fix: stage config-profile mounts as directories so ~/.config stays writable

- Switch apply_resolved_profile from per-file bind mounts to one
  directory-level bind mount per ResolvedMount target.
- Stage all configured files under instance_dir/mounts/<sanitized_target>
  and bind-mount that directory, so Docker no longer creates a root-owned
  parent directory such as ~/.config.
- Propagate read-only mode ('ro') as the 'readonly' flag on volume entries.
- Update unit tests to expect directory-level mounts and add coverage for
  readonly/writable flags.

Quality gates: python3 -m py_compile, pytest (313 passed, 34 skipped),
npm run typecheck, npm run lint.

apps/api/tests/unit/test_config_profile_resolver.py

@@ -1,4 +1,6 @@
 import uuid
+from pathlib import Path
+
 import pytest
 from sqlalchemy.ext.asyncio import AsyncSession
 
@@ -483,10 +485,10 @@ class TestResolveProfile:
 
 
 class TestApplyResolvedProfile:
-    """Unit tests for apply_resolved_profile file-level mount behavior."""
+    """Unit tests for apply_resolved_profile directory-level mount behavior."""
 
-    def test_mounts_individual_files_not_directory(self, tmp_path) -> None:
-        """Each file in a ResolvedMount should be mounted individually, not the staging dir."""
+    def test_mounts_directory_not_individual_files(self, tmp_path) -> None:
+        """Each ResolvedMount should produce one directory-level bind mount."""
         resolved = ResolvedProfile(
             profile_id=uuid.uuid4(),
             profile_name="test",
@@ -503,15 +505,15 @@ class TestApplyResolvedProfile:
         )
         env, files, volumes, hints = apply_resolved_profile(str(tmp_path), resolved)
 
-        assert len(volumes) == 2
-        targets = {v["target"] for v in volumes}
-        assert "/app/config.json" in targets
-        assert "/app/nested/file.txt" in targets
-        # No directory-level mount
-        assert "/app" not in targets
+        assert len(volumes) == 1
+        assert volumes[0]["target"] == "/app"
+        assert Path(volumes[0]["source"]).name == "app"
+        assert Path(volumes[0]["source"]).is_dir()
+        assert (Path(volumes[0]["source"]) / "config.json").exists()
+        assert (Path(volumes[0]["source"]) / "nested" / "file.txt").exists()
 
-    def test_file_mount_preserves_sibling_files(self, tmp_path) -> None:
-        """File-level mounts should not hide sibling files from other mounts."""
+    def test_directory_mount_target(self, tmp_path) -> None:
+        """A directory-level mount targets the configured directory path."""
         resolved = ResolvedProfile(
             profile_id=uuid.uuid4(),
             profile_name="test",
@@ -526,8 +528,9 @@ class TestApplyResolvedProfile:
         env, files, volumes, hints = apply_resolved_profile(str(tmp_path), resolved)
 
         assert len(volumes) == 1
-        assert volumes[0]["target"] == "/workspace/x/y/z.json"
-        assert volumes[0]["source"].endswith("z.json")
+        assert volumes[0]["target"] == "/workspace/x/y"
+        assert Path(volumes[0]["source"]).name == "workspace_x_y"
+        assert (Path(volumes[0]["source"]) / "z.json").exists()
 
     def test_empty_mount_produces_no_volumes(self, tmp_path) -> None:
         """A mount with no files should not produce any volume entries."""
@@ -539,8 +542,8 @@ class TestApplyResolvedProfile:
         env, files, volumes, hints = apply_resolved_profile(str(tmp_path), resolved)
         assert volumes == []
 
-    def test_home_expansion_in_file_mount_target(self, tmp_path) -> None:
-        """~ in mount target should be expanded to home_dir for file mounts."""
+    def test_home_expansion_in_directory_mount_target(self, tmp_path) -> None:
+        """~ in mount target should be expanded to home_dir for directory mounts."""
         resolved = ResolvedProfile(
             profile_id=uuid.uuid4(),
             profile_name="test",
@@ -555,7 +558,47 @@ class TestApplyResolvedProfile:
         env, files, volumes, hints = apply_resolved_profile(
             str(tmp_path), resolved, home_dir="/home/user"
         )
-        assert volumes[0]["target"] == "/home/user/.config/app.toml"
+        assert len(volumes) == 1
+        assert volumes[0]["target"] == "/home/user/.config"
+        assert (Path(volumes[0]["source"]) / "app.toml").exists()
+
+    def test_readonly_mount_sets_readonly_flag(self, tmp_path) -> None:
+        """A mount with mode 'ro' should set readonly on the volume entry."""
+        resolved = ResolvedProfile(
+            profile_id=uuid.uuid4(),
+            profile_name="test",
+            mounts={
+                "/etc/app": ResolvedMount(
+                    target="/etc/app",
+                    mode="ro",
+                    files={"config.cfg": "value"},
+                )
+            },
+        )
+        env, files, volumes, hints = apply_resolved_profile(str(tmp_path), resolved)
+
+        assert len(volumes) == 1
+        assert volumes[0]["target"] == "/etc/app"
+        assert volumes[0].get("readonly") is True
+
+    def test_writable_mount_does_not_set_readonly_flag(self, tmp_path) -> None:
+        """A mount with mode 'rw' should not set readonly on the volume entry."""
+        resolved = ResolvedProfile(
+            profile_id=uuid.uuid4(),
+            profile_name="test",
+            mounts={
+                "/app": ResolvedMount(
+                    target="/app",
+                    mode="rw",
+                    files={"config.json": "{}"},
+                )
+            },
+        )
+        env, files, volumes, hints = apply_resolved_profile(str(tmp_path), resolved)
+
+        assert len(volumes) == 1
+        assert volumes[0]["target"] == "/app"
+        assert volumes[0].get("readonly") is False
 
 
 class TestCheckIncludeCycle: