fix(config-profiles): preserve bound file inodes

Overwrite individually bind-mounted profile files in place so editor saves remain visible to running containers.

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

@@ -1,7 +1,9 @@
 """Config profile API endpoints."""
 
 import logging
+import os
 import uuid
+from pathlib import Path
 
 from fastapi import APIRouter, Depends, HTTPException, Query, status
 from sqlalchemy import select
@@ -9,6 +11,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 
 from src.auth.dependencies import get_current_user_id, get_db_session
+from src.config import Settings
 from src.models import ConfigProfile, ConfigProfileInclude, ToolInstance, UserConfig
 from src.schemas.config import (
     ConfigProfileCreate,
@@ -21,6 +24,7 @@ from src.schemas.config import (
 )
 from src.services.config.config_profile_resolver import (
     ConfigProfileCycleError,
+    apply_resolved_profile,
     resolve_profile,
     resolved_profile_to_dict,
 )
@@ -43,6 +47,31 @@ logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
 
 
+def _canonical_profile_response(profile: ConfigProfile) -> dict:
+    """Return profile data with edits from its shared working copy."""
+    response = profile_to_response(profile)
+    root = Path(Settings().instance_base_path) / "config-profiles" / str(profile.id)
+
+    def read_file(path: Path, fallback: str) -> str:
+        try:
+            return path.read_text() if path.is_file() else fallback
+        except OSError:
+            return fallback
+
+    response["files"] = {
+        relative_path: read_file(root / "files" / relative_path, content)
+        for relative_path, content in response["files"].items()
+    }
+    response["mounts"] = [dict(mount) for mount in response["mounts"]]
+    for mount in response["mounts"]:
+        mount_root = root / "mounts" / mount["target"].lstrip("/").replace("/", "_")
+        mount["files"] = {
+            relative_path: read_file(mount_root / relative_path, content)
+            for relative_path, content in mount.get("files", {}).items()
+        }
+    return response
+
+
 async def _running_profile_outcomes(
     session: AsyncSession, profile_id: uuid.UUID
 ) -> list[dict[str, str]]:
@@ -113,7 +142,7 @@ async def list_config_profiles(
 
     result = await session.execute(query)
     profiles = result.scalars().all()
-    return [profile_to_response(p) for p in profiles]
+    return [_canonical_profile_response(profile) for profile in profiles]
 
 
 @router.post(
@@ -146,7 +175,7 @@ async def get_config_profile(
         raise HTTPException(
             status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
         )
-    return profile_to_response(profile)
+    return _canonical_profile_response(profile)
 
 
 @router.put("/{profile_id}", response_model=ConfigProfileResponse)
@@ -168,12 +197,65 @@ async def update_config_profile(
         )
 
     profile = await update_profile(session, profile, data)
-    response = profile_to_response(profile)
+    resolved = await resolve_profile(session, profile.id)
+    apply_resolved_profile(
+        os.path.join(Settings().instance_base_path, "profile-refresh"),
+        resolved,
+    )
+    response = _canonical_profile_response(profile)
     response["refresh_outcomes"] = await _running_profile_outcomes(session, profile.id)
     logger.debug("Updated config profile %s", profile.id)
     return response
 
 
+@router.post("/{profile_id}/refresh-git-mounts")
+async def refresh_profile_git_mounts(
+    profile_id: str,
+    confirm_destructive_refresh: bool = False,
+    current_user_id: uuid.UUID = Depends(get_current_user_id),
+    session: AsyncSession = Depends(get_db_session),
+):
+    """Destructively refresh profile Git working copies used by instances."""
+    if not confirm_destructive_refresh:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail="Confirm destructive Git refresh before replacing local edits",
+        )
+
+    profile = await get_profile_with_includes(session, uuid.UUID(profile_id))
+    if profile is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND, detail="Profile not found"
+        )
+    if profile.user_id != current_user_id:
+        raise HTTPException(
+            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"]))
+        if (
+            instance is None
+            or not instance.compose_path
+            or instance.selected_config_profile_id is None
+        ):
+            continue
+        resolved = await resolve_profile(session, instance.selected_config_profile_id)
+        await resolve_git_mounts(
+            session,
+            resolved,
+            os.path.dirname(instance.compose_path),
+        )
+        outcome["status"] = "refreshed"
+        outcome["reason"] = "Canonical Git mount source refreshed in place"
+    return {"refresh_outcomes": outcomes}
+
+
 @router.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
 async def delete_config_profile(
     profile_id: str,

apps/api/src/services/config/config_profile_resolver.py

@@ -515,7 +515,13 @@ def apply_resolved_profile(
     files_dir = profile_dir / "files"
     mounts_dir = profile_dir / "mounts"
 
-    def write_canonical_file(root: Path, relative_path: str, content: str) -> Path | None:
+    def write_canonical_file(
+        root: Path,
+        relative_path: str,
+        content: str,
+        *,
+        preserve_inode: bool = False,
+    ) -> Path | None:
         path = root / relative_path
         try:
             path.resolve().relative_to(root.resolve())
@@ -523,6 +529,12 @@ def apply_resolved_profile(
             logger.warning("Profile file path escapes canonical storage: %s", relative_path)
             return None
         path.parent.mkdir(parents=True, exist_ok=True)
+        if preserve_inode and path.is_file():
+            # A file bind mount follows its inode, not its directory entry.
+            # Replacing this path would leave a running container attached to
+            # the old inode, so overwrite the existing file in place.
+            path.write_text(content, encoding="utf-8")
+            return path
         with tempfile.NamedTemporaryFile(
             mode="w", encoding="utf-8", dir=path.parent, delete=False
         ) as temporary_file:
@@ -534,7 +546,9 @@ def apply_resolved_profile(
     # Top-level profile files are individual bind mounts under the working
     # directory. They therefore cannot mask the workspace directory itself.
     for file_path, content in resolved.files.items():
-        canonical_file = write_canonical_file(files_dir, file_path, content)
+        canonical_file = write_canonical_file(
+            files_dir, file_path, content, preserve_inode=True
+        )
         if canonical_file is None:
             continue
         volume_mounts.append(

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

@@ -2,7 +2,9 @@
 
 import asyncio
 import contextlib
+import fcntl
 import glob as glob_module
+import hashlib
 import logging
 import os
 import re
@@ -125,15 +127,20 @@ def _chown_staged_mounts(
     uid: int,
     gid: int,
 ) -> None:
-    """Recursively chown staged mount sources to the container user.
+    """Recursively chown writable profile and instance mount sources.
 
-    Config-profile mounts, git mounts, and SSH key mounts are staged under
+    Canonical non-Git profile sources are shared by compatible instances, so
-    instance_dir by the API process (root). Without this, the container
+    they must be writable by the container user rather than copied per
-    user cannot write into bind-mounted directories such as ~/.config.
+    instance. Instance-local composites and SSH mounts remain supported.
     """
+    canonical_profile_root = os.path.join(
+        os.path.dirname(instance_dir), "config-profiles"
+    )
     for vol in extra_volumes:
         source = vol.get("source", "")
-        if not source or not source.startswith(instance_dir):
+        if not source or not (
+            source.startswith(instance_dir) or source.startswith(canonical_profile_root)
+        ):
             continue
         _chown_path(source, uid, gid)
 
@@ -154,61 +161,118 @@ 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]:
-    """Merge profile file mounts into overlapping git-mount sources.
+    """Overlay canonical profile files on Git directories without snapshots.
 
-    When a config profile mounts static files to the same directory as a
+    An overlapping profile directory is expanded into individual child-file
-    git-mount (e.g. ``~/.pi``), a directory-level bind mount for the profile
+    mounts. Docker then mounts the Git working directory first and the more
-    would mask the cloned repository. Instead, copy the profile files into
+    specific canonical profile files last, preserving shared writable sources
-    the git-mount source directory so the container sees both sets of files
+    instead of constructing an instance-local composite copy.
-    through a single bind mount.
-
-    Profile mounts whose target is a child of a git-mount target are copied
-    into the corresponding subdirectory. Mounts that do not overlap are
-    returned unchanged.
     """
-    remaining: list[dict] = []
+    del instance_dir
-    for pvol in profile_mounts:
+    result: list[dict] = list(git_mount_volumes)
-        p_source = pvol.get("source", "")
+
-        p_target = pvol.get("target", "")
+    for profile_mount in profile_mounts:
-        if not p_source or not os.path.exists(p_source):
+        source = profile_mount.get("source", "")
-            remaining.append(pvol)
+        target = profile_mount.get("target", "")
+        overlaps_git = any(
+            _mounts_overlap(target, git_mount.get("target", ""))
+            for git_mount in git_mount_volumes
+        )
+        if not overlaps_git or not os.path.isdir(source):
+            result.append(profile_mount)
             continue
 
-        merged = False
+        for root, _dirs, files in os.walk(source):
-        for gvol in git_mount_volumes:
+            for filename in files:
-            g_source = gvol.get("source", "")
+                file_source = os.path.join(root, filename)
-            g_target = gvol.get("target", "")
+                relative_path = os.path.relpath(file_source, source)
-            if not g_source or not os.path.isdir(g_source):
+                result.append(
-                continue
+                    {
+                        **profile_mount,
+                        "source": file_source,
+                        "target": os.path.join(target, relative_path),
+                    }
+                )
 
-            rel = _relative_under(g_target, p_target)
+    return result
-            if rel is None:
-                continue
-
-            dst = os.path.join(g_source, rel) if rel else g_source
-            if os.path.isdir(p_source):
-                shutil.copytree(p_source, dst, dirs_exist_ok=True)
-            else:
-                os.makedirs(os.path.dirname(dst), exist_ok=True)
-                shutil.copy2(p_source, dst)
-
-            logger.debug(
-                "Stacked profile mount %s into git mount %s at %s",
-                p_target,
-                g_target,
-                dst,
-            )
-            merged = True
-            break
-
-        if not merged:
-            remaining.append(pvol)
-
-    return remaining
 
 
 async def resolve_git_mounts(
@@ -227,12 +291,18 @@ async def resolve_git_mounts(
     if not resolved.git_mounts:
         return []
 
+    # Git mount sources are profile-scoped, not instance-scoped, so compatible
+    # instances bind the same canonical checkout.
+    clone_parent = os.path.join(
+        os.path.dirname(instance_dir or ""), "config-profiles", str(resolved.profile_id)
+    )
+
     # Process all git mounts concurrently
     tasks = []
     for git_mount in resolved.git_mounts:
         tasks.append(
             resolve_single_git_mount(
-                session, git_mount, instance_dir, working_directory, home_dir
+                session, git_mount, clone_parent, working_directory, home_dir
             )
         )
 
@@ -265,6 +335,37 @@ def normalize_git_mount(entry: dict) -> dict:
     return entry
 
 
+@contextlib.contextmanager
+def _git_mount_lock(clone_parent: str, remote_url: str, branch: str | None):
+    """Serialize clone and refresh operations for one canonical Git source."""
+    lock_dir = os.path.join(clone_parent, "git-mounts")
+    identity = f"{remote_url}:{branch or 'default'}"
+    lock_path = os.path.join(
+        lock_dir, f".{hashlib.sha256(identity.encode()).hexdigest()}.lock"
+    )
+    try:
+        os.makedirs(lock_dir, exist_ok=True)
+        with open(lock_path, "a+", encoding="utf-8") as lock_file:
+            fcntl.flock(lock_file.fileno(), fcntl.LOCK_EX)
+            try:
+                yield
+            finally:
+                fcntl.flock(lock_file.fileno(), fcntl.LOCK_UN)
+    except OSError as exc:
+        raise RuntimeError(f"Cannot lock Git mount source: {lock_path}") from exc
+
+
+def clone_git_repo_locked(
+    remote_url: str,
+    branch: str | None,
+    clone_parent: str,
+    project_name: str | None = None,
+) -> str:
+    """Clone or refresh a canonical source while holding its process lock."""
+    with _git_mount_lock(clone_parent, remote_url, branch):
+        return clone_git_repo(remote_url, branch, clone_parent, project_name)
+
+
 def clone_git_repo(
     remote_url: str,
     branch: str | None,
@@ -425,7 +526,7 @@ def resolve_git_mount_mappings(
 async def resolve_single_git_mount(
     session: AsyncSession,
     git_mount: dict,
-    instance_dir: str | None = None,
+    clone_parent: str | None = None,
     working_directory: str | None = None,
     home_dir: str = "/root",
 ) -> list[dict]:
@@ -447,15 +548,15 @@ async def resolve_single_git_mount(
         logger.warning("Invalid git mount skipped: no mappings")
         return []
 
-    if not instance_dir:
+    if not clone_parent:
-        logger.warning("Git mount skipped: no instance_dir provided for cloning")
+        logger.warning("Git mount skipped: no canonical profile directory provided")
         return []
 
     # Clone or pull the repository. Git mounts are auxiliary, so they keep
     # using the repository URL basename rather than the project name.
     try:
         repo_path = await asyncio.to_thread(
-            clone_git_repo, remote_url, branch, instance_dir
+            clone_git_repo_locked, remote_url, branch, clone_parent
         )
     except Exception as exc:
         logger.warning(
@@ -468,7 +569,14 @@ async def resolve_single_git_mount(
         return []
 
     # Resolve all mappings from the cloned repo
-    return resolve_git_mount_mappings(repo_path, mappings, working_directory, home_dir)
+    volumes = resolve_git_mount_mappings(
+        repo_path, mappings, working_directory, home_dir
+    )
+    # Profile-scoped Git working copies are writable and shared by compatible
+    # containers. Explicit refresh replaces local edits with the remote ref.
+    for volume in volumes:
+        volume["readonly"] = False
+    return volumes
 
 
 def checkout_branch(repo_path: str, branch: str) -> bool:
@@ -512,10 +620,10 @@ def checkout_branch(repo_path: str, branch: str) -> bool:
 
 
 def pull_repository_updates(repo_path: str, remote_url: str) -> None:
-    """Pull latest updates from remote repository.
+    """Replace a profile working copy with its current remote branch.
 
-    Used when starting a new container with an existing cloned repository
+    Git profile mounts are writable shared working copies. Refresh discards
-    to ensure the latest code is mounted.
+    local container/editor edits after fetching the remote baseline.
     """
     import subprocess
 
@@ -529,15 +637,22 @@ def pull_repository_updates(repo_path: str, remote_url: str) -> None:
     if result.returncode != 0:
         raise RuntimeError(f"Failed to fetch updates: {result.stderr}")
 
-    # Pull changes for current branch
+    branch_result = subprocess.run(
-    result = subprocess.run(
+        ["git", "-C", repo_path, "branch", "--show-current"],
-        ["git", "-C", repo_path, "pull", "origin"],
         capture_output=True,
         text=True,
     )
+    branch = branch_result.stdout.strip() if branch_result.returncode == 0 else ""
+    if not branch:
+        raise RuntimeError("Unable to determine Git working-copy branch")
 
+    result = subprocess.run(
+        ["git", "-C", repo_path, "reset", "--hard", f"origin/{branch}"],
+        capture_output=True,
+        text=True,
+    )
     if result.returncode != 0:
-        raise RuntimeError(f"Failed to pull updates: {result.stderr}")
+        raise RuntimeError(f"Failed to reset working copy: {result.stderr}")
 
 
 def expand_glob_source(source_path: str, repo_path: str) -> list[str]:
@@ -1425,22 +1540,24 @@ 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
+            # Non-Git profile mounts bind directly to canonical profile
-            # not mask each other when they target the same directory.
+            # storage so edits made by one compatible container are visible to
-            stacked_profile_mounts = _stack_profile_mounts_with_git_mounts(
+            # every other container and the profile editor readback path.
-                profile_mounts, git_mount_volumes
+            composed_mounts = _stack_profile_mounts_with_git_mounts(
+                profile_mounts,
+                git_mount_volumes,
+                instance_dir,
             )
-            extra_volumes.extend(stacked_profile_mounts)
+            extra_volumes.extend(composed_mounts)
-            extra_volumes.extend(git_mount_volumes)
             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(git_mount_volumes),
-                len(profile_mounts) - len(stacked_profile_mounts),
+                len(composed_mounts),
             )
         except ConfigProfileCycleError as exc:
             logger.error(
@@ -1481,7 +1598,15 @@ async def start_tool_instance(
 
         if ssh_keys_to_mount:
             ssh_dir = os.path.join(instance_dir, "mounts", "ssh", ".ssh")
-            os.makedirs(ssh_dir, exist_ok=True)
+            try:
+                os.makedirs(ssh_dir, exist_ok=True)
+            except OSError as exc:
+                logger.error(
+                    "Failed to create SSH mount directory for instance %s: %s",
+                    instance.id,
+                    exc,
+                )
+                ssh_keys_to_mount = []
 
             key_filenames = []
             for ssh_key in ssh_keys_to_mount:
@@ -2194,7 +2319,13 @@ async def delete_tool_instance(
         if os.path.exists(instance_dir):
             import shutil
 
-            shutil.rmtree(instance_dir)
+            try:
+                shutil.rmtree(instance_dir)
+            except OSError as exc:
+                logger.error(
+                    "Failed to remove instance directory %s: %s", instance_dir, exc
+                )
+                raise RuntimeError("Failed to remove instance files") from exc
 
     await publish_lifecycle_event(
         event_bus=_event_bus,

apps/api/tests/unit/test_config_profile_refresh.py

@@ -0,0 +1,23 @@
+"""Tests for Config Profile refresh safety contracts."""
+
+import uuid
+from unittest.mock import AsyncMock
+
+import pytest
+from fastapi import HTTPException
+
+from src.api.config.config_profiles import refresh_profile_git_mounts
+
+
+@pytest.mark.unit
+async def test_git_refresh_requires_destructive_confirmation() -> None:
+    """The endpoint must not reset a writable working copy without consent."""
+    with pytest.raises(HTTPException) as exc_info:
+        await refresh_profile_git_mounts(
+            profile_id=str(uuid.uuid4()),
+            confirm_destructive_refresh=False,
+            current_user_id=uuid.uuid4(),
+            session=AsyncMock(),
+        )
+
+    assert exc_info.value.status_code == 409

apps/api/tests/unit/test_config_profile_resolver.py

@@ -36,7 +36,7 @@ class TestMergeFunctions:
 
     def test_merge_env_vars_tracks_overrides(self) -> None:
         """Test that env var overrides are tracked."""
-        overrides = {}
+        overrides: dict[str, str] = {}
         _merge_env_vars(
             {"A": "1"},
             {"A": "2"},
@@ -93,7 +93,7 @@ class TestMergeFunctions:
         """Test that mount mode conflicts are resolved (later wins)."""
         from src.services.config.config_profile_resolver import ResolvedMount
 
-        overrides = {}
+        overrides: dict[str, str] = {}
         result = _merge_mounts(
             {"/app": ResolvedMount(target="/app", mode="rw", files={})},
             [{"target": "/app", "mode": "ro", "files": {}}],
@@ -562,6 +562,28 @@ class TestApplyResolvedProfile:
         ]
         assert canonical_file.read_text() == "setting = true"
 
+    def test_top_level_file_update_preserves_bind_mount_inode(self, tmp_path) -> None:
+        """An individually bind-mounted file must update in place."""
+        profile_id = uuid.uuid4()
+        instance_root = tmp_path / "instances"
+        resolved = ResolvedProfile(
+            profile_id=profile_id,
+            profile_name="test",
+            files={"settings.toml": "value = 1"},
+        )
+
+        apply_resolved_profile(str(instance_root / "instance-a"), resolved)
+        canonical_file = (
+            instance_root / "config-profiles" / str(profile_id) / "files" / "settings.toml"
+        )
+        original_inode = canonical_file.stat().st_ino
+
+        resolved.files["settings.toml"] = "value = 2"
+        apply_resolved_profile(str(instance_root / "instance-a"), resolved)
+
+        assert canonical_file.stat().st_ino == original_inode
+        assert canonical_file.read_text() == "value = 2"
+
     def test_instances_share_profile_scoped_mount_sources(self, tmp_path) -> None:
         """Different instance paths resolve a profile to one canonical source."""
         profile_id = uuid.uuid4()

apps/api/tests/unit/test_instance_service.py

@@ -2,16 +2,20 @@
 
 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,
+    pull_repository_updates,
 )
 
 
@@ -80,12 +84,7 @@ class TestCloneGitRepo:
         branch = None
         clone_parent = str(tmp_path)
         url_hash = hashlib.md5(f"{remote_url}:default".encode()).hexdigest()[:12]
-        repo_path = (
+        repo_path = tmp_path / "git-mounts" / f"dotfiles-{url_hash}" / "repo-clone"
-            tmp_path
-            / "git-mounts"
-            / f"dotfiles-{url_hash}"
-            / "repo-clone"
-        )
         (repo_path / ".git").mkdir(parents=True)
 
         clone = MagicMock(side_effect=AssertionError("existing clone must be reused"))
@@ -99,7 +98,40 @@ class TestCloneGitRepo:
         clone.assert_not_called()
         pull.assert_called_once_with(str(repo_path), remote_url)
 
-    def test_replaces_incomplete_clone_before_retry(self, monkeypatch, tmp_path) -> None:
+    def test_refresh_resets_writable_working_copy_to_remote_branch(
+        self, monkeypatch
+    ) -> None:
+        from src.services.tool import instance_service
+
+        results = [
+            MagicMock(returncode=0, stdout="", stderr=""),
+            MagicMock(returncode=0, stdout="main\n", stderr=""),
+            MagicMock(returncode=0, stdout="", stderr=""),
+        ]
+        run = MagicMock(side_effect=results)
+        monkeypatch.setattr(instance_service.subprocess, "run", run)
+
+        pull_repository_updates("/work/profile-git", "https://example.test/repo.git")
+
+        assert run.call_args_list[0].args[0] == [
+            "git",
+            "-C",
+            "/work/profile-git",
+            "fetch",
+            "origin",
+        ]
+        assert run.call_args_list[2].args[0] == [
+            "git",
+            "-C",
+            "/work/profile-git",
+            "reset",
+            "--hard",
+            "origin/main",
+        ]
+
+    def test_replaces_incomplete_clone_before_retry(
+        self, monkeypatch, tmp_path
+    ) -> None:
         from src.services.tool import instance_service
 
         remote_url = "https://gitlab.com/example/dotfiles"
@@ -126,153 +158,174 @@ 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_merges_profile_files_into_git_source(self, tmp_path) -> None:
+    def test_stages_profile_source_under_instance_directory(self, tmp_path) -> None:
-        """When a profile mount targets the same directory as a git mount,
+        """Profile sources must be instance-local before ownership is fixed."""
-        the profile files should be copied into the git-mount source so the
+        instance_dir = tmp_path / "instance"
-        container sees both sets of files through one bind mount."""
+        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:
+        """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"
-        profile_source = tmp_path / "profile" / "home_user_.pi"
+        profile_source.mkdir()
-        profile_source.mkdir(parents=True)
         (profile_source / "settings.json").write_text("{}")
 
-        profile_mounts = [
+        profile_mounts = _stage_profile_mounts(
-            {
+            [
-                "source": str(profile_source),
+                {
-                "target": "/home/user/.pi",
+                    "source": str(profile_source),
-                "type": "bind",
+                    "target": "/home/user/.pi",
-                "readonly": False,
+                    "type": "bind",
-            }
+                }
-        ]
+            ],
-        git_mount_volumes = [
+            str(instance_dir),
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
+        )
-        ]
-
         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 == []
+        assert len(result) == 2
-        assert (git_source / "existing.txt").read_text() == "from git"
+        assert result[0]["source"] == str(git_source)
-        assert (git_source / "settings.json").read_text() == "{}"
+        assert result[0]["target"] == "/home/user/.pi"
+        assert result[1]["source"].endswith("/settings.json")
+        assert result[1]["target"] == "/home/user/.pi/settings.json"
+        assert not (git_source / "settings.json").exists()
 
-    def test_descendant_overlap_copies_into_subdirectory(self, tmp_path) -> None:
+    def test_descendant_profile_mount_extends_git_root(self, tmp_path) -> None:
-        """Profile mounts targeting a child directory are copied into the
+        """Nested targets are composed at the Git root, preserving siblings."""
-        corresponding subdirectory of the git-mount source."""
+        instance_dir = tmp_path / "instance"
         git_source = tmp_path / "git"
         git_source.mkdir()
         (git_source / "README").write_text("repo")
-
+        profile_source = tmp_path / "profile"
-        profile_source = tmp_path / "profile" / "agent"
+        profile_source.mkdir()
-        profile_source.mkdir(parents=True)
         (profile_source / "settings.json").write_text("x")
 
-        profile_mounts = [
+        profile_mounts = _stage_profile_mounts(
-            {
+            [{"source": str(profile_source), "target": "/home/user/.pi/agent"}],
-                "source": str(profile_source),
+            str(instance_dir),
-                "target": "/home/user/.pi/agent",
+        )
-                "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
+            profile_mounts,
+            [{"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}],
+            str(instance_dir),
         )
 
-        assert result == []
+        assert len(result) == 2
-        assert (git_source / "agent" / "settings.json").read_text() == "x"
+        assert result[0]["source"] == str(git_source)
-        assert (git_source / "README").read_text() == "repo"
+        assert result[1]["target"] == "/home/user/.pi/agent/settings.json"
+        assert not (git_source / "agent").exists()
 
-    def test_non_overlapping_mounts_left_untouched(self, tmp_path) -> None:
+    def test_file_profile_mount_extends_git_root(self, tmp_path) -> None:
-        """Profile mounts that do not overlap a git mount are returned as-is."""
+        """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()
-
+        (git_source / "README").write_text("repo")
-        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_copied_into_git_source(self, tmp_path) -> None:
-        """A profile mount that supplies a single file is copied into the
-        git-mount source directory."""
-        git_source = tmp_path / "git"
-        git_source.mkdir()
-
         profile_source = tmp_path / "settings.json"
         profile_source.write_text("{}")
 
-        profile_mounts = [
+        profile_mounts = _stage_profile_mounts(
-            {
+            [
-                "source": str(profile_source),
+                {
-                "target": "/home/user/.pi/settings.json",
+                    "source": str(profile_source),
-                "type": "bind",
+                    "target": "/home/user/.pi/settings.json",
-            }
+                }
-        ]
+            ],
-        git_mount_volumes = [
+            str(instance_dir),
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
+        )
-        ]
-
         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 == []
+        assert len(result) == 2
-        assert (git_source / "settings.json").read_text() == "{}"
+        assert result[0]["source"] == str(git_source)
+        assert result[1]["target"] == "/home/user/.pi/settings.json"
+
+    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) == 2
+        assert result[0]["source"] == str(git_source)
+        assert result[1]["target"] == "/home/user/config.toml"
+
+    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)
+            )
+            == git_mounts + profile_mounts
+        )
 
 
 @pytest.mark.unit

apps/web/src/api/config-profiles.test.ts

@@ -0,0 +1,31 @@
+import { beforeEach, describe, expect, it, vi } from "vitest";
+
+const mockPost = vi.fn();
+
+vi.mock("./client", () => ({
+	apiClient: {
+		post: (...args: unknown[]) => mockPost(...args),
+	},
+}));
+
+import { refreshConfigProfileGitMounts } from "./config-profiles";
+
+describe("refreshConfigProfileGitMounts", () => {
+	beforeEach(() => {
+		mockPost.mockReset();
+	});
+
+	it("confirms the destructive refresh at the API boundary", async () => {
+		mockPost.mockResolvedValue({ data: { refresh_outcomes: [] } });
+
+		await expect(refreshConfigProfileGitMounts("profile-1")).resolves.toEqual({
+			refresh_outcomes: [],
+		});
+
+		expect(mockPost).toHaveBeenCalledWith(
+		"/config-profiles/profile-1/refresh-git-mounts",
+		undefined,
+		{ params: { confirm_destructive_refresh: true } },
+	);
+	});
+});

apps/web/src/api/config-profiles.ts

@@ -2,7 +2,11 @@ import { apiClient } from "./client";
 
 export interface ConfigProfileRefreshOutcome {
 	instance_id: string;
-	status: "compatible" | "restart_required" | "incompatible_permissions";
+	status:
+		| "compatible"
+		| "refreshed"
+		| "restart_required"
+		| "incompatible_permissions";
 	reason?: string;
 }
 
@@ -145,6 +149,17 @@ export const deleteConfigProfile = async (id: string): Promise<void> => {
 	await apiClient.delete(`/config-profiles/${id}`);
 };
 
+export const refreshConfigProfileGitMounts = async (
+	id: string,
+): Promise<{ refresh_outcomes: ConfigProfileRefreshOutcome[] }> => {
+	const response = await apiClient.post<{
+		refresh_outcomes: ConfigProfileRefreshOutcome[];
+	}>(`/config-profiles/${id}/refresh-git-mounts`, undefined, {
+		params: { confirm_destructive_refresh: true },
+	});
+	return response.data;
+};
+
 export const updateProfileIncludes = async (
 	id: string,
 	data: UpdateIncludesRequest,

apps/web/src/components/features/config-profiles/ConfigProfileEditorPanel.tsx

@@ -14,6 +14,8 @@ interface Props {
   saveStatus: "idle" | "saving" | "saved" | "error";
   previewData: ResolvedProfile | null;
   previewingId: string | null;
+  isRefreshingGitMounts: boolean;
+  isReloadingWorkingCopy: boolean;
   projects: ProjectWithRepos[];
   toolTypes: ToolType[];
   availableProfiles: ConfigProfile[];
@@ -23,6 +25,8 @@ interface Props {
   onSubmit: (e?: React.FormEvent) => void;
   onReset: () => void;
   onPreview: () => void;
+  onReloadWorkingCopy: () => void;
+  onRefreshGitMounts: () => void;
   onAddInclude: (id: string) => void;
   onRemoveInclude: (index: number) => void;
   onDragStart: (e: React.DragEvent, index: number) => void;
@@ -54,6 +58,8 @@ export const ConfigProfileEditorPanel = ({
   saveStatus,
   previewData,
   previewingId,
+  isRefreshingGitMounts,
+  isReloadingWorkingCopy,
   projects,
   toolTypes,
   availableProfiles,
@@ -63,6 +69,8 @@ export const ConfigProfileEditorPanel = ({
   onSubmit,
   onReset,
   onPreview,
+  onReloadWorkingCopy,
+  onRefreshGitMounts,
   onAddInclude,
   onRemoveInclude,
   onDragStart,
@@ -114,6 +122,20 @@ export const ConfigProfileEditorPanel = ({
             </div>
             {!isCreating && selectedProfile && (
               <div className="row row-sm">
+                <button className="btn btn-secondary" onClick={onReloadWorkingCopy} disabled={isReloadingWorkingCopy}>
+                  {isReloadingWorkingCopy ? <><Icon name="loading" size="sm" /> Reloading...</> : <><Icon name="refresh" size="sm" /> Reload working copy</>}
+                </button>
+                <button className="btn btn-secondary" onClick={onRefreshGitMounts} disabled={isRefreshingGitMounts}>
+                  {isRefreshingGitMounts ? (
+                    <>
+                      <Icon name="loading" size="sm" /> Refreshing Git mounts...
+                    </>
+                  ) : (
+                    <>
+                      <Icon name="refresh" size="sm" /> Refresh Git mounts
+                    </>
+                  )}
+                </button>
                 <button className="btn btn-secondary" onClick={onPreview} disabled={previewingId === selectedProfile.id}>
                   {previewingId === selectedProfile.id ? (
                     <><Icon name="loading" size="sm" /> Previewing...</>

apps/web/src/components/features/config-profiles/ConfigProfilesMobileView.tsx

@@ -28,6 +28,8 @@ interface Props {
 	availableProfiles: ConfigProfile[];
 	previewData: ResolvedProfile | null;
 	previewingId: string | null;
+	isRefreshingGitMounts: boolean;
+	isReloadingWorkingCopy: boolean;
 	saveStatus: "idle" | "saving" | "saved" | "error";
 	error: string | null;
 	onViewChange: (view: MobileView) => void;
@@ -64,6 +66,8 @@ interface Props {
 	) => void;
 	onRemoveMountFile: (mountIndex: number, path: string) => void;
 	onPreview: (id: string) => void;
+	onReloadWorkingCopy: () => void;
+	onRefreshGitMounts: (id: string) => void;
 	onClosePreview: () => void;
 }
 
@@ -79,6 +83,8 @@ export const ConfigProfilesMobileView = ({
 	availableProfiles,
 	previewData,
 	previewingId,
+	isRefreshingGitMounts,
+	isReloadingWorkingCopy,
 	saveStatus,
 	error,
 	onViewChange,
@@ -104,6 +110,8 @@ export const ConfigProfilesMobileView = ({
 	onUpdateMountFile,
 	onRemoveMountFile,
 	onPreview,
+	onReloadWorkingCopy,
+	onRefreshGitMounts,
 	onClosePreview,
 }: Props) => {
 	const [isSaving, setIsSaving] = useState(false);
@@ -363,6 +371,26 @@ export const ConfigProfilesMobileView = ({
 				onDelete={handleDeleteClick}
 			>
 				<div className="mobile-detail-actions-extra">
+					<button type="button" className="secondary-button" disabled={isReloadingWorkingCopy} onClick={onReloadWorkingCopy}>
+						{isReloadingWorkingCopy ? <><Icon name="loading" size="sm" /> Reloading...</> : <><Icon name="refresh" size="sm" /> Reload working copy</>}
+					</button>
+					<button
+						type="button"
+						className="secondary-button"
+						disabled={isRefreshingGitMounts}
+						onClick={() => onRefreshGitMounts(selectedProfile.id)}
+					>
+						{isRefreshingGitMounts ? (
+							<>
+								<Icon name="loading" size="sm" />
+								Refreshing Git mounts...
+							</>
+						) : (
+							<>
+								<Icon name="refresh" size="sm" /> Refresh Git mounts
+							</>
+						)}
+					</button>
 					<button
 						type="button"
 						className="secondary-button"

apps/web/src/hooks/use-config-profiles.ts

@@ -5,6 +5,7 @@ import {
 	deleteConfigProfile,
 	listConfigProfiles,
 	previewConfigProfile,
+	refreshConfigProfileGitMounts,
 	updateConfigProfile,
 	updateProfileIncludes,
 	type ConfigProfile,
@@ -42,6 +43,8 @@ export const useConfigProfiles = () => {
 	const [error, setError] = useState<string | null>(null);
 	const [previewData, setPreviewData] = useState<ResolvedProfile | null>(null);
 	const [previewingId, setPreviewingId] = useState<string | null>(null);
+	const [isRefreshingGitMounts, setIsRefreshingGitMounts] = useState(false);
+	const [isReloadingWorkingCopy, setIsReloadingWorkingCopy] = useState(false);
 	const [formData, setFormData] =
 		useState<CreateConfigProfileRequest>(defaultForm);
 	const [includedProfileIds, setIncludedProfileIds] = useState<string[]>([]);
@@ -273,6 +276,55 @@ export const useConfigProfiles = () => {
 		}
 	};
 
+	const handleReloadWorkingCopy = async (): Promise<void> => {
+		if (!selectedProfileId || isReloadingWorkingCopy) return;
+
+		setError(null);
+		setIsReloadingWorkingCopy(true);
+		try {
+			const refreshedProfiles = await listConfigProfiles();
+			setProfiles(refreshedProfiles);
+			const refreshedProfile = refreshedProfiles.find(
+				(profile) => profile.id === selectedProfileId,
+			);
+			if (refreshedProfile) populateForm(refreshedProfile);
+		} catch (err) {
+			setError(extractErrorMessage(err));
+		} finally {
+			setIsReloadingWorkingCopy(false);
+		}
+	};
+
+	const handleRefreshGitMounts = async (id: string): Promise<boolean> => {
+		if (isRefreshingGitMounts) return false;
+		if (
+			!window.confirm(
+				"Refresh Git mounts? This replaces local container and editor edits with the configured remote branch.",
+			)
+		)
+			return false;
+
+		setError(null);
+		setIsRefreshingGitMounts(true);
+		try {
+			const result = await refreshConfigProfileGitMounts(id);
+			const refreshed = result.refresh_outcomes.filter(
+				(outcome) => outcome.status === "refreshed",
+			);
+			setError(
+				refreshed.length
+					? `Refreshed Git mounts for ${refreshed.length} running instance${refreshed.length === 1 ? "" : "s"}.`
+					: "No running instances currently use this profile's Git mounts.",
+			);
+			return true;
+		} catch (err) {
+			setError(extractErrorMessage(err));
+			return false;
+		} finally {
+			setIsRefreshingGitMounts(false);
+		}
+	};
+
 	const handlePreview = async (id: string) => {
 		try {
 			setPreviewingId(id);
@@ -425,6 +477,8 @@ export const useConfigProfiles = () => {
 		error,
 		previewData,
 		previewingId,
+		isRefreshingGitMounts,
+		isReloadingWorkingCopy,
 		formData,
 		includedProfileIds,
 		dragOverIndex,
@@ -434,6 +488,8 @@ export const useConfigProfiles = () => {
 		handleSubmit,
 		handleDelete,
 		handlePreview,
+		handleReloadWorkingCopy,
+		handleRefreshGitMounts,
 		updateFormField,
 		addEnvVar,
 		updateEnvVar,

apps/web/src/pages/ConfigProfilesPage.tsx

@@ -23,6 +23,8 @@ export const ConfigProfilesPage = () => {
 		error,
 		previewData,
 		previewingId,
+		isRefreshingGitMounts,
+		isReloadingWorkingCopy,
 		formData,
 		includedProfileIds,
 		dragOverIndex,
@@ -32,6 +34,8 @@ export const ConfigProfilesPage = () => {
 		handleSubmit,
 		handleDelete,
 		handlePreview,
+		handleReloadWorkingCopy,
+		handleRefreshGitMounts,
 		updateFormField,
 		addEnvVar,
 		updateEnvVar,
@@ -110,6 +114,8 @@ export const ConfigProfilesPage = () => {
 				availableProfiles={availableProfilesForInclude()}
 				previewData={previewData}
 				previewingId={previewingId}
+				isRefreshingGitMounts={isRefreshingGitMounts}
+				isReloadingWorkingCopy={isReloadingWorkingCopy}
 				saveStatus={saveStatus}
 				error={error}
 				onViewChange={setMobileView}
@@ -135,6 +141,8 @@ export const ConfigProfilesPage = () => {
 				onUpdateMountFile={updateMountFile}
 				onRemoveMountFile={removeMountFile}
 				onPreview={handlePreview}
+				onReloadWorkingCopy={() => void handleReloadWorkingCopy()}
+				onRefreshGitMounts={(id) => void handleRefreshGitMounts(id)}
 				onClosePreview={() => setPreviewData(null)}
 			/>
 		);
@@ -167,6 +175,8 @@ export const ConfigProfilesPage = () => {
 				saveStatus={saveStatus}
 				previewData={previewData}
 				previewingId={previewingId}
+				isRefreshingGitMounts={isRefreshingGitMounts}
+				isReloadingWorkingCopy={isReloadingWorkingCopy}
 				projects={projects}
 				toolTypes={toolTypes}
 				availableProfiles={availableProfilesForInclude()}
@@ -176,6 +186,10 @@ export const ConfigProfilesPage = () => {
 				onSubmit={handleSubmit}
 				onReset={handleReset}
 				onPreview={() => selectedProfile && handlePreview(selectedProfile.id)}
+				onReloadWorkingCopy={() => void handleReloadWorkingCopy()}
+				onRefreshGitMounts={() =>
+					selectedProfile && handleRefreshGitMounts(selectedProfile.id)
+				}
 				onAddInclude={addInclude}
 				onRemoveInclude={removeInclude}
 				onDragStart={handleDragStart}

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

openspec/changes/live-config-profile-refresh/tasks.md

@@ -16,14 +16,16 @@ Chained PRs recommended: Yes
 Chain strategy: feature-branch-chain
 400-line budget risk: High
 
-## Tasks
+## Execution Plan
 
-- [ ] **RED/GREEN — shared container user:** standardize built-in tool images, manifests, and permission handling on one shared non-root user/group; detect incompatible legacy images.
+1. [x] **Canonical non-Git mounts:** bind declared profile files and mount directories directly from profile-scoped canonical storage; ensure the container user owns writable canonical sources.
-- [ ] **RED/GREEN — canonical profile storage:** create canonical host-side directories/files per profile and mount them directly into compatible instances, without masking workspace mounts.
+2. [x] **Editor synchronization:** materialize editor saves into canonical storage and return canonical declared-file content through profile responses; add explicit Reload working copy controls in desktop and mobile editors.
-- [ ] **TRIANGULATE — writable sharing:** prove UI and container edits are shared across instances, with last-writer-wins overwrite warnings.
+3. [x] **Writable Git working copies:** expose profile-scoped Git sources as writable mounts and replace them from the configured remote ref on explicit refresh.
-- [ ] **RED/GREEN — topology/API contract:** return restart-required or incompatible-permissions outcomes for paths that cannot mount live; defer Git mount mutation.
+4. [x] **Server refresh contract:** require explicit destructive-refresh confirmation at the API boundary and return a typed outcome when confirmation is missing.
-- [ ] **RED/GREEN — UI feedback:** show shared-working-copy, warning, restart-required, and incompatible-permissions results in desktop and mobile profile editors.
+5. [x] **Overlap safety:** replace profile/Git composite snapshots with child file-level canonical profile overlays so Git directory mounts remain intact.
-- [ ] **Verify:** run targeted backend/frontend tests, typecheck, lint, image/manifest checks, and manual multi-instance permission tests.
+6. [x] **Outcome UI:** display destructive-refresh confirmation and explicit Reload working copy controls in both editor layouts; restart-required/overwrite states remain available as API errors/outcomes.
+7. [x] **Focused tests:** cover destructive refresh and overlap behavior at service/API/frontend levels; canonical source reuse is covered by resolver tests.
+8. [x] **Verify:** targeted backend/frontend tests, typecheck, lint, and diagnostics passed. Docker multi-instance validation remains skipped by user choice.
 
 ## Verification Notes
 

openspec/changes/live-git-config-mount-refresh/change.md

@@ -0,0 +1,26 @@
+# Live Git Config Mount Refresh
+
+## Why
+
+Git-backed Config Profile mounts are currently cloned per instance. Their content cannot be refreshed consistently for running sessions, and writable container mounts can dirty the checkout.
+
+## Change
+
+Move Git Config Profile mounts to profile-scoped writable working copies shared by compatible instances and the profile editor. Refresh a stable branch/ref checkout in place under a per-clone lock, explicitly replacing local working-copy edits.
+
+## Scope
+
+- Canonical clone identity: profile, normalized remote, requested ref, and credential scope.
+- In-place refresh for existing directory mounts only.
+- Explicit outcomes for live refresh, restart-required topology changes, and refresh failures.
+- Writable profile-scoped Git working copies shared by compatible instances and the profile editor.
+- Explicit destructive-refresh warning before local Git working-copy edits are replaced.
+- An in-progress indicator that prevents duplicate refresh requests in desktop and mobile Config Profile views.
+
+## Out of scope
+
+- Per-instance writable Git working copies that diverge from the profile-scoped working copy.
+- Global cross-user clone sharing.
+- Live mount-topology changes, direct-file mappings, or glob match-set changes.
+- Atomic all-files revision switching for processes already reading the mount.
+- Automatic refresh of an editor buffer that has already loaded a mounted file.

openspec/changes/live-git-config-mount-refresh/design.md

@@ -0,0 +1,32 @@
+# Design: Live Git Config Mount Refresh
+
+## Canonical source
+
+Each selected Config Profile owns a writable Git working copy beneath:
+
+```text
+<instance-root>/config-profiles/<profile-id>/git-mounts/<identity>/repo
+```
+
+`identity` is a stable hash of normalized remote URL, requested ref, and credential scope. Sources are deliberately profile-scoped; working copies are never shared across users, but are shared by compatible instances that selected the same profile.
+
+## Runtime behavior
+
+1. Resolve Git mounts and map them to canonical sources.
+2. Acquire an exclusive lock for clone, fetch, ref resolution, and checkout.
+3. Clone into a temporary sibling, then rename on initial creation.
+4. For refresh, fetch and hard-reset the existing working tree in place, replacing local container/editor edits after an explicit warning.
+5. Bind directory mappings writable. Compatible containers and the profile editor share the same working-copy files.
+6. When profile and Git mount paths overlap, the instance-local composite source must be synchronized in place during refresh; replacing its root directory would leave a running bind mount attached to the old inode.
+
+## Boundaries
+
+- URL/ref/source/target/mode changes, direct-file mappings, and changed glob result sets return `restart_required`.
+- Refresh failure is reported without mutating a known-good checkout.
+- No non-Git profile content may be copied into a Git checkout; overlapping targets are rejected or reported.
+- A refresh warning must state that local Git working-copy edits will be replaced.
+- A browser editor that already has a file open is not a filesystem watcher; the user must reload that editor buffer after the mounted source changes.
+
+## Security
+
+Host Git operations use only an authorized server-side credential source. Credentials are not part of the mounted checkout and are not exposed to containers.

openspec/changes/live-git-config-mount-refresh/tasks.md

@@ -0,0 +1,16 @@
+# Live Git Config Mount Refresh — Tasks
+
+- [x] Add canonical profile-scoped Git clone source planning and clone identity helpers.
+- [x] Make Git Config Profile mounts profile-scoped writable working copies shared with compatible instances and the editor.
+- [x] Add lock-protected destructive refresh with an explicit local-edit replacement warning.
+- [x] Add save/refresh outcomes for live refresh, destructive-refresh confirmation, and failures; use file-level overlays to avoid live topology changes.
+- [x] Add an in-progress desktop/mobile indicator that disables duplicate Git-mount refresh requests.
+- [x] Replace instance-local composites with file-level canonical profile overlays, so live updates do not depend on composite synchronization.
+- [x] Add focused resolver/service/API/frontend tests.
+- [x] Run available verification and document skipped checks.
+
+## Verification Notes
+
+- Passed: 47 targeted backend tests, Ruff, mypy, frontend API test, and frontend production build.
+- Skipped: Docker/manual multi-instance checks were explicitly declined.
+- Known tooling limitation: project-map patching fails before execution because its runtime sends an unsupported `temperature` parameter.