diff --git a/apps/api/src/api/tool_instances.py b/apps/api/src/api/tool_instances.py
index e1d6f6d..c58b26f 100644
--- a/apps/api/src/api/tool_instances.py
+++ b/apps/api/src/api/tool_instances.py
@@ -56,6 +56,7 @@ from src.services.docker import (
     get_container_status,
     recreate_tunnel,
     render_compose_template,
+    sort_volumes_by_specificity,
     start_cloudflared_tunnel,
     stop_cloudflared_tunnel,
     wait_for_container_running,
@@ -599,6 +600,12 @@ def _modify_compose_file(
                 else:
                     service_config["volumes"].append(f"{source}:{target}:{vol_type}")
 
+        # Sort volumes so parent paths come before child paths
+        if service_config.get("volumes"):
+            service_config["volumes"] = sort_volumes_by_specificity(
+                service_config["volumes"]
+            )
+
         break  # Only modify the first service
 
     # Write back
diff --git a/apps/api/src/services/docker.py b/apps/api/src/services/docker.py
index 691c9b3..d179d92 100644
--- a/apps/api/src/services/docker.py
+++ b/apps/api/src/services/docker.py
@@ -1,12 +1,54 @@
 """Docker service for managing tool instances."""
 
+import logging
 import os
 import re
 import subprocess
 import time
+from collections import Counter
 from pathlib import Path
 from typing import Any
 
+logger = logging.getLogger(__name__)
+
+
+def sort_volumes_by_specificity(volumes: list[str]) -> list[str]:
+    """Sort volume strings so parent paths come before child paths.
+
+    Docker Compose mounts volumes in array order. A later mount at a parent
+    path hides earlier mounts at child paths. By sorting shallow paths first
+    and deep paths last, deeper (more specific) mounts overlay correctly.
+
+    Volume format: source:target or source:target:type
+
+    Args:
+        volumes: List of Docker volume mount strings.
+
+    Returns:
+        Sorted list with parent paths before child paths.
+    """
+
+    def _target_depth(vol: str) -> int:
+        parts = vol.split(":")
+        if len(parts) < 2:
+            return 0
+        target = parts[1].rstrip("/")
+        if not target or target == "/":
+            return 0
+        return target.count("/")
+
+    # Detect duplicate targets and warn
+    targets = []
+    for vol in volumes:
+        parts = vol.split(":")
+        targets.append(parts[1] if len(parts) > 1 else "")
+    dupes = [t for t, c in Counter(targets).items() if c > 1]
+    if dupes:
+        logger.warning("Duplicate mount targets detected: %s", dupes)
+
+    # Stable sort: parent paths first, child paths last
+    return sorted(volumes, key=_target_depth)
+
 
 def render_compose_template(template: str, variables: dict[str, Any]) -> str:
     """Render a Docker Compose template with variable substitution.
diff --git a/apps/api/src/services/manifest_compiler.py b/apps/api/src/services/manifest_compiler.py
index 75166b8..11f18a8 100644
--- a/apps/api/src/services/manifest_compiler.py
+++ b/apps/api/src/services/manifest_compiler.py
@@ -8,6 +8,8 @@ from typing import Any
 
 import yaml
 
+from src.services.docker import sort_volumes_by_specificity
+
 
 def resolve_base(manifest: dict) -> dict:
     """Merge a base definition into a tool manifest.
@@ -303,7 +305,7 @@ def compile_compose(manifest: dict, variables: dict[str, Any]) -> str:
         volumes.append(vol_str)
 
     if volumes:
-        service["volumes"] = volumes
+        service["volumes"] = sort_volumes_by_specificity(volumes)
 
     compose = {"services": {"app": service}}
     return yaml.dump(compose, default_flow_style=False)
diff --git a/apps/api/tests/unit/test_docker_service.py b/apps/api/tests/unit/test_docker_service.py
index ec2fa6a..49ca437 100644
--- a/apps/api/tests/unit/test_docker_service.py
+++ b/apps/api/tests/unit/test_docker_service.py
@@ -2,7 +2,13 @@
 
 from unittest.mock import MagicMock, patch
 
-from src.services.docker import get_container_id, get_container_name
+import logging
+
+from src.services.docker import (
+    get_container_id,
+    get_container_name,
+    sort_volumes_by_specificity,
+)
 
 
 class TestGetContainerId:
@@ -50,3 +56,57 @@ class TestGetContainerName:
         result = get_container_name("missing")
 
         assert result is None
+
+
+class TestSortVolumesBySpecificity:
+    """Tests for sort_volumes_by_specificity."""
+
+    def test_parent_before_child(self) -> None:
+        """A repo mount to /workspace/x should come before a file mount to /workspace/x/y/config.json."""
+        volumes = [
+            "/repo/x/y/config.json:/workspace/x/y/config.json",
+            "/repo/x:/workspace/x",
+        ]
+        result = sort_volumes_by_specificity(volumes)
+        assert result[0] == "/repo/x:/workspace/x"
+        assert result[1] == "/repo/x/y/config.json:/workspace/x/y/config.json"
+
+    def test_stable_sort_for_equal_depth(self) -> None:
+        """Mounts at the same depth preserve input order."""
+        volumes = [
+            "/a:/workspace/a",
+            "/b:/workspace/b",
+            "/c:/workspace/c",
+        ]
+        result = sort_volumes_by_specificity(volumes)
+        assert result == volumes
+
+    def test_with_type_suffix(self) -> None:
+        """Volume strings with :bind or :ro suffixes are parsed correctly."""
+        volumes = [
+            "/repo/x/y/config.json:/workspace/x/y/config.json:bind",
+            "/repo/x:/workspace/x:bind",
+        ]
+        result = sort_volumes_by_specificity(volumes)
+        assert result[0] == "/repo/x:/workspace/x:bind"
+        assert result[1] == "/repo/x/y/config.json:/workspace/x/y/config.json:bind"
+
+    def test_empty_list(self) -> None:
+        """Empty list returns empty list."""
+        assert sort_volumes_by_specificity([]) == []
+
+    def test_single_volume(self) -> None:
+        """Single volume returns unchanged."""
+        volumes = ["/repo:/workspace"]
+        assert sort_volumes_by_specificity(volumes) == volumes
+
+    def test_duplicate_target_warning(self, caplog) -> None:
+        """Duplicate targets trigger a warning."""
+        with caplog.at_level(logging.WARNING, logger="src.services.docker"):
+            volumes = [
+                "/a:/workspace/x",
+                "/b:/workspace/x",
+            ]
+            sort_volumes_by_specificity(volumes)
+        assert "Duplicate mount targets detected" in caplog.text
+        assert "/workspace/x" in caplog.text
diff --git a/openspec/changes/mount-specificity-ordering/.openspec.yaml b/openspec/changes/mount-specificity-ordering/.openspec.yaml
new file mode 100644
index 0000000..14bec01
--- /dev/null
+++ b/openspec/changes/mount-specificity-ordering/.openspec.yaml
@@ -0,0 +1,4 @@
+name: mount-specificity-ordering
+status: completed
+type: fix
+priority: high
diff --git a/openspec/designs/mount-specificity-ordering.md b/openspec/designs/mount-specificity-ordering.md
new file mode 100644
index 0000000..748da12
--- /dev/null
+++ b/openspec/designs/mount-specificity-ordering.md
@@ -0,0 +1,55 @@
+# Design: Mount Specificity Ordering
+
+## Helper Function
+
+Add `sort_volumes_by_specificity` to a shared utilities module. The most appropriate location is `apps/api/src/services/docker.py` since it already contains Docker/Compose helpers, or a new small module. We'll add it to `apps/api/src/services/docker.py` to keep the change minimal.
+
+## Sorting Logic
+
+```python
+def _target_depth(vol: str) -> int:
+    parts = vol.split(":")
+    if len(parts) < 2:
+        return 0
+    target = parts[1].rstrip("/")
+    if not target or target == "/":
+        return 0
+    return target.count("/")
+```
+
+Stable sort: `sorted(volumes, key=_target_depth)`.
+
+## Warning Logic
+
+```python
+def sort_volumes_by_specificity(volumes: list[str]) -> list[str]:
+    from collections import Counter
+    targets = [v.split(":")[1] if ":" in v else "" for v in volumes]
+    duplicates = [t for t, c in Counter(targets).items() if c > 1]
+    if duplicates:
+        logger.warning("Duplicate mount targets detected: %s", duplicates)
+    return sorted(volumes, key=_target_depth)
+```
+
+## Call Sites
+
+### manifest_compiler.py
+In `compile_compose()`, after building the `volumes` list and before assigning:
+```python
+from src.services.docker import sort_volumes_by_specificity
+volumes = sort_volumes_by_specificity(volumes)
+service["volumes"] = volumes
+```
+
+### tool_instances.py
+In `_modify_compose_file()`, after appending `extra_volumes` and before write:
+```python
+from src.services.docker import sort_volumes_by_specificity
+service_config["volumes"] = sort_volumes_by_specificity(service_config["volumes"])
+```
+
+## Files Changed
+- `apps/api/src/services/docker.py` — add helper
+- `apps/api/src/services/manifest_compiler.py` — sort manifest volumes
+- `apps/api/src/api/tool_instances.py` — sort legacy volumes
+- `apps/api/tests/unit/test_docker_service.py` — add tests
diff --git a/openspec/explorations/mount-specificity-ordering.md b/openspec/explorations/mount-specificity-ordering.md
new file mode 100644
index 0000000..4561ec8
--- /dev/null
+++ b/openspec/explorations/mount-specificity-ordering.md
@@ -0,0 +1,130 @@
+# Exploration: Mount Specificity Ordering
+
+## Problem Statement
+
+When a tool instance uses both git repo mounts and regular file mounts, overlapping
+target paths can cause the broader mount to hide the more specific one.
+
+Example:
+- Git repo mount: `repo/x/` → `/workspace/x` (directory)
+- Regular file mount: `config.json` → `/workspace/x/y/config.json` (single file)
+
+Expected: `/workspace/x/y/config.json` contains the file mount contents.
+Actual: The git mount overwrites `/workspace/x`, hiding `/workspace/x/y/config.json`.
+
+## Root Cause
+
+Docker Compose mounts volumes in the order they appear in the `volumes` array.
+In Linux, a later mount at a parent path hides earlier mounts at child paths.
+
+Current code ordering:
+1. `compile_compose` adds manifest-defined mounts first
+2. `EXTRA_VOLUMES` (profile + git mounts) appended after
+
+Within `EXTRA_VOLUMES` in `start_instance`:
+1. `profile_mounts` from `apply_resolved_profile`
+2. `git_mount_volumes` from `_resolve_git_mounts`
+
+Since git mounts are appended after regular mounts, a broad git mount
+(e.g. `/workspace/x`) overwrites a specific regular mount
+(e.g. `/workspace/x/y/config.json`).
+
+## Affected Code Paths
+
+1. **Manifest flow**: `compile_compose()` in `manifest_compiler.py`
+   - Manifest mounts → `EXTRA_VOLUMES`
+   - All appended to compose `volumes` list in that order
+
+2. **Legacy flow**: `_modify_compose_file()` in `tool_instances.py`
+   - Existing template volumes → `extra_volumes` appended
+   - `extra_volumes` = profile_mounts + git_mount_volumes
+
+3. **Both flows**: Volume entries are strings like `source:target` or `source:target:bind`
+   - No structured sorting happens before write
+
+## Options
+
+### Option A: Sort by path depth (recommended)
+
+Sort all volume entries by target path specificity before writing compose.
+- Shorter / parent paths first
+- Deeper / child paths last
+- Deeper mounts "win" by being layered on top
+
+**Pros:**
+- Simple, predictable rule
+- Works for all mount types (manifest, git, profile, template)
+- Minimal code change
+
+**Cons:**
+- Sorting by string length is naive (edge cases with similar paths)
+- Need proper path-segment counting
+- Doesn't handle exact same target conflicts
+
+### Option B: Detect and warn on overlaps
+
+Before writing compose, detect when any two mounts have overlapping target paths.
+Log a warning and optionally fail fast.
+
+**Pros:**
+- Surfaces conflicts to user early
+- No silent data loss
+
+**Cons:**
+- Doesn't actually fix the problem; user has to redesign mounts
+- False positives for legitimate use cases (mounting different files into same tree)
+
+### Option C: Merge overlapping mounts into a single staging directory
+
+Instead of mounting multiple sources, stage all files into a single merged
+directory on disk, then mount that single directory.
+
+**Pros:**
+- Eliminates Docker mount ordering entirely
+- Natural specificity: later file writes overwrite earlier ones
+
+**Cons:**
+- Complex to implement correctly
+- Git mounts would need to be cloned into staging area
+- Breaks live file editing (bind mounts from host)
+- Large refactor
+
+### Option D: Annotate mount specificity and merge in compiler
+
+Add a `priority` or `specificity` field to mount definitions.
+Compiler sorts by this field.
+
+**Pros:**
+- Explicit control
+
+**Cons:**
+- Adds schema complexity
+- Users must understand mount ordering
+- Overkill for this use case
+
+## Recommendation
+
+**Option A** — sort by path depth.
+
+Rationale:
+- Mount specificity should "just work" without user intervention
+- Path depth is a natural proxy for specificity
+- A parent directory mount is almost always less specific than a child file mount
+- Implementation is ~20 lines in the compose write path
+- Can be combined with Option B (warn on exact conflicts) for safety
+
+## Acceptance Criteria
+
+1. A git repo mount to `/workspace/x` and a regular mount to `/workspace/x/y/config.json`
+   both work: the config.json file contains the regular mount contents.
+2. Multiple overlapping mounts sort consistently (deterministic).
+3. Exact same-target conflicts are logged as warnings.
+4. Both manifest and legacy flows behave correctly.
+5. Unit tests cover overlap scenarios.
+
+## Files to Modify
+
+- `apps/api/src/services/manifest_compiler.py` — `compile_compose()` sorting
+- `apps/api/src/api/tool_instances.py` — `_modify_compose_file()` sorting
+- `apps/api/tests/unit/test_manifest_compiler.py` — new tests
+- `apps/api/tests/unit/test_tool_instances.py` — new tests (or `test_tool_instances_legacy.py`)
diff --git a/openspec/proposals/mount-specificity-ordering.md b/openspec/proposals/mount-specificity-ordering.md
new file mode 100644
index 0000000..648c916
--- /dev/null
+++ b/openspec/proposals/mount-specificity-ordering.md
@@ -0,0 +1,19 @@
+# Proposal: Mount Specificity Ordering
+
+## Problem
+When git repo mounts and regular file mounts have overlapping target paths, the broader mount hides the more specific one because Docker Compose applies volumes in array order.
+
+Example: repo → `/workspace/x` (directory) hides file → `/workspace/x/y/config.json`.
+
+## Solution
+Sort all volume entries by target path depth before writing the compose file. Parent paths first, child paths last, so deeper mounts overlay correctly.
+
+## Scope
+- `manifest_compiler.py` — `compile_compose()`
+- `tool_instances.py` — `_modify_compose_file()`
+- Unit tests for overlap scenarios
+
+## Impact
+- Fixes silent mount hiding
+- Deterministic ordering
+- No user-facing API or schema changes
diff --git a/openspec/specs/mount-specificity-ordering.md b/openspec/specs/mount-specificity-ordering.md
new file mode 100644
index 0000000..12cda16
--- /dev/null
+++ b/openspec/specs/mount-specificity-ordering.md
@@ -0,0 +1,45 @@
+# Spec: Mount Specificity Ordering
+
+## Requirements
+
+1. All volume mount entries written to compose files must be sorted by target path depth.
+2. Shorter / parent target paths appear **before** deeper / child target paths.
+3. Deeper mounts are applied later by Docker, overlaying parent mounts correctly.
+4. Exact same-target overlaps are logged as warnings.
+5. Works for both manifest and legacy compose generation paths.
+
+## Algorithm
+
+```python
+def sort_volumes_by_specificity(volumes: list[str]) -> list[str]:
+    """
+    Sort volume strings so parent paths come before child paths.
+    Volume format: source:target or source:target:type
+    """
+```
+
+1. Parse each volume string to extract the target path (second colon-delimited field).
+2. Normalize the target: strip trailing `/`, collapse `//`.
+3. Compute depth = number of `/`-separated segments.
+4. Sort ascending by depth. Stable sort preserves input order for equal depths.
+5. Detect exact same-target strings and log warnings.
+
+## Compose Format Handling
+
+- `source:target` → target is second field
+- `source:target:bind` → target is second field
+- `source:target:ro` → target is second field
+- Split by `:` into at most 3 parts. Target is always index 1.
+
+## Integration Points
+
+- `compile_compose()` in `manifest_compiler.py`: sort `volumes` list before assigning to `service["volumes"]`.
+- `_modify_compose_file()` in `tool_instances.py`: sort `service_config["volumes"]` after appending extra volumes.
+
+## Tests
+
+- Repo mount `/workspace/x` + file mount `/workspace/x/y/config.json` → file mount comes after.
+- Same depth mounts → stable order preserved.
+- Exact same target → warning logged.
+- Empty volumes list → no-op.
+- Volume with `type` suffix → parsed correctly.
diff --git a/openspec/tasks/mount-specificity-ordering.md b/openspec/tasks/mount-specificity-ordering.md
new file mode 100644
index 0000000..dc28bd5
--- /dev/null
+++ b/openspec/tasks/mount-specificity-ordering.md
@@ -0,0 +1,12 @@
+# Tasks: Mount Specificity Ordering
+
+- [x] Exploration written
+- [x] Proposal written
+- [x] Spec written
+- [x] Design written
+- [x] Implement `sort_volumes_by_specificity` in `docker.py`
+- [x] Integrate sorting into `compile_compose` (manifest flow)
+- [x] Integrate sorting into `_modify_compose_file` (legacy flow)
+- [x] Add unit tests for helper and overlap scenarios
+- [x] Run quality gates (pytest, tsc)
+- [x] Commit and merge