diff --git a/apps/api/src/api/config/config_profiles.py b/apps/api/src/api/config/config_profiles.py
index ce39976..b31e05c 100644
--- a/apps/api/src/api/config/config_profiles.py
+++ b/apps/api/src/api/config/config_profiles.py
@@ -9,7 +9,7 @@ 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 +43,34 @@ 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 +168,10 @@ 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.delete("/{profile_id}", status_code=status.HTTP_204_NO_CONTENT)
@@ -161,6 +191,16 @@ 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()
 
diff --git a/apps/api/src/schemas/config/config_profile.py b/apps/api/src/schemas/config/config_profile.py
index 282525a..3486807 100644
--- a/apps/api/src/schemas/config/config_profile.py
+++ b/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):
diff --git a/apps/api/src/seeds/builtin_tool_types.py b/apps/api/src/seeds/builtin_tool_types.py
index c93d02f..0382abd 100644
--- a/apps/api/src/seeds/builtin_tool_types.py
+++ b/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"])
             )
diff --git a/apps/api/src/services/config/config_profile_resolver.py b/apps/api/src/services/config/config_profile_resolver.py
index 2cfa1f5..e04f164 100644
--- a/apps/api/src/services/config/config_profile_resolver.py
+++ b/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:
diff --git a/apps/api/src/services/tool/instance_service.py b/apps/api/src/services/tool/instance_service.py
index 5f81441..d61540c 100644
--- a/apps/api/src/services/tool/instance_service.py
+++ b/apps/api/src/services/tool/instance_service.py
@@ -1402,17 +1402,22 @@ 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)
diff --git a/apps/api/tests/unit/test_builtin_tool_users.py b/apps/api/tests/unit/test_builtin_tool_users.py
new file mode 100644
index 0000000..084e426
--- /dev/null
+++ b/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"]
diff --git a/apps/api/tests/unit/test_config_profile_resolver.py b/apps/api/tests/unit/test_config_profile_resolver.py
index 32d92fb..9c9ee70 100644
--- a/apps/api/tests/unit/test_config_profile_resolver.py
+++ b/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:
diff --git a/apps/web/src/api/config-profiles.ts b/apps/web/src/api/config-profiles.ts
index c8959b2..7539a95 100644
--- a/apps/web/src/api/config-profiles.ts
+++ b/apps/web/src/api/config-profiles.ts
@@ -1,5 +1,11 @@
 import { apiClient } from "./client";
 
+export interface ConfigProfileRefreshOutcome {
+	instance_id: string;
+	status: "compatible" | "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 {
diff --git a/apps/web/src/hooks/use-config-profiles.ts b/apps/web/src/hooks/use-config-profiles.ts
index a4db0cf..b54d321 100644
--- a/apps/web/src/hooks/use-config-profiles.ts
+++ b/apps/web/src/hooks/use-config-profiles.ts
@@ -34,17 +34,21 @@ 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 +93,9 @@ 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 +214,39 @@ 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 +258,8 @@ 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 +268,8 @@ export const useConfigProfiles = () => {
 				resetForm();
 			}
 			await loadData();
-		} catch {
-			alert("Failed to delete config profile");
+		} catch (err) {
+			setError(extractErrorMessage(err));
 		}
 	};
 
@@ -268,7 +294,10 @@ 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 +352,10 @@ 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 };
diff --git a/openspec/changes/live-config-profile-refresh/change.md b/openspec/changes/live-config-profile-refresh/change.md
new file mode 100644
index 0000000..abe9ad0
--- /dev/null
+++ b/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.
diff --git a/openspec/changes/live-config-profile-refresh/design.md b/openspec/changes/live-config-profile-refresh/design.md
new file mode 100644
index 0000000..f9b9b41
--- /dev/null
+++ b/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.
diff --git a/openspec/changes/live-config-profile-refresh/implementation-plan.md b/openspec/changes/live-config-profile-refresh/implementation-plan.md
new file mode 100644
index 0000000..1a907f9
--- /dev/null
+++ b/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.
diff --git a/openspec/changes/live-config-profile-refresh/tasks.md b/openspec/changes/live-config-profile-refresh/tasks.md
new file mode 100644
index 0000000..da73e4d
--- /dev/null
+++ b/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.
diff --git a/openspec/changes/live-config-profile-refresh/test-plan.md b/openspec/changes/live-config-profile-refresh/test-plan.md
new file mode 100644
index 0000000..99209ba
--- /dev/null
+++ b/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.
diff --git a/tool-images/base.dockerfile b/tool-images/base.dockerfile
index 2459699..406ce04 100644
--- a/tool-images/base.dockerfile
+++ b/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
diff --git a/tool-images/code-server.dockerfile b/tool-images/code-server.dockerfile
index ffa73e5..e6a991b 100644
--- a/tool-images/code-server.dockerfile
+++ b/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
\ No newline at end of file
diff --git a/tool-images/jupyter.dockerfile b/tool-images/jupyter.dockerfile
index c997ba1..bfd2313 100644
--- a/tool-images/jupyter.dockerfile
+++ b/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
\ No newline at end of file
diff --git a/tool-images/opencode.dockerfile b/tool-images/opencode.dockerfile
index 1127ec6..566d8e9 100644
--- a/tool-images/opencode.dockerfile
+++ b/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
diff --git a/tool-images/pi-agent.dockerfile b/tool-images/pi-agent.dockerfile
index b71c117..d36b4cf 100644
--- a/tool-images/pi-agent.dockerfile
+++ b/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