            profile_mounts, git_mount_volumes
+            profile_mounts,
+            [{"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}],
+            str(instance_dir),
         )
 
-        assert result == profile_mounts
-        assert not (git_source / "settings.json").exists()
+        assert len(result) == 1
+        composite = Path(result[0]["source"])
+        assert result[0]["target"] == "/home/user/.pi"
+        assert (composite / "README").read_text() == "repo"
+        assert (composite / "settings.json").read_text() == "{}"
+
+    def test_parent_profile_mount_extends_nested_git_mount(self, tmp_path) -> None:
+        """A profile parent mount keeps Git content and its own sibling files."""
+        instance_dir = tmp_path / "instance"
+        git_source = tmp_path / "git"
+        git_source.mkdir()
+        (git_source / "plugin.toml").write_text("git")
+        profile_source = tmp_path / "profile"
+        profile_source.mkdir()
+        (profile_source / "config.toml").write_text("profile")
+
+        profile_mounts = _stage_profile_mounts(
+            [{"source": str(profile_source), "target": "/home/user"}], str(instance_dir)
+        )
+        result = _stack_profile_mounts_with_git_mounts(
+            profile_mounts,
+            [{"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}],
+            str(instance_dir),
+        )
+
+        assert len(result) == 1
+        composite = Path(result[0]["source"])
+        assert result[0]["target"] == "/home/user"
+        assert (composite / "config.toml").read_text() == "profile"
+        assert (composite / ".pi" / "plugin.toml").read_text() == "git"
+
+    def test_non_overlapping_mounts_remain_separate(self, tmp_path) -> None:
+        """Unrelated profile and Git mounts retain their independent sources."""
+        instance_dir = tmp_path / "instance"
+        git_source = tmp_path / "git"
+        git_source.mkdir()
+        profile_source = tmp_path / "profile"
+        profile_source.mkdir()
+
+        profile_mounts = _stage_profile_mounts(
+            [{"source": str(profile_source), "target": "/home/user/.config"}],
+            str(instance_dir),
+        )
+        git_mounts = [{"source": str(git_source), "target": "/home/user/.pi"}]
+
+        assert (
+            _stack_profile_mounts_with_git_mounts(
+                profile_mounts, git_mounts, str(instance_dir)
+            )
+            == profile_mounts + git_mounts
+        )
 
 
 @pytest.mark.unit

openspec/changes/fix-pi-container-mount-permissions/change.md

@@ -12,6 +12,7 @@ After implementing configurable tool container home directories, new `pi-agent`
 4. `npm_global` packages are installed with `RUN npm install -g ...` as root into the system npm prefix, so the non-root container user cannot update them.
 5. Once the repo mount moves out of `/workspace`, the generated `/workspace` compatibility symlink is created in the image as root. The non-root entrypoint cannot replace it (write permission is required on `/`), so container startup fails.
 6. Older images baked a literal `{{WORKSPACE_NAME}}` directory into `/home/user`, which survives alongside the real repo-named mount directory.
+7. Config-profile file mounts use canonical profile storage owned by the API process. A non-root container user therefore cannot write to writable bind mounts. When a directory-level profile mount and a Git mount share or nest under the same target, Docker bind mounting masks the earlier source rather than merging their files.
 
 ## Fix
 
@@ -40,7 +41,9 @@ After implementing configurable tool container home directories, new `pi-agent`
 6. Remove the explicit repo mount from the built-in `pi-agent` manifest so the repo mount is synthesized by `compile_compose` rather than depending on tool config. Add a follow-up Alembic data migration that strips the `source_type: repo` mount from the manifest.
 7. Add `_get_repository_mount_name()` helper. When the instance is bound to a workspace, the helper returns the basename of `workspace.path`. For legacy repo-only instances it falls back to parsing the remote URL like `git clone` would, then to the user-provided repository name.
 8. Switch workspace storage layout to `/data/working-copies/{workspace_id}/{repo_name}/` so `git clone` creates the repo-named directory naturally, making `workspace.path.basename` the correct container mount name. This replaces the previous `/data/working-copies/{repo_id}/{workspace_name}/` layout.
-9. Update unit tests for the new behavior.
+9. Stage every config-profile bind-mount source into the instance directory before compose generation. This makes writable mounts user-owned without changing the shared canonical profile source.
+10. Replace overlapping profile and Git bind mounts with a per-instance composite source. The composite copies Git content first and profile content second, preserving Git siblings while allowing profile files to override matching paths; it is then chowned with the other staged mounts. This removes duplicate/nested Docker mounts rather than relying on mount order to merge them.
+11. Update unit tests for the new behavior.
 
 ## Affected files
 

openspec/changes/fix-pi-container-mount-permissions/tasks.md

@@ -12,5 +12,8 @@
 - [x] Remove compose-level `user: 0:0` override so entrypoint can drop privileges
 - [x] Pass manifest-declared container user to terminal sessions via `docker exec --user`
 - [x] Update unit tests for container user/terminal changes
+- [x] Stage profile bind mounts per instance so writable sources are owned by the container user
+- [x] Composite overlapping profile and Git mounts into one per-instance bind source
+- [x] Add regression tests for mount composition, ownership staging, and mount order
 - [ ] Run quality gates for container user/terminal changes
 - [ ] Commit and push