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/src/services/config/config_profile_resolver.py

@@ -476,9 +476,19 @@ def apply_resolved_profile(
         full_path.parent.mkdir(parents=True, exist_ok=True)
         full_path.write_text(content)
 
-    # Stage mount files and prepare volume mounts
+    # Stage mount directories and prepare directory-level volume mounts.
+    # Each ResolvedMount targets a container directory; we stage all of its
+    # files under a single host directory and bind-mount that directory. This
+    # keeps the target directory writable by the container user, instead of
+    # having Docker create a root-owned parent directory when only individual
+    # files are mounted.
     for mount in resolved.mounts.values():
-        expanded_target = expand_container_path(mount.target, home_dir)
+        if not mount.files:
+            continue
+
+        expanded_target = os.path.normpath(
+            expand_container_path(mount.target, home_dir)
+        )
         mount_dir = (
             instance_path / "mounts" / expanded_target.lstrip("/").replace("/", "_")
         )
@@ -494,16 +504,14 @@ def apply_resolved_profile(
             full_path.parent.mkdir(parents=True, exist_ok=True)
             full_path.write_text(content)
 
-            # Mount each file individually so sibling files from other mounts
-            # (e.g. git repo directories) are preserved.
-            file_target = os.path.join(expanded_target, file_path)
-            volume_mounts.append(
-                {
-                    "source": str(full_path),
-                    "target": file_target,
-                    "type": "bind",
-                }
-            )
+        volume_mounts.append(
+            {
+                "source": str(mount_dir),
+                "target": expanded_target,
+                "type": "bind",
+                "readonly": mount.mode in ("ro", "readonly"),
+            }
+        )
 
     return env_vars, files, volume_mounts, resolved.runtime_hints