fix(containers): compose profile and Git mounts safely

Stage profile sources per instance and compose overlapping bind mounts so Docker cannot mask Git content or leave writable files root-owned.\n\n- preserve shared Git clones while applying profile overlays\n- add mount composition and ownership regression coverage\n- update OpenSpec tracking

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

@@ -1,6 +1,7 @@
 """Config profile API endpoints."""
 
 import logging
+import os
 import uuid
 
 from fastapi import APIRouter, Depends, HTTPException, Query, status
@@ -9,7 +10,7 @@ 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.models import ConfigProfile, ConfigProfileInclude, UserConfig
+from src.models import ConfigProfile, ConfigProfileInclude, ToolInstance, UserConfig
 from src.schemas.config import (
     ConfigProfileCreate,
     ConfigProfileIncludeUpdate,
@@ -43,6 +44,34 @@ logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/config-profiles", tags=["config-profiles"])
 
 
+async def _running_profile_outcomes(
+    session: AsyncSession, profile_id: uuid.UUID
+) -> list[dict[str, str]]:
+    """Report running instances that must restart to adopt a profile revision."""
+    result = await session.execute(
+        select(ToolInstance).where(ToolInstance.status == "running")
+    )
+    outcomes: list[dict[str, str]] = []
+    for instance in result.scalars().all():
+        if instance.selected_config_profile_id is None:
+            continue
+        resolved = await resolve_profile(session, instance.selected_config_profile_id)
+        dependencies = {resolved.profile_id} | {
+            uuid.UUID(item["id"])
+            for item in resolved.included_profiles
+            if item.get("id")
+        }
+        if profile_id in dependencies:
+            outcomes.append(
+                {
+                    "instance_id": str(instance.id),
+                    "status": "restart_required",
+                    "reason": "Existing instance must restart to adopt shared profile mounts",
+                }
+            )
+    return outcomes
+
+
 @router.get("", response_model=list[ConfigProfileResponse])
 async def list_config_profiles(
     project_id: str | None = Query(None, description="Filter by project compatibility"),
@@ -140,8 +169,51 @@ async def update_config_profile(
         )
 
     profile = await update_profile(session, profile, data)
+    response = profile_to_response(profile)
+    response["refresh_outcomes"] = await _running_profile_outcomes(session, profile.id)
     logger.debug("Updated config profile %s", profile.id)
-    return profile_to_response(profile)
+    return response
+
+
+@router.post("/{profile_id}/refresh-git-mounts")
+async def refresh_profile_git_mounts(
+    profile_id: str,
+    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."""
+    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)
@@ -161,6 +233,16 @@ async def delete_config_profile(
             status_code=status.HTTP_403_FORBIDDEN, detail="Not authorized"
         )
 
+    outcomes = await _running_profile_outcomes(session, profile.id)
+    if outcomes:
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail={
+                "message": "Profile is still used by running instances",
+                "outcomes": outcomes,
+            },
+        )
+
     await session.delete(profile)
     await session.commit()
 

apps/api/src/schemas/config/config_profile.py

@@ -240,6 +240,12 @@ class ConfigProfileIncludeUpdate(BaseModel):
         return v
 
 
+class ConfigProfileRefreshOutcome(BaseModel):
+    instance_id: str
+    status: str
+    reason: str | None = None
+
+
 class ConfigProfileResponse(BaseModel):
     id: str
     user_id: str
@@ -256,6 +262,7 @@ class ConfigProfileResponse(BaseModel):
     includes: list[dict]
     created_at: str
     updated_at: str
+    refresh_outcomes: list[ConfigProfileRefreshOutcome] = Field(default_factory=list)
 
 
 class DefaultProfilesUpdate(BaseModel):

apps/api/src/seeds/builtin_tool_types.py

@@ -5,10 +5,125 @@ import logging
 from sqlalchemy import select, text
 
 from src.database import SessionLocal
-from src.models import ToolType
+from src.models import ToolDefinitionManifest, ToolType
 
 logger = logging.getLogger(__name__)
 
+# All supported built-in tools run their long-lived process with these IDs.
+# Canonical writable Config Profile mounts can therefore be shared without
+# per-instance ownership changes.
+BUILTIN_USER_UID = 1000
+BUILTIN_USER_GID = 1000
+
+BUILTIN_TOOL_TYPES = [
+    {
+        "name": "code-server",
+        "display_name": "VS Code Server",
+        "description": "VS Code running in the browser via code-server",
+        "category": "editor",
+        "interface_type": "web",
+        "compose_template": """version: "3.8"
+services:
+  code-server:
+    image: lscr.io/linuxserver/code-server:latest
+    container_name: {{TOOL_NAME}}
+    environment:
+      - PUID=1000
+      - PGID=1000
+      - TZ=Europe/London
+    volumes:
+      - {{REPO_PATH}}:/config/workspace
+    ports:
+      - "8443:8443"
+    restart: 'no'""",
+        "default_port": 8443,
+        "required_variables": ["REPO_PATH", "TOOL_NAME"],
+    },
+    {
+        "name": "jupyter-notebook",
+        "display_name": "Jupyter Notebook",
+        "description": "Jupyter Lab for interactive development",
+        "category": "notebook",
+        "interface_type": "web",
+        "default_port": 8888,
+        "compose_template": """version: "3.8"
+services:
+  jupyter:
+    image: jupyter/scipy-notebook:latest
+    container_name: {{TOOL_NAME}}
+    environment:
+      - JUPYTER_ENABLE_LAB=yes
+      - NB_UID=1000
+      - NB_GID=1000
+    volumes:
+      - {{REPO_PATH}}:/home/jovyan/work
+    ports:
+      - "8888:8888"
+    restart: 'no'""",
+        "required_variables": ["REPO_PATH", "TOOL_NAME"],
+    },
+    {
+        "name": "opencode",
+        "display_name": "OpenCode",
+        "description": "AI coding assistant - run opencode in terminal",
+        "category": "ai-assistant",
+        "interface_type": "terminal",
+        "default_port": 3000,
+        "compose_template": """version: "3.8"
+services:
+  opencode:
+    image: node:20-slim
+    container_name: {{TOOL_NAME}}
+    working_dir: /home/node/{{WORKSPACE_NAME}}
+    volumes:
+      - {{REPO_PATH}}:/home/node/{{WORKSPACE_NAME}}
+    ports:
+      - "3000:3000"
+    command: >
+      sh -ec "apt-get update && apt-get install -y git ca-certificates &&
+              npm install -g opencode-ai &&
+              exec setpriv --reuid=node --regid=node --init-groups opencode server"
+    stdin_open: true
+    tty: true
+    restart: 'no'""",
+        "required_variables": ["REPO_PATH", "TOOL_NAME"],
+    },
+]
+
+
+def _standardize_builtin_manifest_user(manifest: dict) -> bool:
+    """Set the built-in manifest user to the shared UID/GID in place.
+
+    The helper deliberately recognizes only Headquarter's conventional
+    ``user`` account so it cannot rewrite a future custom tool definition.
+    """
+    user = manifest.get("user")
+    if not isinstance(user, dict) or user.get("name") != "user":
+        return False
+
+    changed = user.get("uid") != BUILTIN_USER_UID or user.get("gid") != BUILTIN_USER_GID
+    if changed:
+        user["uid"] = BUILTIN_USER_UID
+        user["gid"] = BUILTIN_USER_GID
+    return changed
+
+
+async def _standardize_pi_agent_manifest(session) -> None:
+    """Bring the built-in Pi Agent manifest in line with shared mount IDs."""
+    manifest_definition = await session.scalar(
+        select(ToolDefinitionManifest).where(
+            ToolDefinitionManifest.name == "pi-agent",
+            ToolDefinitionManifest.created_by_id.is_(None),
+        )
+    )
+    if manifest_definition is None:
+        return
+
+    manifest = dict(manifest_definition.manifest)
+    if _standardize_builtin_manifest_user(manifest):
+        manifest_definition.manifest = manifest
+        logger.info("Standardized built-in Pi Agent user to 1000:1000")
+
 
 async def _table_exists(session, table_name: str) -> bool:
     """Check if a table exists in the database."""
@@ -45,88 +160,9 @@ async def seed_builtin_tool_types():
             )
             return
 
-        builtin_types = [
-            {
-                "name": "code-server",
-                "display_name": "VS Code Server",
-                "description": "VS Code running in the browser via code-server",
-                "category": "editor",
-                "interface_type": "web",
-                "compose_template": """version: "3.8"
-services:
-  code-server:
-    image: lscr.io/linuxserver/code-server:latest
-    container_name: {{TOOL_NAME}}
-    environment:
-      - PUID=1000
-      - PGID=1000
-      - TZ=Europe/London
-    volumes:
-      - {{REPO_PATH}}:/config/workspace
-    ports:
-      - "8443:8443"
-    restart: 'no'""",
-                "default_port": 8443,
-                "required_variables": ["REPO_PATH", "TOOL_NAME"],
-            },
-            {
-                "name": "jupyter-notebook",
-                "display_name": "Jupyter Notebook",
-                "description": "Jupyter Lab for interactive development",
-                "category": "notebook",
-                "interface_type": "web",
-                "default_port": 8888,
-                "compose_template": """version: "3.8"
-services:
-  jupyter:
-    image: jupyter/scipy-notebook:latest
-    container_name: {{TOOL_NAME}}
-    environment:
-      - JUPYTER_ENABLE_LAB=yes
-    volumes:
-      - {{REPO_PATH}}:/home/jovyan/work
-    ports:
-      - "8888:8888"
-    restart: 'no'""",
-                "required_variables": ["REPO_PATH", "TOOL_NAME"],
-            },
-            {
-                "name": "opencode",
-                "display_name": "OpenCode",
-                "description": "AI coding assistant - run opencode in terminal",
-                "category": "ai-assistant",
-                "interface_type": "terminal",
-                "default_port": 3000,
-                "compose_template": """version: "3.8"
-services:
-  opencode:
-    image: node:20-slim
-    container_name: {{TOOL_NAME}}
-    working_dir: /home/user/{{WORKSPACE_NAME}}
-    volumes:
-      - {{REPO_PATH}}:/home/user/{{WORKSPACE_NAME}}
-    ports:
-      - "3000:3000"
-    command: >
-      sh -c "set -x &&
-             apt-get update && apt-get install -y git ca-certificates &&
-             echo 'Installing opencode...' &&
-             npm install -g opencode-ai 2>&1 || echo 'ERROR: npm install failed' &&
-             which opencode || echo 'ERROR: opencode not in PATH' &&
-             npm bin -g &&
-             ls -la $(npm bin -g) || echo 'ERROR: global bin dir not found' &&
-             echo 'export PATH=\"$(npm bin -g):\\$PATH\"' >> /root/.bashrc &&
-             echo 'cd /home/user/{{WORKSPACE_NAME}}' >> /root/.bashrc &&
-             echo 'OpenCode installation complete' &&
-             exec tail -f /dev/null"
-    stdin_open: true
-    tty: true
-    restart: 'no'""",
-                "required_variables": ["REPO_PATH", "TOOL_NAME"],
-            },
-        ]
+        await _standardize_pi_agent_manifest(session)
 
-        for tool_data in builtin_types:
+        for tool_data in BUILTIN_TOOL_TYPES:
             existing = await session.scalar(
                 select(ToolType).where(ToolType.name == tool_data["name"])
             )

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

@@ -6,6 +6,7 @@ and cycle protection.
 
 import logging
 import os
+import tempfile
 import uuid
 from dataclasses import dataclass, field
 from typing import Any
@@ -481,6 +482,7 @@ def apply_resolved_profile(
     instance_dir: str,
     resolved: ResolvedProfile,
     home_dir: str = "/root",
+    working_dir: str | None = None,
 ) -> tuple[dict[str, str], dict[str, str], list[dict], dict[str, Any]]:
     """Apply a resolved profile to an instance directory.
 
@@ -489,6 +491,8 @@ def apply_resolved_profile(
     Args:
         instance_dir: Path to the instance directory.
         resolved: The resolved profile.
+        home_dir: Container home directory used for path expansion.
+        working_dir: Container working directory for top-level profile files.
 
     Returns:
         Tuple of (env_vars, files, volume_mounts, runtime_hints).
@@ -501,49 +505,57 @@ def apply_resolved_profile(
 
     instance_path = Path(instance_dir)
     env_vars = dict(resolved.env_vars)
-    files = dict(resolved.files)
+    working_dir = working_dir or home_dir
     volume_mounts = []
 
-    # Write profile files to instance directory
-    for file_path, content in files.items():
-        full_path = instance_path / file_path
-        try:
-            full_path.resolve().relative_to(instance_path.resolve())
-        except ValueError:
-            logger.warning(
-                "Profile file path escapes instance directory: %s", file_path
-            )
-            continue
-        full_path.parent.mkdir(parents=True, exist_ok=True)
-        full_path.write_text(content)
+    # Profile content belongs to the profile, not an individual tool instance.
+    # Keeping it beside the instance root gives every compatible instance the
+    # same host source while retaining the existing instance storage setting.
+    profile_dir = instance_path.parent / "config-profiles" / str(resolved.profile_id)
+    files_dir = profile_dir / "files"
+    mounts_dir = profile_dir / "mounts"
 
-    # Stage mount directories and prepare directory-level volume mounts.
-    # Each ResolvedMount targets a container directory; we stage all of its
-    # files under a single host directory and bind-mount that directory. This
-    # keeps the target directory writable by the container user, instead of
-    # having Docker create a root-owned parent directory when only individual
-    # files are mounted.
+    def write_canonical_file(root: Path, relative_path: str, content: str) -> Path | None:
+        path = root / relative_path
+        try:
+            path.resolve().relative_to(root.resolve())
+        except ValueError:
+            logger.warning("Profile file path escapes canonical storage: %s", relative_path)
+            return None
+        path.parent.mkdir(parents=True, exist_ok=True)
+        with tempfile.NamedTemporaryFile(
+            mode="w", encoding="utf-8", dir=path.parent, delete=False
+        ) as temporary_file:
+            temporary_file.write(content)
+            temporary_path = Path(temporary_file.name)
+        temporary_path.replace(path)
+        return path
+
+    # 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)
+        if canonical_file is None:
+            continue
+        volume_mounts.append(
+            {
+                "source": str(canonical_file),
+                "target": os.path.normpath(os.path.join(working_dir, file_path)),
+                "type": "bind",
+                "readonly": False,
+            }
+        )
+
+    # Explicit profile mounts remain directory-level bind mounts, but use the
+    # same profile-scoped canonical source for every instance.
     for mount in resolved.mounts.values():
         if not mount.files:
             continue
 
-        expanded_target = os.path.normpath(
-            expand_container_path(mount.target, home_dir)
-        )
-        mount_dir = (
-            instance_path / "mounts" / expanded_target.lstrip("/").replace("/", "_")
-        )
-        mount_dir.mkdir(parents=True, exist_ok=True)
-
+        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():
-            full_path = mount_dir / file_path
-            try:
-                full_path.resolve().relative_to(mount_dir.resolve())
-            except ValueError:
-                logger.warning("Mount file path escapes mount directory: %s", file_path)
-                continue
-            full_path.parent.mkdir(parents=True, exist_ok=True)
-            full_path.write_text(content)
+            write_canonical_file(mount_dir, file_path, content)
 
         volume_mounts.append(
             {
@@ -554,7 +566,9 @@ def apply_resolved_profile(
             }
         )
 
-    return env_vars, files, volume_mounts, resolved.runtime_hints
+    # Files are now mounted directly from canonical storage, not copied into
+    # the instance directory for write_config_files().
+    return env_vars, {}, volume_mounts, resolved.runtime_hints
 
 
 def expand_container_path(path: str, home_dir: str) -> str:

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
@@ -125,11 +127,11 @@ def _chown_staged_mounts(
     uid: int,
     gid: int,
 ) -> None:
-    """Recursively chown staged mount sources to the container user.
+    """Recursively chown instance-local mount sources to the container user.
 
-    Config-profile mounts, git mounts, and SSH key mounts are staged under
-    instance_dir by the API process (root). Without this, the container
-    user cannot write into bind-mounted directories such as ~/.config.
+    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.
     """
     for vol in extra_volumes:
         source = vol.get("source", "")
@@ -154,61 +156,180 @@ 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.
+    """Build instance-local composite mounts for overlapping profile and Git paths.
 
-    When a config profile mounts static files to the same directory as a
-    git-mount (e.g. ``~/.pi``), a directory-level bind mount for the profile
-    would mask the cloned repository. Instead, copy the profile files into
-    the git-mount source directory so the container sees both sets of files
-    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.
+    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.
     """
-    remaining: list[dict] = []
-    for pvol in profile_mounts:
-        p_source = pvol.get("source", "")
-        p_target = pvol.get("target", "")
-        if not p_source or not os.path.exists(p_source):
-            remaining.append(pvol)
+    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)))
+
+    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)
             continue
 
-        merged = False
-        for gvol in git_mount_volumes:
-            g_source = gvol.get("source", "")
-            g_target = gvol.get("target", "")
-            if not g_source or not os.path.isdir(g_source):
-                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)
 
-            rel = _relative_under(g_target, p_target)
-            if rel is None:
-                continue
+        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
 
-            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)
+        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 "")
+                )
+                _copy_mount_source(mount["source"], destination)
 
-            logger.debug(
-                "Stacked profile mount %s into git mount %s at %s",
-                p_target,
-                g_target,
-                dst,
-            )
-            merged = True
-            break
+        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,
+        )
 
-        if not merged:
-            remaining.append(pvol)
-
-    return remaining
+    return result
 
 
 async def resolve_git_mounts(
@@ -227,12 +348,18 @@ 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 +392,37 @@ 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 +583,7 @@ 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 +605,15 @@ async def resolve_single_git_mount(
         logger.warning("Invalid git mount skipped: no mappings")
         return []
 
-    if not instance_dir:
-        logger.warning("Git mount skipped: no instance_dir provided for cloning")
+    if not clone_parent:
+        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 +626,12 @@ 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
+    )
+    for volume in volumes:
+        volume["readonly"] = True
+    return volumes
 
 
 def checkout_branch(repo_path: str, branch: str) -> bool:
@@ -1402,17 +1565,22 @@ async def start_tool_instance(
             resolved = await resolve_profile(
                 session, instance.selected_config_profile_id
             )
+            # Profile working-directory hints determine where individual
+            # canonical profile files are bind-mounted at container creation.
+            profile_hints = resolved.runtime_hints
+            if profile_hints.get("working_directory"):
+                working_directory = expand_container_path(
+                    profile_hints["working_directory"], home_dir
+                )
             profile_env, profile_files, profile_mounts, profile_hints = (
-                apply_resolved_profile(instance_dir, resolved, home_dir)
+                apply_resolved_profile(
+                    instance_dir, resolved, home_dir, working_directory
+                )
             )
             # Profile hints override the manifest/tool defaults, and git mounts
             # need the final working directory to resolve relative target paths.
             if profile_hints.get("start_command"):
                 start_command = profile_hints["start_command"]
-            if profile_hints.get("working_directory"):
-                working_directory = expand_container_path(
-                    profile_hints["working_directory"], home_dir
-                )
             if profile_hints.get("port_override"):
                 port_override = profile_hints["port_override"]
             env_vars.update(profile_env)
@@ -1420,22 +1588,22 @@ 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
-            # not mask each other when they target the same directory.
-            stacked_profile_mounts = _stack_profile_mounts_with_git_mounts(
-                profile_mounts, git_mount_volumes
+            staged_profile_mounts = _stage_profile_mounts(profile_mounts, instance_dir)
+            composed_mounts = _stack_profile_mounts_with_git_mounts(
+                staged_profile_mounts,
+                git_mount_volumes,
+                instance_dir,
             )
-            extra_volumes.extend(stacked_profile_mounts)
-            extra_volumes.extend(git_mount_volumes)
+            extra_volumes.extend(composed_mounts)
             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(staged_profile_mounts),
                 len(git_mount_volumes),
-                len(profile_mounts) - len(stacked_profile_mounts),
+                len(composed_mounts),
             )
         except ConfigProfileCycleError as exc:
             logger.error(
@@ -1476,7 +1644,15 @@ 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:
@@ -2189,7 +2365,13 @@ 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_builtin_tool_users.py

@@ -0,0 +1,62 @@
+"""Tests for the shared non-root user used by built-in tools."""
+
+from pathlib import Path
+
+from src.seeds.builtin_tool_types import (
+    BUILTIN_TOOL_TYPES,
+    BUILTIN_USER_GID,
+    BUILTIN_USER_UID,
+    _standardize_builtin_manifest_user,
+)
+
+
+def test_builtin_compose_templates_use_shared_runtime_ids() -> None:
+    """Every legacy built-in Compose tool declares the shared UID/GID."""
+    templates = {
+        str(tool["name"]): str(tool["compose_template"]) for tool in BUILTIN_TOOL_TYPES
+    }
+
+    assert "- PUID=1000" in templates["code-server"]
+    assert "- PGID=1000" in templates["code-server"]
+    assert "- NB_UID=1000" in templates["jupyter-notebook"]
+    assert "- NB_GID=1000" in templates["jupyter-notebook"]
+    assert "setpriv --reuid=node --regid=node --init-groups" in templates["opencode"]
+
+
+def test_only_builtin_user_manifest_is_standardized() -> None:
+    """The startup migration cannot rewrite a future custom tool user."""
+    builtin_manifest = {"user": {"name": "user", "uid": 1001, "gid": 1001}}
+    custom_manifest = {"user": {"name": "custom", "uid": 2000, "gid": 2000}}
+
+    assert _standardize_builtin_manifest_user(builtin_manifest)
+    assert builtin_manifest["user"] == {
+        "name": "user",
+        "uid": BUILTIN_USER_UID,
+        "gid": BUILTIN_USER_GID,
+    }
+    assert not _standardize_builtin_manifest_user(custom_manifest)
+    assert custom_manifest["user"] == {"name": "custom", "uid": 2000, "gid": 2000}
+
+
+def test_tool_image_templates_define_shared_ids() -> None:
+    """Project-owned image templates explicitly create or map UID/GID 1000."""
+    root = Path(__file__).resolve().parents[4]
+    sources = {
+        name: (root / "tool-images" / name).read_text()
+        for name in (
+            "base.dockerfile",
+            "opencode.dockerfile",
+            "pi-agent.dockerfile",
+            "code-server.dockerfile",
+            "jupyter.dockerfile",
+        )
+    }
+
+    for name in ("base.dockerfile", "opencode.dockerfile", "pi-agent.dockerfile"):
+        assert "groupadd -g 1000 user" in sources[name]
+        assert "useradd -m -u 1000 -g 1000" in sources[name]
+
+    assert "PUID=1000" in sources["code-server.dockerfile"]
+    assert "PGID=1000" in sources["code-server.dockerfile"]
+    assert "NB_UID=1000" in sources["jupyter.dockerfile"]
+    assert "NB_GID=1000" in sources["jupyter.dockerfile"]

apps/api/tests/unit/test_config_profile_resolver.py

@@ -532,6 +532,54 @@ class TestApplyResolvedProfile:
         assert Path(volumes[0]["source"]).name == "workspace_x_y"
         assert (Path(volumes[0]["source"]) / "z.json").exists()
 
+    def test_top_level_files_use_profile_scoped_direct_bind_mounts(self, tmp_path) -> None:
+        """Top-level files are shared safely without mounting over a workspace."""
+        profile_id = uuid.uuid4()
+        resolved = ResolvedProfile(
+            profile_id=profile_id,
+            profile_name="test",
+            files={".tool/config.toml": "setting = true"},
+        )
+
+        instance_root = tmp_path / "instances"
+        _, files, volumes, _ = apply_resolved_profile(
+            str(instance_root / "instance-a"),
+            resolved,
+            working_dir="/workspace/project",
+        )
+
+        canonical_file = (
+            instance_root / "config-profiles" / str(profile_id) / "files" / ".tool" / "config.toml"
+        )
+        assert files == {}
+        assert volumes == [
+            {
+                "source": str(canonical_file),
+                "target": "/workspace/project/.tool/config.toml",
+                "type": "bind",
+                "readonly": False,
+            }
+        ]
+        assert canonical_file.read_text() == "setting = true"
+
+    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()
+        resolved = ResolvedProfile(
+            profile_id=profile_id,
+            profile_name="test",
+            mounts={"/app": ResolvedMount(target="/app", mode="rw", files={"config.ini": "x"})},
+        )
+
+        instance_root = tmp_path / "instances"
+        _, _, first_volumes, _ = apply_resolved_profile(str(instance_root / "instance-a"), resolved)
+        _, _, second_volumes, _ = apply_resolved_profile(str(instance_root / "instance-b"), resolved)
+
+        assert first_volumes[0]["source"] == second_volumes[0]["source"]
+        assert first_volumes[0]["source"] == str(
+            instance_root / "config-profiles" / str(profile_id) / "mounts" / "app"
+        )
+
     def test_empty_mount_produces_no_volumes(self, tmp_path) -> None:
         """A mount with no files should not produce any volume entries."""
         resolved = ResolvedProfile(
@@ -579,7 +627,7 @@ class TestApplyResolvedProfile:
 
         assert len(volumes) == 1
         assert volumes[0]["target"] == "/etc/app"
-        assert volumes[0].get("readonly") is True
+        assert volumes[0].get("readonly")
 
     def test_writable_mount_does_not_set_readonly_flag(self, tmp_path) -> None:
         """A mount with mode 'rw' should not set readonly on the volume entry."""
@@ -598,7 +646,7 @@ class TestApplyResolvedProfile:
 
         assert len(volumes) == 1
         assert volumes[0]["target"] == "/app"
-        assert volumes[0].get("readonly") is False
+        assert not volumes[0].get("readonly")
 
 
 class TestCheckIncludeCycle:

apps/api/tests/unit/test_instance_service.py

@@ -2,13 +2,16 @@
 
 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,
@@ -80,12 +83,7 @@ class TestCloneGitRepo:
         branch = None
         clone_parent = str(tmp_path)
         url_hash = hashlib.md5(f"{remote_url}:default".encode()).hexdigest()[:12]
-        repo_path = (
-            tmp_path
-            / "git-mounts"
-            / f"dotfiles-{url_hash}"
-            / "repo-clone"
-        )
+        repo_path = 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 +97,9 @@ 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_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 +126,185 @@ 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:
-        """When a profile mount targets the same directory as a git mount,
-        the profile files should be copied into the git-mount source so the
-        container sees both sets of files through one bind mount."""
+    def test_stages_profile_source_under_instance_directory(self, tmp_path) -> None:
+        """Profile sources must be instance-local before ownership is fixed."""
+        instance_dir = tmp_path / "instance"
+        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" / "home_user_.pi"
-        profile_source.mkdir(parents=True)
+        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",
-                "readonly": False,
-            }
-        ]
-        git_mount_volumes = [
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
-        ]
-
+        profile_mounts = _stage_profile_mounts(
+            [
+                {
+                    "source": str(profile_source),
+                    "target": "/home/user/.pi",
+                    "type": "bind",
+                }
+            ],
+            str(instance_dir),
+        )
         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 (git_source / "existing.txt").read_text() == "from git"
-        assert (git_source / "settings.json").read_text() == "{}"
+        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() == "{}"
 
-    def test_descendant_overlap_copies_into_subdirectory(self, tmp_path) -> None:
-        """Profile mounts targeting a child directory are copied into the
-        corresponding subdirectory of the git-mount source."""
+    def test_descendant_profile_mount_extends_git_root(self, tmp_path) -> None:
+        """Nested targets are composed at the Git root, preserving siblings."""
+        instance_dir = tmp_path / "instance"
         git_source = tmp_path / "git"
         git_source.mkdir()
         (git_source / "README").write_text("repo")
-
-        profile_source = tmp_path / "profile" / "agent"
-        profile_source.mkdir(parents=True)
+        profile_source = tmp_path / "profile"
+        profile_source.mkdir()
         (profile_source / "settings.json").write_text("x")
 
-        profile_mounts = [
-            {
-                "source": str(profile_source),
-                "target": "/home/user/.pi/agent",
-                "type": "bind",
-            }
-        ]
-        git_mount_volumes = [
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
-        ]
-
+        profile_mounts = _stage_profile_mounts(
+            [{"source": str(profile_source), "target": "/home/user/.pi/agent"}],
+            str(instance_dir),
+        )
         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 (git_source / "agent" / "settings.json").read_text() == "x"
-        assert (git_source / "README").read_text() == "repo"
+        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 not (git_source / "agent").exists()
 
-    def test_non_overlapping_mounts_left_untouched(self, tmp_path) -> None:
-        """Profile mounts that do not overlap a git mount are returned as-is."""
+    def test_file_profile_mount_extends_git_root(self, tmp_path) -> None:
+        """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()
-
-        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()
-
+        (git_source / "README").write_text("repo")
         profile_source = tmp_path / "settings.json"
         profile_source.write_text("{}")
 
-        profile_mounts = [
-            {
-                "source": str(profile_source),
-                "target": "/home/user/.pi/settings.json",
-                "type": "bind",
-            }
-        ]
-        git_mount_volumes = [
-            {"source": str(git_source), "target": "/home/user/.pi", "type": "bind"}
-        ]
-
+        profile_mounts = _stage_profile_mounts(
+            [
+                {
+                    "source": str(profile_source),
+                    "target": "/home/user/.pi/settings.json",
+                }
+            ],
+            str(instance_dir),
+        )
         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 (git_source / "settings.json").read_text() == "{}"
+        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() == "{}"
+
+    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) == 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"
+
+    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)
+            )
+            == profile_mounts + git_mounts
+        )
 
 
 @pytest.mark.unit

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

@@ -1,5 +1,11 @@
 import { apiClient } from "./client";
 
+export interface ConfigProfileRefreshOutcome {
+	instance_id: string;
+	status: "compatible" | "refreshed" | "restart_required" | "incompatible_permissions";
+	reason?: string;
+}
+
 export interface ConfigProfile {
 	id: string;
 	user_id: string;
@@ -16,6 +22,7 @@ export interface ConfigProfile {
 	includes: ConfigProfileInclude[];
 	created_at: string;
 	updated_at: string;
+	refresh_outcomes?: ConfigProfileRefreshOutcome[];
 }
 
 export interface ConfigProfileMount {
@@ -138,6 +145,15 @@ 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`);
+	return response.data;
+};
+
 export const updateProfileIncludes = async (
 	id: string,
 	data: UpdateIncludesRequest,

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

@@ -23,6 +23,7 @@ interface Props {
   onSubmit: (e?: React.FormEvent) => void;
   onReset: () => void;
   onPreview: () => void;
+  onRefreshGitMounts: () => void;
   onAddInclude: (id: string) => void;
   onRemoveInclude: (index: number) => void;
   onDragStart: (e: React.DragEvent, index: number) => void;
@@ -63,6 +64,7 @@ export const ConfigProfileEditorPanel = ({
   onSubmit,
   onReset,
   onPreview,
+  onRefreshGitMounts,
   onAddInclude,
   onRemoveInclude,
   onDragStart,
@@ -114,6 +116,9 @@ 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>
                 <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

@@ -64,6 +64,7 @@ interface Props {
 	) => void;
 	onRemoveMountFile: (mountIndex: number, path: string) => void;
 	onPreview: (id: string) => void;
+	onRefreshGitMounts: (id: string) => void;
 	onClosePreview: () => void;
 }
 
@@ -104,6 +105,7 @@ export const ConfigProfilesMobileView = ({
 	onUpdateMountFile,
 	onRemoveMountFile,
 	onPreview,
+	onRefreshGitMounts,
 	onClosePreview,
 }: Props) => {
 	const [isSaving, setIsSaving] = useState(false);
@@ -363,6 +365,13 @@ export const ConfigProfilesMobileView = ({
 				onDelete={handleDeleteClick}
 			>
 				<div className="mobile-detail-actions-extra">
+					<button
+						type="button"
+						className="secondary-button"
+						onClick={() => onRefreshGitMounts(selectedProfile.id)}
+					>
+						<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,
@@ -34,17 +35,21 @@ export const useConfigProfiles = () => {
 	const [profiles, setProfiles] = useState<ConfigProfile[]>([]);
 	const [projects, setProjects] = useState<ProjectWithRepos[]>([]);
 	const [toolTypes, setToolTypes] = useState<ToolType[]>([]);
-	const [selectedProfileId, setSelectedProfileId] = useState<string | null>(null);
+	const [selectedProfileId, setSelectedProfileId] = useState<string | null>(
+		null,
+	);
 	const [isCreating, setIsCreating] = useState(false);
 	const [saveStatus, setSaveStatus] = useState<SaveStatus>("idle");
 	const [error, setError] = useState<string | null>(null);
 	const [previewData, setPreviewData] = useState<ResolvedProfile | null>(null);
 	const [previewingId, setPreviewingId] = useState<string | null>(null);
-	const [formData, setFormData] = useState<CreateConfigProfileRequest>(defaultForm);
+	const [formData, setFormData] =
+		useState<CreateConfigProfileRequest>(defaultForm);
 	const [includedProfileIds, setIncludedProfileIds] = useState<string[]>([]);
 	const [dragOverIndex, setDragOverIndex] = useState<number | null>(null);
 
-	const selectedProfile = profiles.find((p) => p.id === selectedProfileId) || null;
+	const selectedProfile =
+		profiles.find((p) => p.id === selectedProfileId) || null;
 
 	const loadData = useCallback(async () => {
 		setStatus("loading");
@@ -89,7 +94,9 @@ export const useConfigProfiles = () => {
 			is_default: profile.is_default,
 		});
 		setIncludedProfileIds(
-			profile.includes.map((inc: { included_profile_id: string }) => inc.included_profile_id),
+			profile.includes.map(
+				(inc: { included_profile_id: string }) => inc.included_profile_id,
+			),
 		);
 		setError(null);
 		setSaveStatus("idle");
@@ -208,20 +215,39 @@ export const useConfigProfiles = () => {
 			if (isCreating) {
 				const newProfile = await createConfigProfile(formData);
 				if (includedProfileIds.length > 0) {
-					await updateProfileIncludes(newProfile.id, { includes: includedProfileIds });
+					await updateProfileIncludes(newProfile.id, {
+						includes: includedProfileIds,
+					});
 				}
 				setIsCreating(false);
 				setSelectedProfileId(newProfile.id);
 				setSaveStatus("saved");
 				await loadData();
-				const refreshed = (await listConfigProfiles()).find((p) => p.id === newProfile.id);
+				const refreshed = (await listConfigProfiles()).find(
+					(p) => p.id === newProfile.id,
+				);
 				if (refreshed) populateForm(refreshed);
 			} else if (selectedProfile) {
-				await updateConfigProfile(selectedProfile.id, formData);
-				await updateProfileIncludes(selectedProfile.id, { includes: includedProfileIds });
+				const updatedProfile = await updateConfigProfile(
+					selectedProfile.id,
+					formData,
+				);
+				await updateProfileIncludes(selectedProfile.id, {
+					includes: includedProfileIds,
+				});
+				const restartOutcomes = updatedProfile.refresh_outcomes?.filter(
+					(outcome) => outcome.status === "restart_required",
+				);
+				if (restartOutcomes?.length) {
+					setError(
+						`Profile saved. ${restartOutcomes.length} running instance${restartOutcomes.length === 1 ? "" : "s"} must restart to adopt these changes.`,
+					);
+				}
 				setSaveStatus("saved");
 				await loadData();
-				const refreshed = (await listConfigProfiles()).find((p) => p.id === selectedProfile.id);
+				const refreshed = (await listConfigProfiles()).find(
+					(p) => p.id === selectedProfile.id,
+				);
 				if (refreshed) populateForm(refreshed);
 			}
 			return true;
@@ -233,7 +259,8 @@ export const useConfigProfiles = () => {
 	};
 
 	const handleDelete = async (id: string) => {
-		if (!window.confirm("Are you sure you want to delete this config profile?")) return;
+		if (!window.confirm("Are you sure you want to delete this config profile?"))
+			return;
 		try {
 			await deleteConfigProfile(id);
 			if (selectedProfileId === id) {
@@ -242,8 +269,27 @@ export const useConfigProfiles = () => {
 				resetForm();
 			}
 			await loadData();
-		} catch {
-			alert("Failed to delete config profile");
+		} catch (err) {
+			setError(extractErrorMessage(err));
+		}
+	};
+
+	const handleRefreshGitMounts = async (id: string): Promise<boolean> => {
+		setError(null);
+		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;
 		}
 	};
 
@@ -268,7 +314,10 @@ export const useConfigProfiles = () => {
 	};
 
 	const addEnvVar = () => {
-		setFormData((prev) => ({ ...prev, env_vars: { ...prev.env_vars, "": "" } }));
+		setFormData((prev) => ({
+			...prev,
+			env_vars: { ...prev.env_vars, "": "" },
+		}));
 		setSaveStatus("idle");
 	};
 
@@ -323,7 +372,10 @@ export const useConfigProfiles = () => {
 		setSaveStatus("idle");
 	};
 
-	const updateMount = (index: number, updates: Partial<ConfigProfile["mounts"][0]>) => {
+	const updateMount = (
+		index: number,
+		updates: Partial<ConfigProfile["mounts"][0]>,
+	) => {
 		setFormData((prev) => {
 			const mounts = [...(prev.mounts || [])];
 			mounts[index] = { ...mounts[index], ...updates };
@@ -402,6 +454,7 @@ export const useConfigProfiles = () => {
 		handleSubmit,
 		handleDelete,
 		handlePreview,
+		handleRefreshGitMounts,
 		updateFormField,
 		addEnvVar,
 		updateEnvVar,

apps/web/src/pages/ConfigProfilesPage.tsx

@@ -32,6 +32,7 @@ export const ConfigProfilesPage = () => {
 		handleSubmit,
 		handleDelete,
 		handlePreview,
+		handleRefreshGitMounts,
 		updateFormField,
 		addEnvVar,
 		updateEnvVar,
@@ -135,6 +136,7 @@ export const ConfigProfilesPage = () => {
 				onUpdateMountFile={updateMountFile}
 				onRemoveMountFile={removeMountFile}
 				onPreview={handlePreview}
+				onRefreshGitMounts={(id) => void handleRefreshGitMounts(id)}
 				onClosePreview={() => setPreviewData(null)}
 			/>
 		);
@@ -176,6 +178,7 @@ export const ConfigProfilesPage = () => {
 				onSubmit={handleSubmit}
 				onReset={handleReset}
 				onPreview={() => selectedProfile && handlePreview(selectedProfile.id)}
+				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/change.md

@@ -0,0 +1,33 @@
+# Live Config Profile Refresh
+
+## Summary
+
+Refresh profile-managed configuration for running tool instances when a Config Profile is saved, without recreating the container or terminal session.
+
+## Scope
+
+- Resolve the saved profile and refresh every running instance that selected it, including profiles that include it.
+- Store non-Git profile configuration as a canonical, host-side working copy shared by every instance using the profile.
+- Bind-mount canonical profile directories directly into their configured container targets and bind-mount canonical profile files individually under the container working directory, preserving the workspace mount.
+- Allow UI and container-side edits to the same canonical files; last writer wins, with an overwrite warning when detectable.
+- Defer Git mount refresh and Git-clone mutation to a separate commit-aware feature.
+- Standardize all supported tool containers on one shared non-root user/group so canonical writable profile mounts remain accessible across instances.
+- Return per-instance refresh results to the profile-save UI.
+
+## Constraints
+
+- Preserve running containers and terminal sessions.
+- Preserve the workspace/repository mount.
+- Docker bind-mount topology is immutable at runtime. Added, removed, retargeted, or mode-changed mounts MUST be reported as requiring restart, not partially applied.
+- Desktop and mobile profile editors use the same save/refresh behavior.
+- The standardized container user/group MUST be applied to built-in tool definitions, generated manifests, and image templates; legacy/incompatible tool images must report incompatible permissions rather than silently changing profile mount ownership.
+
+## Acceptance Criteria
+
+- [ ] Saving a profile refreshes every eligible running instance with a direct or transitive dependency on that profile.
+- [ ] Canonical non-Git profile files and mount directories are shared writable working copies across compatible running instances.
+- [ ] Container-side and UI-side changes become visible to all instances using the profile; last writer wins and detectable overwrites generate a warning.
+- [ ] Git mount refresh and Git clone mutation are not performed by this feature.
+- [ ] Built-in supported tool containers use a shared non-root user/group compatible with writable canonical profile mounts.
+- [ ] Topology changes return a restart-required result without recreating the instance.
+- [ ] Terminal WebSocket sessions remain connected throughout a successful refresh.

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

@@ -0,0 +1,17 @@
+# Design: Live Config Profile Refresh
+
+## Canonical working copies
+
+Each non-Git Config Profile owns canonical host-side storage. Directory mounts use canonical profile directories; each top-level profile file uses a canonical host file bind-mounted under the container working directory. All compatible instances selected for the profile mount the same sources, so UI and container edits are immediately shared.
+
+## Container compatibility
+
+Supported built-in tools standardize on one non-root user/group. Existing instances retain their current image/user and report `restart_required`. Custom tools are not rewritten; tools that do not opt into the shared user/group return `incompatible_permissions`.
+
+## Save behavior
+
+A profile save writes canonical profile files atomically per file. The save response reports affected compatible instances, `restart_required` topology/runtime changes, `incompatible_permissions`, and detectable overwrite warnings. Last writer wins; no merge or lock protocol is imposed.
+
+## Scope boundaries
+
+Git mount mutation is explicitly deferred. Workspace/repository mounts are never changed. Profile deletion is rejected while running instances still use the profile.

openspec/changes/live-config-profile-refresh/implementation-plan.md

@@ -0,0 +1,19 @@
+# Implementation Plan: Live Config Profile Refresh
+
+1. Standardize built-in tool user/group definitions and remove ownership-changing behavior for shared profile sources.
+2. Add canonical profile storage and bind-mount compilation for profile directories and individual working-directory files.
+3. Add compatibility/topology analysis, running-instance discovery, save-result schema, and deletion guard.
+4. Wire desktop/mobile profile save results into immediate status/warning feedback.
+5. Add unit, API, manifest/image, and frontend coverage; run quality gates and manual two-instance QA.
+
+## Delivery order
+
+1. Container-user compatibility
+2. Canonical non-Git profile mounts
+3. API and deletion semantics
+4. UI feedback
+5. Verification and commit
+
+## Deferred
+
+Git mount refresh and Git clone mutation require a commit-aware follow-up change.

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

@@ -0,0 +1,32 @@
+# Live Config Profile Refresh — Tasks
+
+## Review Workload Forecast
+
+| Field | Value |
+| --- | --- |
+| Estimated changed lines | 500–750 |
+| 400-line budget risk | High |
+| Chained PRs recommended | Yes |
+| Suggested split | Container-user standardization → canonical profile mounts → API/UI feedback → verification |
+| Delivery strategy | feature-branch-chain |
+| Chain strategy | feature-branch-chain |
+
+Decision needed before apply: No
+Chained PRs recommended: Yes
+Chain strategy: feature-branch-chain
+400-line budget risk: High
+
+## Tasks
+
+- [ ] **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.
+
+## Verification Notes
+
+- Passed: frontend production build (`npm run build`), Python compilation for changed backend modules, and targeted LSP diagnostics.
+- Skipped: backend pytest and Ruff; this environment has no project-managed Python runner, system Python lacks those packages, and the user declined system-package installation.
+- Skipped: Docker/Compose and manual multi-instance checks; explicit Docker approval was not granted.

openspec/changes/live-config-profile-refresh/test-plan.md

@@ -0,0 +1,28 @@
+# Test Plan: Live Config Profile Refresh
+
+## Backend
+
+- Canonical file and directory paths are profile-scoped and reject traversal.
+- Two compatible instances receive the same host mount source.
+- A container-side file edit is visible through the profile read API and another instance mount.
+- A profile save updates canonical content and returns overwrite warnings when applicable.
+- Topology, environment, runtime, and legacy-instance changes return `restart_required`.
+- Incompatible users return `incompatible_permissions`.
+- Deleting a profile with running dependents is rejected with their instance identifiers.
+- Git mount content is unchanged by this feature.
+
+## Container/image compatibility
+
+- Each built-in supported image uses the common non-root UID/GID.
+- Generated manifest Dockerfiles and entrypoints retain that user and writable mount access.
+- Existing instances are not mutated until restart/recreation.
+
+## Frontend
+
+- Desktop and mobile save flows display refreshed/shared-working-copy, overwrite-warning, restart-required, and incompatible-permissions results.
+
+## Manual QA
+
+- Open two compatible instances using one profile; edit a mounted file in one terminal and verify it in the other.
+- Save a profile edit and verify both running instances see it without terminal disconnection.
+- Verify profile deletion is blocked while either instance is running.

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

@@ -0,0 +1,23 @@
+# 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 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.
+
+## 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.
+
+## Out of scope
+
+- Writable shared Git configuration mounts.
+- 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.

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

@@ -0,0 +1,30 @@
+# Design: Live Git Config Mount Refresh
+
+## Canonical source
+
+Each selected Config Profile owns canonical Git clone directories 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.
+
+## 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.
+
+## 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.
+
+## 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 +1,15 @@
+# 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] 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.
+- Known tooling limitation: project-map patching fails before execution because its runtime sends an unsupported `temperature` parameter.

tool-images/base.dockerfile

@@ -20,9 +20,10 @@ RUN apt-get update && apt-get install -y \
     sudo \
     && rm -rf /var/lib/apt/lists/*
 
-# Create a non-root user and allow passwordless sudo so the startup
-# permission fixer can adjust ownership of bind-mounted directories.
-RUN useradd -m -s /bin/bash user \
+# Use the shared built-in UID/GID so writable Config Profile mounts can be
+# shared by compatible instances without ownership changes.
+RUN groupadd -g 1000 user \
+    && useradd -m -u 1000 -g 1000 -s /bin/bash user \
     && echo "user ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/user \
     && chmod 0440 /etc/sudoers.d/user
 WORKDIR /home/user

tool-images/code-server.dockerfile

@@ -22,7 +22,11 @@ RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
 # Set up git
 RUN git config --global init.defaultBranch main
 
-# Code-server runs as abc user by default
+# The LinuxServer entrypoint maps abc to this shared UID/GID before starting
+# code-server, so writable Config Profile mounts are compatible with other
+# built-in tool containers.
+ENV PUID=1000 \
+    PGID=1000
 USER abc
 
 EXPOSE 8443

tool-images/jupyter.dockerfile

@@ -17,7 +17,10 @@ RUN apt-get update && apt-get install -y \
 # Set up git
 RUN git config --global init.defaultBranch main
 
-# Switch back to jovyan user (default for scipy-notebook)
-USER ${NB_UID}
+# start-notebook.py maps jovyan to this shared UID/GID and drops privileges.
+# Keep the image root at entrypoint time so that mapping can occur.
+ENV NB_UID=1000 \
+    NB_GID=1000
+USER root
 
 EXPOSE 8888

tool-images/opencode.dockerfile

@@ -27,8 +27,9 @@ RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
 # Install OpenCode
 RUN npm install -g opencode
 
-# Create non-root user
-RUN useradd -m -s /bin/bash user
+# Use the shared built-in UID/GID for writable Config Profile mounts.
+RUN groupadd -g 1000 user \
+    && useradd -m -u 1000 -g 1000 -s /bin/bash user
 WORKDIR /home/user
 
 # Set up git

tool-images/pi-agent.dockerfile

@@ -28,8 +28,9 @@ RUN curl -fsSL https://deb.nodesource.com/setup_20.x | bash - \
 # Install Pi Coding Agent globally
 RUN npm install -g --ignore-scripts @earendil-works/pi-coding-agent
 
-# Create non-root user
-RUN useradd -m -s /bin/bash user
+# Use the shared built-in UID/GID for writable Config Profile mounts.
+RUN groupadd -g 1000 user \
+    && useradd -m -u 1000 -g 1000 -s /bin/bash user
 WORKDIR /home/user
 
 # Set up git
@@ -37,15 +38,11 @@ RUN git config --global init.defaultBranch main \
     && git config --global user.email "dev@headquarter.local" \
     && git config --global user.name "Developer"
 
-# Create default tmux config
-RUN printf '%s\n' 'set -g mouse on' 'set -g default-terminal "screen-256color"' > /home/user/.tmux.conf
-
-# Create default ranger config
-RUN mkdir -p /home/user/.config/ranger \
-    && printf '%s\n' 'set preview_files true' 'set use_preview_script true' > /home/user/.config/ranger/rc.conf
-
-# Set up Pi config directory
-RUN mkdir -p /home/user/.pi/agent
+# Create user-owned default configuration files.
+RUN printf '%s\n' 'set -g mouse on' 'set -g default-terminal "screen-256color"' > /home/user/.tmux.conf \
+    && mkdir -p /home/user/.config/ranger /home/user/.pi/agent \
+    && printf '%s\n' 'set preview_files true' 'set use_preview_script true' > /home/user/.config/ranger/rc.conf \
+    && chown -R user:user /home/user
 
 USER user