fix(config-profiles): preserve mounted file inodes

Update files within profile directory mounts in place so editor saves reach running containers.

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

@@ -3,6 +3,7 @@
 import logging
 import os
 import uuid
+from pathlib import Path
 
 from fastapi import APIRouter, Depends, HTTPException, Query, status
 from sqlalchemy import select
@@ -10,6 +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,
@@ -22,6 +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,
 )
@@ -44,6 +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]]:
@@ -114,7 +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(
@@ -147,7 +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)
@@ -169,7 +197,12 @@ 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
@@ -178,10 +211,17 @@ async def update_config_profile(
 @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),
 ):
-    """Refresh canonical Git mount sources used by running profile instances."""
+    """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(

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(
@@ -555,7 +569,7 @@ def apply_resolved_profile(
         expanded_target = os.path.normpath(expand_container_path(mount.target, home_dir))
         mount_dir = mounts_dir / expanded_target.lstrip("/").replace("/", "_")
         for file_path, content in mount.files.items():
-            write_canonical_file(mount_dir, file_path, content)
+            write_canonical_file(mount_dir, file_path, content, preserve_inode=True)
 
         volume_mounts.append(
             {

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

@@ -127,15 +127,20 @@ def _chown_staged_mounts(
     uid: int,
     gid: int,
 ) -> None:
-    """Recursively chown instance-local mount sources to the container user.
+    """Recursively chown writable profile and instance mount sources.
 
-    Profile copies, profile/Git composites, and SSH key mounts are created by
-    the API process. Their sources must be owned by the target container user
-    before Docker bind-mounts them into writable paths.
+    Canonical non-Git profile sources are shared by compatible instances, so
+    they must be writable by the container user rather than copied per
+    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)
 
@@ -234,100 +239,38 @@ def _stack_profile_mounts_with_git_mounts(
     git_mount_volumes: list[dict],
     instance_dir: str,
 ) -> list[dict]:
-    """Build instance-local composite mounts for overlapping profile and Git paths.
+    """Overlay canonical profile files on Git directories without snapshots.
 
-    Docker applies one bind mount per target; it never merges their contents.
-    A composite therefore copies shared Git content first and profile content
-    second, so profile files extend (and intentionally override) the Git tree
-    without dirtying the shared clone.
+    An overlapping profile directory is expanded into individual child-file
+    mounts. Docker then mounts the Git working directory first and the more
+    specific canonical profile files last, preserving shared writable sources
+    instead of constructing an instance-local composite copy.
     """
-    records: list[tuple[str, dict]] = [
-        ("profile", mount) for mount in profile_mounts
-    ] + [("git", mount) for mount in git_mount_volumes]
-    components: list[list[int]] = []
-    remaining: set[int] = set(range(len(records)))
+    del instance_dir
+    result: list[dict] = list(git_mount_volumes)
 
-    while remaining:
-        component_indices: set[int] = {min(remaining)}
-        remaining.difference_update(component_indices)
-        pending = list(component_indices)
-        while pending:
-            current_index = pending.pop()
-            current_target = records[current_index][1].get("target", "")
-            for candidate_index in list(remaining):
-                candidate_target = records[candidate_index][1].get("target", "")
-                if _mounts_overlap(current_target, candidate_target):
-                    remaining.remove(candidate_index)
-                    component_indices.add(candidate_index)
-                    pending.append(candidate_index)
-        components.append(sorted(component_indices))
-
-    result: list[dict] = []
-    for component_indexes in components:
-        component_records = [records[index] for index in component_indexes]
-        kinds = {kind for kind, _mount in component_records}
-        if kinds != {"profile", "git"}:
-            result.extend(mount for _kind, mount in component_records)
+    for profile_mount in profile_mounts:
+        source = profile_mount.get("source", "")
+        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
 
-        targets = [
-            os.path.normpath(mount["target"]) for _kind, mount in component_records
-        ]
-        composite_target = os.path.commonpath(targets)
-        if any(
-            not os.path.isdir(mount["source"])
-            and os.path.normpath(mount["target"]) == composite_target
-            for _kind, mount in component_records
-        ):
-            composite_target = os.path.dirname(composite_target)
-
-        digest_input = "\0".join(
-            f"{kind}:{mount['source']}:{mount['target']}"
-            for kind, mount in component_records
-        )
-        composite_source = os.path.join(
-            instance_dir,
-            "mounts",
-            "composites",
-            hashlib.sha256(digest_input.encode()).hexdigest()[:16],
-        )
-        try:
-            if os.path.lexists(composite_source):
-                shutil.rmtree(composite_source)
-            os.makedirs(composite_source, exist_ok=True)
-        except OSError as exc:
-            raise RuntimeError(
-                f"Unable to prepare composite mount directory {composite_source}: {exc}"
-            ) from exc
-
-        for kind in ("git", "profile"):
-            for record_kind, mount in component_records:
-                if record_kind != kind:
-                    continue
-                relative_target = _relative_under(composite_target, mount["target"])
-                destination = (
-                    composite_source
-                    if relative_target == ""
-                    else os.path.join(composite_source, relative_target or "")
+        for root, _dirs, files in os.walk(source):
+            for filename in files:
+                file_source = os.path.join(root, filename)
+                relative_path = os.path.relpath(file_source, source)
+                result.append(
+                    {
+                        **profile_mount,
+                        "source": file_source,
+                        "target": os.path.join(target, relative_path),
+                    }
                 )
-                _copy_mount_source(mount["source"], destination)
-
-        result.append(
-            {
-                "source": composite_source,
-                "target": composite_target,
-                "type": "bind",
-                "readonly": all(
-                    mount.get("readonly", False) for _kind, mount in component_records
-                ),
-            }
-        )
-        logger.info(
-            "Composed %d profile/Git mounts at %s into %s",
-            len(component_records),
-            composite_target,
-            composite_source,
-        )
 
     return result
 
@@ -629,8 +572,10 @@ async def resolve_single_git_mount(
     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"] = True
+        volume["readonly"] = False
     return volumes
 
 
@@ -675,10 +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
-    to ensure the latest code is mounted.
+    Git profile mounts are writable shared working copies. Refresh discards
+    local container/editor edits after fetching the remote baseline.
     """
     import subprocess
 
@@ -692,15 +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
-    result = subprocess.run(
-        ["git", "-C", repo_path, "pull", "origin"],
+    branch_result = subprocess.run(
+        ["git", "-C", repo_path, "branch", "--show-current"],
         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]:
@@ -1588,9 +1540,11 @@ async def start_tool_instance(
             git_mount_volumes = await resolve_git_mounts(
                 session, resolved, instance_dir, working_directory, home_dir
             )
-            staged_profile_mounts = _stage_profile_mounts(profile_mounts, instance_dir)
+            # Non-Git profile mounts bind directly to canonical profile
+            # storage so edits made by one compatible container are visible to
+            # every other container and the profile editor readback path.
             composed_mounts = _stack_profile_mounts_with_git_mounts(
-                staged_profile_mounts,
+                profile_mounts,
                 git_mount_volumes,
                 instance_dir,
             )
@@ -1601,7 +1555,7 @@ async def start_tool_instance(
                 instance.id,
                 len(profile_env),
                 len(profile_files),
-                len(staged_profile_mounts),
+                len(profile_mounts),
                 len(git_mount_volumes),
                 len(composed_mounts),
             )

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 +562,59 @@ 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_mounted_file_update_preserves_bind_mount_inode(self, tmp_path) -> None:
+        """A file inside a profile directory mount must update in place."""
+        profile_id = uuid.uuid4()
+        instance_root = tmp_path / "instances"
+        resolved = ResolvedProfile(
+            profile_id=profile_id,
+            profile_name="test",
+            mounts={
+                "/etc/tool": ResolvedMount(
+                    target="/etc/tool", mode="rw", files={"settings.toml": "value = 1"}
+                )
+            },
+        )
+
+        apply_resolved_profile(str(instance_root / "instance-a"), resolved)
+        canonical_file = (
+            instance_root
+            / "config-profiles"
+            / str(profile_id)
+            / "mounts"
+            / "etc_tool"
+            / "settings.toml"
+        )
+        original_inode = canonical_file.stat().st_ino
+
+        resolved.mounts["/etc/tool"].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

@@ -15,6 +15,7 @@ from src.services.tool.instance_service import (
     clone_git_repo,
     modify_compose_file,
     prepare_manifest_instance,
+    pull_repository_updates,
 )
 
 
@@ -97,6 +98,37 @@ class TestCloneGitRepo:
         clone.assert_not_called()
         pull.assert_called_once_with(str(repo_path), remote_url)
 
+    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:
@@ -191,17 +223,12 @@ class TestStackProfileMountsWithGitMounts:
             str(instance_dir),
         )
 
-        assert len(result) == 1
-        composite = result[0]
-        assert composite["target"] == "/home/user/.pi"
-        assert composite["source"].startswith(str(instance_dir))
-        assert not (tmp_path / "git" / "repo-clone" / "settings.json").exists()
-        assert (
-            tmp_path / "git" / "repo-clone" / "existing.txt"
-        ).read_text() == "from git"
-        assert (tmp_path / "instance" / "mounts" / "composites").exists()
-        assert (Path(composite["source"]) / "existing.txt").read_text() == "from git"
-        assert (Path(composite["source"]) / "settings.json").read_text() == "{}"
+        assert len(result) == 2
+        assert result[0]["source"] == str(git_source)
+        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_profile_mount_extends_git_root(self, tmp_path) -> None:
         """Nested targets are composed at the Git root, preserving siblings."""
@@ -223,11 +250,9 @@ class TestStackProfileMountsWithGitMounts:
             str(instance_dir),
         )
 
-        assert len(result) == 1
-        composite = Path(result[0]["source"])
-        assert result[0]["target"] == "/home/user/.pi"
-        assert (composite / "README").read_text() == "repo"
-        assert (composite / "agent" / "settings.json").read_text() == "x"
+        assert len(result) == 2
+        assert result[0]["source"] == str(git_source)
+        assert result[1]["target"] == "/home/user/.pi/agent/settings.json"
         assert not (git_source / "agent").exists()
 
     def test_file_profile_mount_extends_git_root(self, tmp_path) -> None:
@@ -254,11 +279,9 @@ class TestStackProfileMountsWithGitMounts:
             str(instance_dir),
         )
 
-        assert len(result) == 1
-        composite = Path(result[0]["source"])
-        assert result[0]["target"] == "/home/user/.pi"
-        assert (composite / "README").read_text() == "repo"
-        assert (composite / "settings.json").read_text() == "{}"
+        assert len(result) == 2
+        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."""
@@ -279,11 +302,9 @@ class TestStackProfileMountsWithGitMounts:
             str(instance_dir),
         )
 
-        assert len(result) == 1
-        composite = Path(result[0]["source"])
-        assert result[0]["target"] == "/home/user"
-        assert (composite / "config.toml").read_text() == "profile"
-        assert (composite / ".pi" / "plugin.toml").read_text() == "git"
+        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."""
@@ -303,7 +324,7 @@ class TestStackProfileMountsWithGitMounts:
             _stack_profile_mounts_with_git_mounts(
                 profile_mounts, git_mounts, str(instance_dir)
             )
-            == profile_mounts + git_mounts
+            == git_mounts + profile_mounts
         )
 
 

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" | "refreshed" | "restart_required" | "incompatible_permissions";
+	status:
+		| "compatible"
+		| "refreshed"
+		| "restart_required"
+		| "incompatible_permissions";
 	reason?: string;
 }
 
@@ -150,7 +154,9 @@ export const refreshConfigProfileGitMounts = async (
 ): Promise<{ refresh_outcomes: ConfigProfileRefreshOutcome[] }> => {
 	const response = await apiClient.post<{
 		refresh_outcomes: ConfigProfileRefreshOutcome[];
-	}>(`/config-profiles/${id}/refresh-git-mounts`);
+	}>(`/config-profiles/${id}/refresh-git-mounts`, undefined, {
+		params: { confirm_destructive_refresh: true },
+	});
 	return response.data;
 };
 

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 +25,7 @@ interface Props {
   onSubmit: (e?: React.FormEvent) => void;
   onReset: () => void;
   onPreview: () => void;
+  onReloadWorkingCopy: () => void;
   onRefreshGitMounts: () => void;
   onAddInclude: (id: string) => void;
   onRemoveInclude: (index: number) => void;
@@ -55,6 +58,8 @@ export const ConfigProfileEditorPanel = ({
   saveStatus,
   previewData,
   previewingId,
+  isRefreshingGitMounts,
+  isReloadingWorkingCopy,
   projects,
   toolTypes,
   availableProfiles,
@@ -64,6 +69,7 @@ export const ConfigProfileEditorPanel = ({
   onSubmit,
   onReset,
   onPreview,
+  onReloadWorkingCopy,
   onRefreshGitMounts,
   onAddInclude,
   onRemoveInclude,
@@ -116,8 +122,19 @@ export const ConfigProfileEditorPanel = ({
             </div>
             {!isCreating && selectedProfile && (
               <div className="row row-sm">
-                <button className="btn btn-secondary" onClick={onRefreshGitMounts}>
-                  <Icon name="refresh" size="sm" /> Refresh Git mounts
+                <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 ? (

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 +66,7 @@ interface Props {
 	) => void;
 	onRemoveMountFile: (mountIndex: number, path: string) => void;
 	onPreview: (id: string) => void;
+	onReloadWorkingCopy: () => void;
 	onRefreshGitMounts: (id: string) => void;
 	onClosePreview: () => void;
 }
@@ -80,6 +83,8 @@ export const ConfigProfilesMobileView = ({
 	availableProfiles,
 	previewData,
 	previewingId,
+	isRefreshingGitMounts,
+	isReloadingWorkingCopy,
 	saveStatus,
 	error,
 	onViewChange,
@@ -105,6 +110,7 @@ export const ConfigProfilesMobileView = ({
 	onUpdateMountFile,
 	onRemoveMountFile,
 	onPreview,
+	onReloadWorkingCopy,
 	onRefreshGitMounts,
 	onClosePreview,
 }: Props) => {
@@ -365,12 +371,25 @@ 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)}
 					>
-						<Icon name="refresh" size="sm" /> Refresh Git mounts
+						{isRefreshingGitMounts ? (
+							<>
+								<Icon name="loading" size="sm" />
+								Refreshing Git mounts...
+							</>
+						) : (
+							<>
+								<Icon name="refresh" size="sm" /> Refresh Git mounts
+							</>
+						)}
 					</button>
 					<button
 						type="button"

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

@@ -43,6 +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[]>([]);
@@ -274,8 +276,36 @@ export const useConfigProfiles = () => {
 		}
 	};
 
-	const handleRefreshGitMounts = async (id: string): Promise<boolean> => {
+	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(
@@ -290,6 +320,8 @@ export const useConfigProfiles = () => {
 		} catch (err) {
 			setError(extractErrorMessage(err));
 			return false;
+		} finally {
+			setIsRefreshingGitMounts(false);
 		}
 	};
 
@@ -445,6 +477,8 @@ export const useConfigProfiles = () => {
 		error,
 		previewData,
 		previewingId,
+		isRefreshingGitMounts,
+		isReloadingWorkingCopy,
 		formData,
 		includedProfileIds,
 		dragOverIndex,
@@ -454,6 +488,7 @@ export const useConfigProfiles = () => {
 		handleSubmit,
 		handleDelete,
 		handlePreview,
+		handleReloadWorkingCopy,
 		handleRefreshGitMounts,
 		updateFormField,
 		addEnvVar,

apps/web/src/pages/ConfigProfilesPage.tsx

@@ -23,6 +23,8 @@ export const ConfigProfilesPage = () => {
 		error,
 		previewData,
 		previewingId,
+		isRefreshingGitMounts,
+		isReloadingWorkingCopy,
 		formData,
 		includedProfileIds,
 		dragOverIndex,
@@ -32,6 +34,7 @@ export const ConfigProfilesPage = () => {
 		handleSubmit,
 		handleDelete,
 		handlePreview,
+		handleReloadWorkingCopy,
 		handleRefreshGitMounts,
 		updateFormField,
 		addEnvVar,
@@ -111,6 +114,8 @@ export const ConfigProfilesPage = () => {
 				availableProfiles={availableProfilesForInclude()}
 				previewData={previewData}
 				previewingId={previewingId}
+				isRefreshingGitMounts={isRefreshingGitMounts}
+				isReloadingWorkingCopy={isReloadingWorkingCopy}
 				saveStatus={saveStatus}
 				error={error}
 				onViewChange={setMobileView}
@@ -136,6 +141,7 @@ export const ConfigProfilesPage = () => {
 				onUpdateMountFile={updateMountFile}
 				onRemoveMountFile={removeMountFile}
 				onPreview={handlePreview}
+				onReloadWorkingCopy={() => void handleReloadWorkingCopy()}
 				onRefreshGitMounts={(id) => void handleRefreshGitMounts(id)}
 				onClosePreview={() => setPreviewData(null)}
 			/>
@@ -169,6 +175,8 @@ export const ConfigProfilesPage = () => {
 				saveStatus={saveStatus}
 				previewData={previewData}
 				previewingId={previewingId}
+				isRefreshingGitMounts={isRefreshingGitMounts}
+				isReloadingWorkingCopy={isReloadingWorkingCopy}
 				projects={projects}
 				toolTypes={toolTypes}
 				availableProfiles={availableProfilesForInclude()}
@@ -178,7 +186,10 @@ export const ConfigProfilesPage = () => {
 				onSubmit={handleSubmit}
 				onReset={handleReset}
 				onPreview={() => selectedProfile && handlePreview(selectedProfile.id)}
-				onRefreshGitMounts={() => selectedProfile && handleRefreshGitMounts(selectedProfile.id)}
+				onReloadWorkingCopy={() => void handleReloadWorkingCopy()}
+				onRefreshGitMounts={() =>
+					selectedProfile && handleRefreshGitMounts(selectedProfile.id)
+				}
 				onAddInclude={addInclude}
 				onRemoveInclude={removeInclude}
 				onDragStart={handleDragStart}

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.
-- [ ] **RED/GREEN — canonical profile storage:** create canonical host-side directories/files per profile and mount them directly into compatible instances, without masking workspace mounts.
-- [ ] **TRIANGULATE — writable sharing:** prove UI and container edits are shared across instances, with last-writer-wins overwrite warnings.
-- [ ] **RED/GREEN — topology/API contract:** return restart-required or incompatible-permissions outcomes for paths that cannot mount live; defer Git mount mutation.
-- [ ] **RED/GREEN — UI feedback:** show shared-working-copy, warning, restart-required, and incompatible-permissions results in desktop and mobile profile editors.
-- [ ] **Verify:** run targeted backend/frontend tests, typecheck, lint, image/manifest checks, and manual multi-instance permission tests.
+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.
+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.
+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.
+4. [x] **Server refresh contract:** require explicit destructive-refresh confirmation at the API boundary and return a typed outcome when confirmation is missing.
+5. [x] **Overlap safety:** replace profile/Git composite snapshots with child file-level canonical profile overlays so Git directory mounts remain intact.
+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

@@ -6,18 +6,21 @@ Git-backed Config Profile mounts are currently cloned per instance. Their conten
 
 ## Change
 
-Move Git Config Profile mounts to profile-scoped canonical host clones. Bind the already-mounted directory sources read-only into compatible instances and refresh a stable branch/ref checkout in place under a per-clone lock.
+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.
-- Read-only container Git config mounts.
+- 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
 
-- Writable shared Git configuration mounts.
+- 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

@@ -2,28 +2,30 @@
 
 ## Canonical source
 
-Each selected Config Profile owns canonical Git clone directories beneath:
+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; clones are never shared across users.
+`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 update the existing working tree in place.
-5. Bind directory mappings read-only. Existing containers see changed directory contents without recreation.
+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.
-- Containers must not write to shared Git mount sources.
+- 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
 

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

@@ -1,15 +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 read-only and prevent profile-content copy into Git sources.
-- [x] Add lock-protected clone/fetch/ref checkout refresh that preserves a known-good checkout on failure.
-- [x] Add save/refresh outcomes for live refresh, restart-required topology, and failures.
-- [x] Add desktop/mobile feedback for refresh outcomes.
-- [ ] Add focused resolver/service/API/frontend tests.
+- [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: frontend production build and Python compilation for changed backend modules.
-- Skipped: backend pytest and Ruff are unavailable in this environment; Docker/manual live-session checks were not approved.
+- 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.