fix: mount config profile files individually instead of replacing directories

The previous sorting fix exposed a deeper bug: ResolvedMount always
mounted its staging directory as a single bind mount. When a config
profile mount targeted /workspace/x/y and contained a single file
z.json, the staging directory (containing only z.json) replaced the
ENTIRE /workspace/x/y directory, hiding all sibling files from git
repo mounts.

- Change apply_resolved_profile to mount each file individually:
  - source: staging_dir/relative_path
  - target: expanded_target/relative_path
  - Sibling files from other mounts are preserved.
  - Empty mounts produce no volume entries.

- Keep volume sorting (parent paths before child paths) which is
  still necessary for directory mounts and ensures parent dirs exist
  before file mounts inside them.

- Add 4 unit tests for file-level mount behavior.

Quality gates: pytest (218 passed, 6 pre-existing), tsc --noEmit (clean)

apps/api/src/services/config_profile_resolver.py

@@ -494,13 +494,16 @@ def apply_resolved_profile(
             full_path.parent.mkdir(parents=True, exist_ok=True)
             full_path.write_text(content)
 
-        volume_mounts.append(
-            {
-                "source": str(mount_dir),
-                "target": expanded_target,
-                "type": "bind",
-            }
-        )
+            # 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",
+                }
+            )
 
     return env_vars, files, volume_mounts, resolved.runtime_hints
 

apps/api/tests/unit/test_config_profile_resolver.py

@@ -6,6 +6,9 @@ from src.models.config_profile import ConfigProfile, ConfigProfileInclude
 from src.services.config_profile_resolver import (
     ConfigProfileCycleError,
     ConfigProfileNotFoundError,
+    ResolvedMount,
+    ResolvedProfile,
+    apply_resolved_profile,
     check_include_cycle,
     resolve_profile,
     _merge_env_vars,
@@ -479,6 +482,81 @@ class TestResolveProfile:
             await resolve_profile(db_session, uuid.uuid4())
 
 
+class TestApplyResolvedProfile:
+    """Unit tests for apply_resolved_profile file-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."""
+        resolved = ResolvedProfile(
+            profile_id=uuid.uuid4(),
+            profile_name="test",
+            mounts={
+                "/app": ResolvedMount(
+                    target="/app",
+                    mode="rw",
+                    files={"config.json": '{"key": "value"}', "nested/file.txt": "hello"},
+                )
+            },
+        )
+        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
+
+    def test_file_mount_preserves_sibling_files(self, tmp_path) -> None:
+        """File-level mounts should not hide sibling files from other mounts."""
+        resolved = ResolvedProfile(
+            profile_id=uuid.uuid4(),
+            profile_name="test",
+            mounts={
+                "/workspace/x/y": ResolvedMount(
+                    target="/workspace/x/y",
+                    mode="rw",
+                    files={"z.json": "override"},
+                )
+            },
+        )
+        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")
+
+    def test_empty_mount_produces_no_volumes(self, tmp_path) -> None:
+        """A mount with no files should not produce any volume entries."""
+        resolved = ResolvedProfile(
+            profile_id=uuid.uuid4(),
+            profile_name="test",
+            mounts={
+                "/app": ResolvedMount(target="/app", mode="rw", files={})
+            },
+        )
+        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."""
+        resolved = ResolvedProfile(
+            profile_id=uuid.uuid4(),
+            profile_name="test",
+            mounts={
+                "~/.config": ResolvedMount(
+                    target="~/.config",
+                    mode="rw",
+                    files={"app.toml": "setting = 1"},
+                )
+            },
+        )
+        env, files, volumes, hints = apply_resolved_profile(
+            str(tmp_path), resolved, home_dir="/home/user"
+        )
+        assert volumes[0]["target"] == "/home/user/.config/app.toml"
+
+
 class TestCheckIncludeCycle:
     """Unit tests for include cycle checking."""
 

openspec/explorations/mount-file-level-overlays.md

@@ -0,0 +1,68 @@
+# Exploration: File-Level Mount Overlays
+
+## Follow-up to Mount Specificity Ordering
+
+The sorting fix (parent paths before child paths) was correct for directory mounts,
+but it exposed a deeper bug: `ResolvedMount` always mounts its staging directory
+as a single bind mount. When a config profile mount targets `/workspace/x/y` and
+contains a single file `z.json`, the staging directory (containing only `z.json`)
+replaces the ENTIRE `/workspace/x/y` directory, hiding all sibling files from the
+git repo.
+
+## Root Cause
+
+In `apply_resolved_profile`:
+```python
+volume_mounts.append({
+    "source": str(mount_dir),      # staging dir with ONLY z.json
+    "target": expanded_target,     # /workspace/x/y
+    "type": "bind",
+})
+```
+
+This mounts a directory. Docker bind mounts at a directory path completely replace
+the target directory. There is no merge.
+
+## What the User Expects
+
+Git repo mount: `/repo/x` → `/workspace/x` (directory with many files)
+Config profile mount: `z.json` → `/workspace/x/y/z.json` (single file overlay)
+
+Expected: `/workspace/x/y/` contains all repo files PLUS the overlaid `z.json`.
+Actual (before sorting): parent mount hides child mount (child never visible).
+Actual (after sorting): child directory mount replaces parent subdirectory
+(`/workspace/x/y` now contains ONLY `z.json`).
+
+## Solution
+
+Mount each file individually instead of the staging directory.
+
+```python
+for file_path, content in mount.files.items():
+    full_path = mount_dir / file_path
+    full_path.write_text(content)
+    volume_mounts.append({
+        "source": str(full_path),
+        "target": os.path.join(expanded_target, file_path),
+        "type": "bind",
+    })
+```
+
+This creates file-level bind mounts. Docker mounts a single file without affecting
+sibling files in the parent directory.
+
+## Edge Cases
+
+- Empty `files` dict: skip, no mounts created.
+- Nested file paths (`a/b/c.txt`): mount `staging/a/b/c.txt` → `target/a/b/c.txt`.
+  Docker creates parent directories as needed.
+- File target already exists in git repo: file mount wins (desired override behavior).
+- No git repo mount (directory doesn't exist in image): Docker creates parent dirs
+  for the first file mount.
+
+## Sorting Fix Status
+
+KEEP the sorting. It is still correct and necessary for cases where directory
+mounts genuinely override parent directories (e.g., a git mount to `/workspace/x`
+and another git mount to `/workspace/x/sub`). File-level mounts also benefit from
+sorting because the parent directory mount must exist before file mounts inside it.