fix: use host bind mount for repos so tool instances can access workspace files

Replace named Docker volume (repo_data) with bind mount (/data/repos) in both
development and production compose files. The named volume trapped repo files
inside the API container; tool instances started via Docker socket on the host
could not see them, causing /workspace to mount as an empty directory.

Also fix 6 pre-existing test failures in test_tool_instances_legacy.py caused
by get_container_id/get_container_name moving to docker.py and new helpers
(_ensure_web_bind_address, _ensure_container_name_in_compose) being added.

- docker-compose.yml: repo_data:/data/repos -> /data/repos:/data/repos
- docker-compose.traefik.yml: same change + remove repo_data volume decl
- tests: update patch targets and add missing mock parameters

Quality gates: pytest test_tool_instances_legacy.py (10 passed)

AGENTS.md

@@ -4,6 +4,10 @@
 
 OpenSpec is the source of truth. Superpowers is the default workflow. Keep changes small, scoped, and verified.
 
+## Communication
+
+All agent output, code comments, commit messages, documentation, and artifacts must be in **English** unless the user explicitly requests another language.
+
 ## Priority order
 
 1. Current user instruction

apps/api/alembic/versions/2026_05_28_add_tool_definition_manifests.py

@@ -232,14 +232,6 @@ def upgrade() -> None:
                             "writable": True,
                             "owner": "user",
                         },
-                        {
-                            "name": "ssh_keys",
-                            "target": "/home/user/.ssh",
-                            "source_type": "ssh_key",
-                            "mode": "0700",
-                            "file_mode": "0600",
-                            "readonly": True,
-                        },
                         {
                             "name": "pi_state",
                             "target": "/tmp/.pi/agents",

apps/api/alembic/versions/2026_05_29_fix_code_server_bind_addr.py

@@ -0,0 +1,54 @@
+"""fix code-server bind-addr to host in DB template
+
+Revision ID: 2026_05_29_fix_code_server_bind_addr
+Revises: 2026_05_29_fix_web_tool_bind_address
+Create Date: 2026-05-29 15:00:00.000000
+
+"""
+
+from typing import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_fix_code_server_bind_addr"
+down_revision: str | None = "2026_05_29_fix_web_tool_bind_address"
+branch_labels: Sequence[str] | None = None
+depends_on: Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+
+    # Find code-server tool types with broken --bind-addr in compose template
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template
+            FROM tool_types
+            WHERE name = 'code-server'
+            AND compose_template LIKE '%--bind-addr%'
+        """)
+    ).fetchall()
+
+    for tool_id, compose_template in result:
+        updated = compose_template.replace(
+            "--bind-addr 0.0.0.0:8443", "--host 0.0.0.0"
+        ).replace("--bind-addr", "--host 0.0.0.0")
+
+        conn.execute(
+            sa.text("""
+                UPDATE tool_types
+                SET compose_template = :compose_template
+                WHERE id = :id
+            """),
+            {"compose_template": updated, "id": tool_id},
+        )
+
+        print(
+            f"Fixed code-server template ({tool_id}): replaced --bind-addr with --host"
+        )
+
+
+def downgrade() -> None:
+    pass

apps/api/alembic/versions/2026_05_29_fix_code_server_bind_addr_port.py

@@ -0,0 +1,148 @@
+"""Fix code-server bind address to include port
+
+Revision ID: 2026_05_29_fix_code_server_bind_addr_port
+Revises: 2026_05_29_remove_lsio_command_override
+Create Date: 2026-05-29 18:00:00.000000
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+import yaml
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_fix_code_server_bind_addr_port"
+down_revision: Union[str, None] = "2026_05_29_remove_lsio_command_override"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def _fix_tool_type_templates(conn) -> None:
+    """Fix code-server tool type templates with broken --host override."""
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template, default_port
+            FROM tool_types
+            WHERE name = 'code-server'
+            AND compose_template LIKE '%--host%'
+        """)
+    ).fetchall()
+
+    for tool_id, compose_template, default_port in result:
+        port = default_port or 8443
+        expected = f"--bind-addr 0.0.0.0:{port}"
+
+        # Replace any line containing --host with the correct bind-addr
+        lines = compose_template.split("\n")
+        new_lines = []
+        modified = False
+        for line in lines:
+            if "command:" in line and "--host" in line:
+                indent = line[: len(line) - len(line.lstrip())]
+                new_lines.append(f"{indent}command: {expected}")
+                modified = True
+            else:
+                new_lines.append(line)
+
+        if not modified:
+            continue
+
+        updated = "\n".join(new_lines)
+        conn.execute(
+            sa.text("""
+                UPDATE tool_types
+                SET compose_template = :compose_template
+                WHERE id = :id
+            """),
+            {"compose_template": updated, "id": tool_id},
+        )
+        print(f"Fixed code-server template ({tool_id}): replaced --host with {expected}")
+
+
+def _fix_instance_compose_files(conn) -> None:
+    """Fix existing instance compose files on disk with broken --host override."""
+    from pathlib import Path
+
+    # Use information_schema to check if compose_path column exists
+    col_result = conn.execute(
+        sa.text("""
+            SELECT column_name
+            FROM information_schema.columns
+            WHERE table_name = 'tool_instances'
+            AND column_name = 'compose_path'
+        """)
+    ).fetchone()
+
+    if not col_result:
+        print("compose_path column not found, skipping instance file fixes")
+        return
+
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_path, tool_type_id
+            FROM tool_instances
+            WHERE compose_path IS NOT NULL
+        """)
+    ).fetchall()
+
+    for instance_id, compose_path, tool_type_id in result:
+        path = Path(compose_path)
+        if not path.exists():
+            continue
+
+        try:
+            content = path.read_text()
+        except Exception:
+            continue
+
+        if "--host" not in content:
+            continue
+
+        # Get default_port from tool_type
+        port_result = conn.execute(
+            sa.text("""
+                SELECT default_port FROM tool_types WHERE id = :id
+            """),
+            {"id": tool_type_id},
+        ).fetchone()
+        port = port_result[0] if port_result and port_result[0] else 8443
+        expected = f"--bind-addr 0.0.0.0:{port}"
+
+        try:
+            data = yaml.safe_load(content)
+        except Exception:
+            continue
+
+        if not data or "services" not in data:
+            continue
+
+        modified = False
+        for svc in data["services"].values():
+            if "command" in svc:
+                cmd = svc["command"]
+                if "--host" in cmd:
+                    svc["command"] = expected
+                    modified = True
+
+        if not modified:
+            continue
+
+        try:
+            path.write_text(yaml.dump(data, default_flow_style=False))
+            print(
+                f"Fixed code-server instance compose ({instance_id}): "
+                f"replaced --host with {expected}"
+            )
+        except Exception as exc:
+            print(f"Failed to fix instance {instance_id}: {exc}")
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+    _fix_tool_type_templates(conn)
+    _fix_instance_compose_files(conn)
+
+
+def downgrade() -> None:
+    pass

apps/api/alembic/versions/2026_05_29_fix_web_tool_bind_address.py

@@ -0,0 +1,140 @@
+"""fix web tool bind address to 0.0.0.0
+
+Revision ID: 2026_05_29_fix_web_tool_bind_address
+Revises: 2026_05_29_remove_ssh_keys_mount_from_manifest
+Create Date: 2026-05-29 14:00:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_fix_web_tool_bind_address"
+down_revision: Union[str, None] = "2026_05_29_remove_ssh_keys_mount_from_manifest"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def _fix_code_server_compose(conn) -> None:
+    """Update code-server compose template to bind to 0.0.0.0."""
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template, definition_type
+            FROM tool_types
+            WHERE name = 'code-server'
+        """)
+    ).fetchone()
+
+    if result is None:
+        return
+
+    tool_id, compose_template, definition_type = result
+
+    if definition_type != "compose" or not compose_template:
+        return
+
+    # Fix or add command to bind to 0.0.0.0
+    lines = compose_template.split("\n")
+    new_lines = []
+    image_line_idx = -1
+    command_fixed = False
+    for i, line in enumerate(lines):
+        # Replace broken --bind-addr with correct --host
+        if "command:" in line and "--bind-addr" in line:
+            indent = line[: len(line) - len(line.lstrip())]
+            new_lines.append(f"{indent}command: --host 0.0.0.0")
+            command_fixed = True
+            continue
+        new_lines.append(line)
+        if "image:" in line and image_line_idx == -1:
+            image_line_idx = i
+
+    # If no command line exists, insert one after image
+    if not command_fixed and image_line_idx != -1:
+        image_line = lines[image_line_idx]
+        indent = image_line[: len(image_line) - len(image_line.lstrip())]
+        # Insert after the image line in new_lines
+        insert_idx = new_lines.index(image_line) + 1
+        new_lines.insert(insert_idx, f"{indent}command: --host 0.0.0.0")
+        command_fixed = True
+
+    if not command_fixed:
+        return
+
+    updated_compose = "\n".join(new_lines)
+
+    conn.execute(
+        sa.text("""
+            UPDATE tool_types
+            SET compose_template = :compose_template
+            WHERE id = :id
+        """),
+        {"compose_template": updated_compose, "id": tool_id},
+    )
+
+    print(f"Updated code-server tool type ({tool_id}) to bind to 0.0.0.0")
+
+
+def _fix_jupyter_compose(conn) -> None:
+    """Update jupyter-notebook compose template to bind to 0.0.0.0."""
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template, definition_type
+            FROM tool_types
+            WHERE name = 'jupyter-notebook'
+        """)
+    ).fetchone()
+
+    if result is None:
+        return
+
+    tool_id, compose_template, definition_type = result
+
+    if definition_type != "compose" or not compose_template:
+        return
+
+    if "command:" in compose_template:
+        return
+
+    lines = compose_template.split("\n")
+    new_lines = []
+    image_line_idx = -1
+    for i, line in enumerate(lines):
+        new_lines.append(line)
+        if "image:" in line and image_line_idx == -1:
+            image_line_idx = i
+            indent = line[: len(line) - len(line.lstrip())]
+            # Jupyter needs --ip=0.0.0.0 to bind to all interfaces
+            new_lines.append(
+                f"{indent}command: start-notebook.sh --ip=0.0.0.0 --port=8888 --no-browser"
+            )
+
+    if image_line_idx == -1:
+        return
+
+    updated_compose = "\n".join(new_lines)
+
+    conn.execute(
+        sa.text("""
+            UPDATE tool_types
+            SET compose_template = :compose_template
+            WHERE id = :id
+        """),
+        {"compose_template": updated_compose, "id": tool_id},
+    )
+
+    print(f"Updated jupyter-notebook tool type ({tool_id}) to bind to 0.0.0.0:8888")
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+    _fix_code_server_compose(conn)
+    _fix_jupyter_compose(conn)
+
+
+def downgrade() -> None:
+    # Cannot safely downgrade without knowing the original compose_template
+    pass

apps/api/alembic/versions/2026_05_29_remove_lsio_command_override.py

@@ -0,0 +1,121 @@
+"""Remove broken command override from LSIO code-server templates
+
+Revision ID: 2026_05_29_remove_lsio_command_override
+Revises: 2026_05_29_fix_code_server_bind_addr
+Create Date: 2026-05-29 15:05:00.000000
+
+"""
+
+from collections.abc import Sequence
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_remove_lsio_command_override"
+down_revision: str | None = "2026_05_29_fix_code_server_bind_addr"
+branch_labels: Sequence[str] | None = None
+depends_on: Sequence[str] | None = None
+
+
+def upgrade() -> None:
+    conn = op.get_bind()
+
+    # Fix tool_types templates in DB
+    result = conn.execute(
+        sa.text("""
+            SELECT id, compose_template
+            FROM tool_types
+            WHERE name = 'code-server'
+        """)
+    ).fetchall()
+
+    import yaml
+    from pathlib import Path
+
+    for tool_id, compose_template in result:
+        try:
+            data = yaml.safe_load(compose_template)
+        except Exception:
+            continue
+
+        if not data or "services" not in data:
+            continue
+
+        modified = False
+        for svc in data["services"].values():
+            image = svc.get("image", "")
+            if not image or "linuxserver" not in image:
+                continue
+            if "command" in svc:
+                cmd = svc["command"]
+                if "--bind-addr" in cmd or "--host" in cmd:
+                    del svc["command"]
+                    modified = True
+
+        if modified:
+            updated = yaml.dump(data, default_flow_style=False)
+            conn.execute(
+                sa.text("""
+                    UPDATE tool_types
+                    SET compose_template = :compose_template
+                    WHERE id = :id
+                """),
+                {"compose_template": updated, "id": tool_id},
+            )
+            print(f"Removed broken command override from LSIO template ({tool_id})")
+
+    # Fix existing instance compose files on disk
+    # Use information_schema to check if compose_path column exists
+    col_result = conn.execute(
+        sa.text("""
+            SELECT column_name
+            FROM information_schema.columns
+            WHERE table_name = 'tool_instances'
+            AND column_name = 'compose_path'
+        """)
+    ).fetchone()
+
+    if col_result:
+        result = conn.execute(
+            sa.text("""
+                SELECT id, compose_path
+                FROM tool_instances
+                WHERE compose_path IS NOT NULL
+            """)
+        ).fetchall()
+
+        for instance_id, compose_path in result:
+            path = Path(compose_path)
+            if not path.exists():
+                continue
+            try:
+                content = path.read_text()
+                data = yaml.safe_load(content)
+            except Exception:
+                continue
+
+            if not data or "services" not in data:
+                continue
+
+            modified = False
+            for svc in data["services"].values():
+                image = svc.get("image", "")
+                if not image or "linuxserver" not in image:
+                    continue
+                if "command" in svc:
+                    cmd = svc["command"]
+                    if "--bind-addr" in cmd or "--host" in cmd:
+                        del svc["command"]
+                        modified = True
+
+            if modified:
+                path.write_text(yaml.dump(data, default_flow_style=False))
+                print(
+                    f"Removed broken command override from instance compose "
+                    f"({instance_id})"
+                )
+
+
+def downgrade() -> None:
+    pass

apps/api/alembic/versions/2026_05_29_remove_ssh_keys_mount_from_manifest.py

@@ -0,0 +1,105 @@
+"""remove ssh_keys mount from pi-agent manifest
+
+Revision ID: 2026_05_29_remove_ssh_keys_mount_from_manifest
+Revises: 2026_05_29_add_ssh_key_ids_to_tool_instances
+Create Date: 2026-05-29 14:00:00.000000
+
+"""
+
+import json
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+# revision identifiers, used by Alembic.
+revision: str = "2026_05_29_remove_ssh_keys_mount_from_manifest"
+down_revision: Union[str, None] = "2026_05_29_add_ssh_key_ids_to_tool_instances"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Remove the ssh_keys mount from the pi-agent manifest."""
+    conn = op.get_bind()
+
+    # Get the pi-agent manifest
+    result = conn.execute(
+        sa.text(
+            "SELECT id, manifest FROM tool_definition_manifests WHERE name = 'pi-agent'"
+        )
+    )
+    row = result.fetchone()
+    if not row:
+        return
+
+    manifest_id, manifest_json = row
+    manifest = (
+        manifest_json if isinstance(manifest_json, dict) else json.loads(manifest_json)
+    )
+
+    mounts = manifest.get("mounts", [])
+    original_count = len(mounts)
+
+    # Remove any mount named "ssh_keys"
+    filtered_mounts = [m for m in mounts if m.get("name") != "ssh_keys"]
+
+    if len(filtered_mounts) < original_count:
+        manifest["mounts"] = filtered_mounts
+        conn.execute(
+            sa.text(
+                "UPDATE tool_definition_manifests SET manifest = :manifest WHERE id = :id"
+            ),
+            {
+                "manifest": json.dumps(manifest),
+                "id": manifest_id,
+            },
+        )
+
+
+def downgrade() -> None:
+    """Restore the ssh_keys mount to the pi-agent manifest."""
+    conn = op.get_bind()
+
+    result = conn.execute(
+        sa.text(
+            "SELECT id, manifest FROM tool_definition_manifests WHERE name = 'pi-agent'"
+        )
+    )
+    row = result.fetchone()
+    if not row:
+        return
+
+    manifest_id, manifest_json = row
+    manifest = (
+        manifest_json if isinstance(manifest_json, dict) else json.loads(manifest_json)
+    )
+
+    mounts = manifest.get("mounts", [])
+
+    # Check if ssh_keys mount already exists
+    if any(m.get("name") == "ssh_keys" for m in mounts):
+        return
+
+    # Add the ssh_keys mount back
+    mounts.append(
+        {
+            "name": "ssh_keys",
+            "target": "/home/user/.ssh",
+            "source_type": "ssh_key",
+            "mode": "0700",
+            "file_mode": "0600",
+            "readonly": True,
+        }
+    )
+    manifest["mounts"] = mounts
+
+    conn.execute(
+        sa.text(
+            "UPDATE tool_definition_manifests SET manifest = :manifest WHERE id = :id"
+        ),
+        {
+            "manifest": json.dumps(manifest),
+            "id": manifest_id,
+        },
+    )

apps/api/src/api/notifications.py

@@ -47,6 +47,10 @@ class MarkAllReadResponse(BaseModel):
     marked_count: int
 
 
+class ClearAllResponse(BaseModel):
+    cleared_count: int
+
+
 async def _get_mute_categories(
     session: AsyncSession,
     user_id: uuid.UUID,
@@ -131,13 +135,23 @@ async def mark_all_read(
     return MarkAllReadResponse(marked_count=marked)
 
 
+@router.delete("", status_code=status.HTTP_200_OK)
+async def clear_all_notifications(
+    user: User = Depends(get_current_user),
+    session: AsyncSession = Depends(get_db_session),
+) -> ClearAllResponse:
+    """Dismiss all notifications for the authenticated user."""
+    cleared = await notification_service.dismiss_all(session, user.id)
+    return ClearAllResponse(cleared_count=cleared)
+
+
 @router.delete("/{notification_id}", status_code=status.HTTP_204_NO_CONTENT)
 async def dismiss_notification(
     notification_id: uuid.UUID,
     user: User = Depends(get_current_user),
     session: AsyncSession = Depends(get_db_session),
 ) -> None:
-    """Soft-delete (dismiss) a notification."""
+    """Soft-delete (dismiss) a single notification."""
     try:
         await notification_service.dismiss(session, notification_id, user.id)
     except ValueError as exc:

apps/api/src/api/tool_instances.py

@@ -52,7 +52,6 @@ from src.services.docker import (
     find_free_port,
     get_container_id,
     get_container_logs,
-    get_container_name,
     get_container_status,
     recreate_tunnel,
     render_compose_template,
@@ -475,7 +474,7 @@ async def _validate_config_profile(
     Raises:
         HTTPException: If profile is not found, not owned, or incompatible.
     """
-    if profile_id is None:
+    if not profile_id:
         return None
 
     try:
@@ -618,6 +617,137 @@ def _modify_compose_file(
     compose_file.write_text(yaml.dump(compose_data, default_flow_style=False))
 
 
+def _ensure_container_name_in_compose(compose_path: str, container_name: str) -> None:
+    """Ensure compose file has explicit container_name for predictable naming.
+
+    Docker Compose auto-generates container names from the project directory
+    when container_name is absent. This breaks tunnel connectivity because
+    get_container_name(instance.name) cannot find the container. We inject
+    container_name into every service so the container has a predictable name.
+    """
+    import yaml
+    from pathlib import Path
+
+    compose_file = Path(compose_path)
+    if not compose_file.exists():
+        return
+
+    content = compose_file.read_text()
+    compose_data = yaml.safe_load(content)
+
+    if not compose_data or "services" not in compose_data:
+        return
+
+    modified = False
+    for svc_name, svc_config in compose_data["services"].items():
+        if "container_name" not in svc_config:
+            svc_config["container_name"] = container_name.lower()
+            modified = True
+
+    if modified:
+        compose_file.write_text(yaml.dump(compose_data, default_flow_style=False))
+        logger.info(
+            "Injected container_name '%s' into compose file",
+            container_name.lower(),
+        )
+
+
+def _ensure_web_bind_address(
+    compose_path: str, tool_type_name: str, default_port: int
+) -> None:
+    """Auto-inject bind address for known web tools that default to 127.0.0.1.
+
+    Many web tools (code-server, jupyter) bind to localhost by default,
+    making them inaccessible from the Docker network. This function detects
+    known tool images and injects the correct --bind-addr or --ip flag.
+    """
+    import yaml
+    from pathlib import Path
+
+    if default_port <= 0:
+        return
+
+    KNOWN_BIND_FIXES: dict[str, str] = {
+        "code-server": f"--bind-addr 0.0.0.0:{default_port}",
+        "jupyter-notebook": f"start-notebook.sh --ip=0.0.0.0 --port={default_port} --no-browser",
+    }
+
+    bind_command = KNOWN_BIND_FIXES.get(tool_type_name)
+    if not bind_command:
+        return
+
+    compose_file = Path(compose_path)
+    if not compose_file.exists():
+        return
+
+    content = compose_file.read_text()
+    compose_data = yaml.safe_load(content)
+
+    if not compose_data or "services" not in compose_data:
+        return
+
+    for service_config in compose_data["services"].values():
+        image = service_config.get("image", "")
+        if not image:
+            continue
+
+        # LSIO images already bind to 0.0.0.0 — command override breaks s6 init
+        if "linuxserver" in image:
+            existing_command = service_config.get("command", "")
+            if "--bind-addr" in existing_command or "--host" in existing_command:
+                del service_config["command"]
+                compose_file.write_text(
+                    yaml.dump(compose_data, default_flow_style=False)
+                )
+                logger.warning(
+                    "Removed broken command override from LSIO image: %s",
+                    existing_command,
+                )
+                return
+            return
+
+        # Check if the image matches a known tool
+        is_code_server = tool_type_name == "code-server" and (
+            "code-server" in image or "coder" in image
+        )
+        is_jupyter = tool_type_name == "jupyter-notebook" and (
+            "jupyter" in image or "notebook" in image
+        )
+        if not is_code_server and not is_jupyter:
+            continue
+
+        existing_command = service_config.get("command", "")
+        if existing_command:
+            # Already correct — nothing to do
+            if bind_command in existing_command:
+                return
+            # Fix broken or outdated bind flags
+            if (
+                "--bind-addr" in existing_command
+                or "--host" in existing_command
+                or "--ip=" in existing_command
+            ):
+                service_config["command"] = bind_command
+                compose_file.write_text(
+                    yaml.dump(compose_data, default_flow_style=False)
+                )
+                logger.warning(
+                    "Replaced broken bind address for %s: %s → %s",
+                    tool_type_name,
+                    existing_command,
+                    bind_command,
+                )
+                return
+            # Some other command override exists — don't touch it
+            return
+
+        # No command yet — inject the correct bind address
+        service_config["command"] = bind_command
+        compose_file.write_text(yaml.dump(compose_data, default_flow_style=False))
+        logger.info("Injected bind address for %s: %s", tool_type_name, bind_command)
+        return
+
+
 @router.post(
     "/{project_id}/repositories/{repo_id}/instances",
     summary="Create tool instance",
@@ -854,7 +984,7 @@ services:
                     )
 
             # Determine home directory for path expansion
-            home_dir = get_manifest_home_dir(manifest)
+            _home_dir = get_manifest_home_dir(manifest)
 
             image_tag = compute_image_tag(tool_type.name, manifest)
 
@@ -1341,11 +1471,27 @@ async def start_instance(
         manifest_def = await session.get(ToolDefinitionManifest, tool_type.manifest_id)
         if manifest_def:
             manifest = dict(manifest_def.manifest)
+            # Merge with base definition if referenced (user config is often in base)
+            if manifest_def.base_definition_id:
+                base_def = await session.get(
+                    ToolDefinitionManifest, manifest_def.base_definition_id
+                )
+                if base_def:
+                    manifest = resolve_base(
+                        deep_merge(dict(base_def.manifest), manifest)
+                    )
             home_dir = get_manifest_home_dir(manifest)
             user_cfg = manifest.get("user")
             if user_cfg:
                 container_uid = user_cfg.get("uid", 0)
                 container_gid = user_cfg.get("gid", 0)
+            logger.debug(
+                "Manifest user resolved for instance %s: uid=%s, gid=%s, home=%s",
+                instance.id,
+                container_uid,
+                container_gid,
+                home_dir,
+            )
 
     # Apply selected config profile if any
     instance_dir = os.path.dirname(instance.compose_path)
@@ -1534,6 +1680,15 @@ async def start_instance(
     # Sanitize compose file to remove invalid port mappings from old instances
     _sanitize_compose_file(instance.compose_path)
 
+    # Auto-fix bind address for known web tools that default to localhost
+    if tool_type and tool_type.interface_type == "web":
+        _ensure_web_bind_address(
+            instance.compose_path, tool_type.name, tool_type.default_port
+        )
+
+    # Ensure predictable container name for tunnel connectivity
+    _ensure_container_name_in_compose(instance.compose_path, instance.name)
+
     # Execute docker compose up with env file
     logger.debug(
         "Running docker compose up for instance %s (compose_path=%s)",
@@ -1560,24 +1715,23 @@ async def start_instance(
             detail=f"failed to start instance: {stderr}",
         )
 
-    # Get container ID and name
-    container_id = get_container_id(instance.name)
+    # Get container ID and name (use predictable name from compose)
+    expected_container_name = instance.name.lower()
+    container_id = get_container_id(expected_container_name)
     if container_id:
         instance.container_id = container_id
         logger.debug("Container ID for instance %s: %s", instance.id, container_id)
 
-    container_name = get_container_name(instance.name)
-    if container_name:
-        instance.container_name = container_name
-        logger.debug("Container name for instance %s: %s", instance.id, container_name)
+    instance.container_name = expected_container_name
+    logger.debug("Container name for instance %s: %s", instance.id, expected_container_name)
 
-        # Connect container to backend network so API can reach it
-        logger.debug("Connecting container %s to backend network...", container_name)
-        connected = connect_container_to_network(container_name, "backend")
-        if connected:
-            logger.debug("Successfully connected %s to backend network", container_name)
-        else:
-            logger.warning("Failed to connect %s to backend network", container_name)
+    # Connect container to backend network so API can reach it
+    logger.debug("Connecting container %s to backend network...", expected_container_name)
+    connected = connect_container_to_network(expected_container_name, "backend")
+    if connected:
+        logger.debug("Successfully connected %s to backend network", expected_container_name)
+    else:
+        logger.warning("Failed to connect %s to backend network", expected_container_name)
 
     # Verify container reached running state
     if instance.container_id:
@@ -1818,7 +1972,8 @@ async def start_instance(
                 instance_port,
             )
             tunnel_info = start_cloudflared_tunnel(
-                host_port=instance.port,
+                container_name=instance.container_name or instance.name,
+                port=instance_port,
             )
             instance.tunnel_id = tunnel_info["pid"]
             instance.public_url = tunnel_info["url"]
@@ -2003,6 +2158,15 @@ async def restart_instance(
                     exc,
                 )
 
+        # Re-apply compose fixes in case they were updated since last start
+        _sanitize_compose_file(instance.compose_path)
+        tool_type = await session.get(ToolType, instance.tool_type_id)
+        if tool_type and tool_type.interface_type == "web":
+            _ensure_web_bind_address(
+                instance.compose_path, tool_type.name, tool_type.default_port
+            )
+        _ensure_container_name_in_compose(instance.compose_path, instance.name)
+
         returncode, stdout, stderr = execute_compose_command(
             instance.compose_path, "restart"
         )
@@ -2025,12 +2189,15 @@ async def restart_instance(
                     "error": f"Tool type '{tool_type.name if tool_type else 'unknown'}' has no port configured",
                 }
 
+            instance_port = tool_type.default_port
+
             # Only create tunnel for web-enabled tools
             if tool_type.interface_type == "web":
                 # Create new temporary tunnel
                 try:
                     tunnel_info = start_cloudflared_tunnel(
-                        host_port=instance.port or 0,
+                        container_name=instance.name.lower(),
+                        port=instance_port,
                     )
                     instance.tunnel_id = tunnel_info["pid"]
                     instance.public_url = tunnel_info["url"]
@@ -2263,9 +2430,16 @@ async def recreate_tunnel_endpoint(
                 "message": "Tunnel is already healthy",
             }
 
+    # Get tool type for default port
+    tool_type = await session.get(ToolType, instance.tool_type_id)
+    instance_port = (
+        tool_type.default_port if tool_type and tool_type.default_port else 8080
+    )
+
     try:
         tunnel_info = recreate_tunnel(
-            host_port=instance.port or 0,
+            container_name=instance.container_name or instance.name,
+            port=instance_port,
             old_pid=instance.tunnel_id,
         )
         instance.tunnel_id = tunnel_info["pid"]

apps/api/src/services/docker.py

@@ -159,7 +159,7 @@ def execute_compose_command(
         cmd.extend(["--env-file", env_file])
 
     if action == "up":
-        cmd.extend(["up", "-d"])
+        cmd.extend(["up", "-d", "--force-recreate"])
     elif action == "down":
         cmd.extend(["down", "-v"])
     elif action in ("start", "stop", "restart"):
@@ -384,16 +384,96 @@ def find_free_port(start: int = 10000, end: int = 20000) -> int:
     raise RuntimeError(f"No free port found in range {start}-{end}")
 
 
+def _check_app_binding(container_name: str, port: int) -> dict[str, str | bool]:
+    """Diagnose whether the app is bound to 127.0.0.1 or 0.0.0.0.
+
+    Checks from both inside the container (localhost) and outside
+    (via Docker network) to detect binding issues.
+
+    Returns:
+        Dict with 'internal_ok', 'external_ok', 'internal_status',
+        'external_status', and 'diagnosis'.
+    """
+    import subprocess
+
+    result: dict[str, Any] = {
+        "internal_ok": False,
+        "external_ok": False,
+        "internal_status": None,
+        "external_status": None,
+        "diagnosis": "unknown",
+    }
+
+    # Check from inside the container (loopback)
+    internal = subprocess.run(
+        [
+            "docker",
+            "exec",
+            container_name,
+            "sh",
+            "-c",
+            f"curl -s -o /dev/null -w '%{{http_code}}' http://localhost:{port}",
+        ],
+        capture_output=True,
+        text=True,
+        timeout=5,
+    )
+    if internal.returncode == 0:
+        try:
+            result["internal_status"] = int(internal.stdout.strip())
+            result["internal_ok"] = result["internal_status"] > 0
+        except ValueError:
+            pass
+
+    # Check from outside the container (Docker network)
+    external = subprocess.run(
+        [
+            "curl",
+            "-s",
+            "-o",
+            "/dev/null",
+            "-w",
+            "%{http_code}",
+            f"http://{container_name}:{port}",
+        ],
+        capture_output=True,
+        text=True,
+        timeout=5,
+    )
+    if external.returncode == 0:
+        try:
+            result["external_status"] = int(external.stdout.strip())
+            result["external_ok"] = result["external_status"] > 0
+        except ValueError:
+            pass
+
+    # Diagnose binding issue
+    if result["internal_ok"] and not result["external_ok"]:
+        result["diagnosis"] = (
+            f"App appears to be bound to 127.0.0.1:{port} inside the container. "
+            f"It must bind to 0.0.0.0:{port} to be accessible from the tunnel."
+        )
+    elif result["internal_ok"] and result["external_ok"]:
+        result["diagnosis"] = "App is accessible on both interfaces."
+    elif not result["internal_ok"] and not result["external_ok"]:
+        result["diagnosis"] = f"App is not responding on port {port} at all."
+    else:
+        result["diagnosis"] = "Unexpected binding state."
+
+    return result
+
+
 def start_cloudflared_tunnel(
-    host_port: int, timeout: int = 30
+    container_name: str, port: int, timeout: int = 30
 ) -> dict[str, str]:
-    """Start a temporary Cloudflare tunnel to localhost.
+    """Start a temporary Cloudflare tunnel for a container.
 
     Uses 'cloudflared tunnel --url' to create a temporary tunnel
     with a random trycloudflare.com URL.
 
     Args:
-        host_port: Host-mapped port number (e.g. from find_free_port)
+        container_name: Name of the Docker container to tunnel to
+        port: Port number the container listens on
         timeout: Maximum seconds to wait for tunnel URL
 
     Returns:
@@ -404,9 +484,11 @@ def start_cloudflared_tunnel(
 
     logger = logging.getLogger(__name__)
 
-    # First verify the container is accessible via the host-mapped port
-    logger.info("Checking connectivity to localhost:%d...", host_port)
-    for attempt in range(10):
+    # First verify the container is accessible from the Docker network
+    logger.info("Checking connectivity to %s:%d...", container_name, port)
+    accessible = False
+    last_status = None
+    for attempt in range(30):  # 30 attempts × 1s = 30s max wait for app startup
         check = subprocess.run(
             [
                 "curl",
@@ -415,27 +497,65 @@ def start_cloudflared_tunnel(
                 "/dev/null",
                 "-w",
                 "%{http_code}",
-                f"http://localhost:{host_port}",
+                "--max-time",
+                "3",
+                f"http://{container_name}:{port}",
             ],
             capture_output=True,
             text=True,
             timeout=5,
         )
+        status_str = check.stdout.strip()
         logger.info(
-            "Connectivity check %d: http_code=%s", attempt + 1, check.stdout.strip()
+            "Connectivity check %d/%d: http_code=%s (rc=%d)",
+            attempt + 1,
+            30,
+            status_str,
+            check.returncode,
         )
-        if check.returncode == 0:
-            break
+        try:
+            last_status = int(status_str)
+            # Accept 2xx, 3xx, 401, 403 as "app is listening"
+            if last_status in (401, 403) or 200 <= last_status < 400:
+                accessible = True
+                logger.info(
+                    "App on %s:%d is ready (HTTP %d)",
+                    container_name,
+                    port,
+                    last_status,
+                )
+                break
+        except ValueError:
+            pass
+
+        if check.returncode != 0:
+            logger.debug(
+                "curl failed: stderr=%s", check.stderr.strip() if check.stderr else ""
+            )
         time.sleep(1)
-    else:
+
+    if not accessible:
         logger.warning(
-            "localhost:%d not responding to curl checks", host_port
+            "Container %s:%d not responding after 30s (last status: %s). "
+            "Running binding diagnostics...",
+            container_name,
+            port,
+            last_status,
+        )
+        diagnosis = _check_app_binding(container_name, port)
+        logger.warning(
+            "Binding diagnosis: internal=%s (HTTP %s), external=%s (HTTP %s). %s",
+            diagnosis["internal_ok"],
+            diagnosis["internal_status"],
+            diagnosis["external_ok"],
+            diagnosis["external_status"],
+            diagnosis["diagnosis"],
         )
 
     # Run cloudflared in background, capture output
-    logger.info("Starting cloudflared tunnel to http://localhost:%d", host_port)
+    logger.info("Starting cloudflared tunnel to http://%s:%d", container_name, port)
     proc = subprocess.Popen(
-        ["cloudflared", "tunnel", "--url", f"http://localhost:{host_port}"],
+        ["cloudflared", "tunnel", "--url", f"http://{container_name}:{port}"],
         stdout=subprocess.PIPE,
         stderr=subprocess.STDOUT,
         text=True,
@@ -490,14 +610,15 @@ def stop_cloudflared_tunnel(pid: str) -> None:
 
 
 def recreate_tunnel(
-    host_port: int, old_pid: str | None = None
+    container_name: str, port: int, old_pid: str | None = None
 ) -> dict[str, str]:
     """Recreate a temporary Cloudflare tunnel.
 
     Stops the old tunnel (if pid provided) and starts a new one.
 
     Args:
-        host_port: Host-mapped port number (e.g. from find_free_port)
+        container_name: Name of the Docker container to tunnel to
+        port: Port number the container listens on
         old_pid: Optional PID of the old tunnel process to stop
 
     Returns:
@@ -506,7 +627,7 @@ def recreate_tunnel(
     if old_pid:
         stop_cloudflared_tunnel(old_pid)
 
-    return start_cloudflared_tunnel(host_port)
+    return start_cloudflared_tunnel(container_name, port)
 
 
 def check_tunnel_health(url: str, timeout: int = 10) -> dict[str, Any]:

apps/api/src/services/health_monitor.py

@@ -220,18 +220,18 @@ class HealthMonitor:
         await self._event_bus.publish(event_type, payload)
 
         # Create notification for instance owner (fire-and-forget)
+        # Only send warnings and errors; skip "recovered" info notifications.
         if new_status == "error":
             category = "instance"
             severity = "error"
             title = "Container failed"
-        else:
+        elif new_status == "unhealthy":
             category = "health"
-            if new_status == "unhealthy":
-                severity = "warning"
-                title = "Container unhealthy"
-            else:
-                severity = "info"
-                title = "Container recovered"
+            severity = "warning"
+            title = "Container unhealthy"
+        else:
+            # Running/recovered — do not notify
+            return
 
         try:
             await notification_service.create_notification(

apps/api/src/services/lifecycle_hooks.py

@@ -24,6 +24,7 @@ def _derive_title(event_type: str) -> str:
         "instance.restarted": "Container restarted",
         "instance.deleted": "Container deleted",
         "instance.error": "Container error",
+        "instance.health_changed": "Container ready",
     }
     return mapping.get(
         event_type,
@@ -31,6 +32,21 @@ def _derive_title(event_type: str) -> str:
     )
 
 
+def _should_notify(event_type: str, status: str | None) -> bool:
+    """Determine whether a lifecycle event should generate a notification.
+
+    Only warnings, errors, and "container is ready" (health_changed running)
+    are sent to users.
+    """
+    if event_type == "instance.error":
+        return True
+    if event_type == "instance.health_changed" and status == "running":
+        return True
+    # Filter out: created, started, stopped, restarted, deleted, and any
+    # health_changed that is not "running" (unhealthy is handled by health_monitor)
+    return False
+
+
 def _build_payload(
     event_type: str,
     instance: ToolInstance,
@@ -118,15 +134,12 @@ async def publish_lifecycle_event(
     await event_bus.publish(event_type, payload)
 
     # Create notification for instance owner (fire-and-forget)
-    # Skip intermediate "starting" notifications — only notify on terminal states
-    # (failed or successful attempts)
-    _is_starting_intermediate = (
-        event_type == "instance.started" and (status or instance.status) == "starting"
-    )
-    if _is_starting_intermediate:
+    # Only send warnings, errors, and "container is ready" notifications.
+    effective_status = status or instance.status
+    if not _should_notify(event_type, effective_status):
         return
 
-    severity = "error" if event_type == "instance.error" else "info"
+    severity = "error" if event_type == "instance.error" else "success"
     title = _derive_title(event_type)
 
     try:

apps/api/src/services/notification_service.py

@@ -195,6 +195,32 @@ class NotificationService:
         await session.commit()
         return result.rowcount or 0
 
+    async def dismiss_all(
+        self,
+        session: AsyncSession,
+        user_id: uuid.UUID,
+    ) -> int:
+        """Soft-delete all non-dismissed notifications for a user.
+
+        Args:
+            session: Database session.
+            user_id: Owner of the notifications.
+
+        Returns:
+            Number of rows updated.
+        """
+        stmt = (
+            update(Notification)
+            .where(
+                Notification.user_id == user_id,
+                Notification.dismissed_at.is_(None),
+            )
+            .values(dismissed_at=datetime.now(timezone.utc))
+        )
+        result: CursorResult[Any] = await session.execute(stmt)  # type: ignore[assignment]
+        await session.commit()
+        return result.rowcount or 0
+
     async def dismiss(
         self,
         session: AsyncSession,

apps/api/src/services/permission_fixer.py

@@ -40,6 +40,17 @@ def apply_mount_permissions(
             "error": None,
         }
 
+        # Skip read-only mounts — their permissions cannot be changed
+        # post-start because the bind mount is locked.
+        if mount.get("readonly", False):
+            logger.debug(
+                "Skipping permission fix for read-only mount %s (target=%s)",
+                name,
+                target,
+            )
+            results.append(result)
+            continue
+
         # Skip if no permission policy defined
         if not owner and not mode and not file_mode:
             results.append(result)

apps/api/src/services/ssh_keys.py

@@ -1,5 +1,6 @@
 """SSH key service utilities for preparing keys for container use."""
 
+import logging
 import os
 from pathlib import Path
 
@@ -7,6 +8,8 @@ from cryptography.fernet import Fernet
 
 from src.config import Settings
 
+logger = logging.getLogger(__name__)
+
 
 def _get_fernet() -> Fernet:
     """Generate a valid Fernet key from the session secret."""
@@ -75,10 +78,20 @@ def prepare_ssh_key_files(
             os.chown(private_key_path, effective_uid, effective_gid)
             os.chown(public_key_path, effective_uid, effective_gid)
             os.chown(config_path, effective_uid, effective_gid)
-        except PermissionError:
-            # API process may not be running as root; permission fixer will
-            # handle this post-start if the mount is read-write
-            pass
+            logger.debug(
+                "Set SSH key ownership to uid=%s gid=%s for %s",
+                effective_uid,
+                effective_gid,
+                ssh_dir,
+            )
+        except PermissionError as exc:
+            logger.warning(
+                "Cannot chown SSH keys to uid=%s gid=%s (running as uid=%s): %s",
+                effective_uid,
+                effective_gid,
+                os.getuid(),
+                exc,
+            )
 
     return str(ssh_dir)
 

apps/api/tests/integration/test_notifications_lifecycle.py

@@ -149,8 +149,8 @@ async def test_lifecycle_running_creates_notification(
     assert len(notifications) == 1
     n = notifications[0]
     assert n.category == "instance"
-    assert n.severity == "info"
-    assert n.title == "Health Changed"
+    assert n.severity == "success"
+    assert n.title == "Container ready"
     assert n.source_type == "tool_instances"
     assert n.source_id == test_instance.id
 
@@ -315,9 +315,9 @@ async def test_notification_ownership_matches_instance_owner(
         event_bus=event_bus,
         session=db_session,
         instance=instance,
-        event_type="instance.created",
-        status="pending",
-        message="Instance created",
+        event_type="instance.health_changed",
+        status="running",
+        message="Container running",
     )
 
     result = await db_session.execute(

apps/api/tests/integration/test_tool_types_api_extended.py

@@ -6,7 +6,9 @@ from fastapi.testclient import TestClient
 class TestToolTypesAPIExtended:
     """Integration tests for tool types API with new fields."""
 
-    def test_create_tool_type_with_dockerfile(self, authenticated_client: TestClient) -> None:
+    def test_create_tool_type_with_dockerfile(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test creating a tool type with dockerfile definition."""
         response = authenticated_client.post(
             "/tool-types",
@@ -27,7 +29,9 @@ class TestToolTypesAPIExtended:
         assert data["definition_type"] == "dockerfile"
         assert data["dockerfile_template"] == "FROM python:3.11\nRUN pip install flask"
 
-    def test_create_tool_type_with_readiness_probe(self, authenticated_client: TestClient) -> None:
+    def test_create_tool_type_with_readiness_probe(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test creating a tool type with readiness probe."""
         response = authenticated_client.post(
             "/tool-types",
@@ -52,7 +56,9 @@ class TestToolTypesAPIExtended:
         assert data["readiness_probe"]["command"] == "curl -f http://localhost:8080"
         assert data["readiness_probe"]["timeout"] == 30
 
-    def test_create_tool_type_invalid_definition_type(self, authenticated_client: TestClient) -> None:
+    def test_create_tool_type_invalid_definition_type(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test that invalid definition types are rejected."""
         response = authenticated_client.post(
             "/tool-types",
@@ -67,7 +73,9 @@ class TestToolTypesAPIExtended:
         )
         assert response.status_code == 422
 
-    def test_create_tool_type_dockerfile_without_template(self, authenticated_client: TestClient) -> None:
+    def test_create_tool_type_dockerfile_without_template(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test that dockerfile type requires dockerfile_template."""
         response = authenticated_client.post(
             "/tool-types",
@@ -81,7 +89,9 @@ class TestToolTypesAPIExtended:
         )
         assert response.status_code == 422
 
-    def test_update_tool_type_with_new_fields(self, authenticated_client: TestClient) -> None:
+    def test_update_tool_type_with_new_fields(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test updating a tool type with new fields."""
         # Create tool type first
         create_response = authenticated_client.post(
@@ -112,7 +122,9 @@ class TestToolTypesAPIExtended:
         assert response.status_code == 200
         data = response.json()
         assert data["display_name"] == "Updated Name"
-        assert data["readiness_probe"]["command"] == "curl -f http://localhost:8080/health"
+        assert (
+            data["readiness_probe"]["command"] == "curl -f http://localhost:8080/health"
+        )
 
     def test_validate_tool_type_compose(self, authenticated_client: TestClient) -> None:
         """Test validating compose template."""
@@ -127,7 +139,9 @@ class TestToolTypesAPIExtended:
         data = response.json()
         assert data["valid"] is True
 
-    def test_validate_tool_type_invalid_compose(self, authenticated_client: TestClient) -> None:
+    def test_validate_tool_type_invalid_compose(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test validating invalid compose template."""
         response = authenticated_client.post(
             "/tool-types/validate",
@@ -141,7 +155,9 @@ class TestToolTypesAPIExtended:
         assert data["valid"] is False
         assert "errors" in data
 
-    def test_validate_tool_type_dockerfile(self, authenticated_client: TestClient) -> None:
+    def test_validate_tool_type_dockerfile(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test validating dockerfile template."""
         response = authenticated_client.post(
             "/tool-types/validate",
@@ -154,7 +170,9 @@ class TestToolTypesAPIExtended:
         data = response.json()
         assert data["valid"] is True
 
-    def test_get_tool_type_returns_new_fields(self, authenticated_client: TestClient) -> None:
+    def test_get_tool_type_returns_new_fields(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test that GET returns new fields."""
         # Create tool type with all fields
         create_response = authenticated_client.post(
@@ -166,7 +184,7 @@ class TestToolTypesAPIExtended:
                 "interfaces": ["web", "terminal"],
                 "default_port": 8443,
                 "definition_type": "compose",
-                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: code-server\n    ports:\n      - '8443:8443'\n    volumes:\n      - \"{{REPO_PATH}}:/workspace\"",
+                "compose_template": "version: '3.8'\nservices:\n  app:\n    image: code-server\n    command: --bind-addr 0.0.0.0:8443\n    ports:\n      - '8443:8443'\n    volumes:\n      - \"{{REPO_PATH}}:/workspace\"",
                 "readiness_probe": {
                     "command": "curl -f http://localhost:8443",
                     "timeout": 30,
@@ -186,7 +204,9 @@ class TestToolTypesAPIExtended:
         assert data["interfaces"] == ["web", "terminal"]
         assert "readiness_probe" in data
 
-    def test_create_tool_type_without_port_fails(self, authenticated_client: TestClient) -> None:
+    def test_create_tool_type_without_port_fails(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test that creating a tool type without default_port fails validation."""
         response = authenticated_client.post(
             "/tool-types",
@@ -204,7 +224,9 @@ class TestToolTypesAPIExtended:
         data = response.json()
         assert "default_port" in str(data)
 
-    def test_create_tool_type_with_port_mismatch_fails(self, authenticated_client: TestClient) -> None:
+    def test_create_tool_type_with_port_mismatch_fails(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test that port mismatch between default_port and compose template fails."""
         response = authenticated_client.post(
             "/tool-types",
@@ -222,7 +244,9 @@ class TestToolTypesAPIExtended:
         assert response.status_code == 422
         _ = response.json()
 
-    def test_create_tool_type_with_startup_command(self, authenticated_client: TestClient) -> None:
+    def test_create_tool_type_with_startup_command(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test creating a tool type with startup_command."""
         response = authenticated_client.post(
             "/tool-types",
@@ -244,7 +268,9 @@ class TestToolTypesAPIExtended:
         assert data["startup_command"] == "cd /workspace && ls"
         assert data["interface_type"] == "terminal"
 
-    def test_update_tool_type_startup_command(self, authenticated_client: TestClient) -> None:
+    def test_update_tool_type_startup_command(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test updating a tool type's startup_command."""
         # Create tool type first
         create_response = authenticated_client.post(
@@ -273,7 +299,9 @@ class TestToolTypesAPIExtended:
         data = response.json()
         assert data["startup_command"] == "source /etc/profile"
 
-    def test_get_tool_type_returns_startup_command(self, authenticated_client: TestClient) -> None:
+    def test_get_tool_type_returns_startup_command(
+        self, authenticated_client: TestClient
+    ) -> None:
         """Test that GET returns startup_command."""
         create_response = authenticated_client.post(
             "/tool-types",

apps/api/tests/unit/test_lifecycle_hooks.py

@@ -0,0 +1,49 @@
+"""Unit tests for lifecycle hook helpers."""
+
+import pytest
+
+from src.services.lifecycle_hooks import _derive_title, _should_notify
+
+
+class TestDeriveTitle:
+    """Tests for _derive_title."""
+
+    def test_known_event_types(self) -> None:
+        assert _derive_title("instance.created") == "Container created"
+        assert _derive_title("instance.started") == "Container started"
+        assert _derive_title("instance.stopped") == "Container stopped"
+        assert _derive_title("instance.restarted") == "Container restarted"
+        assert _derive_title("instance.deleted") == "Container deleted"
+        assert _derive_title("instance.error") == "Container error"
+        assert _derive_title("instance.health_changed") == "Container ready"
+
+    def test_unknown_event_type(self) -> None:
+        assert _derive_title("instance.custom_event") == "Custom Event"
+
+
+class TestShouldNotify:
+    """Tests for _should_notify filtering."""
+
+    def test_error_events_are_notified(self) -> None:
+        assert _should_notify("instance.error", "error") is True
+        assert _should_notify("instance.error", None) is True
+
+    def test_health_changed_running_is_notified(self) -> None:
+        assert _should_notify("instance.health_changed", "running") is True
+
+    def test_created_started_stopped_restarted_deleted_filtered(self) -> None:
+        for event in [
+            "instance.created",
+            "instance.started",
+            "instance.stopped",
+            "instance.restarted",
+            "instance.deleted",
+        ]:
+            assert _should_notify(event, "pending") is False
+            assert _should_notify(event, "running") is False
+            assert _should_notify(event, None) is False
+
+    def test_health_changed_non_running_filtered(self) -> None:
+        assert _should_notify("instance.health_changed", "unhealthy") is False
+        assert _should_notify("instance.health_changed", "starting") is False
+        assert _should_notify("instance.health_changed", None) is False

apps/api/tests/unit/test_notification_service.py

@@ -308,6 +308,59 @@ async def test_get_unread_count_excludes_dismissed(
     assert count == 0
 
 
+@pytest.mark.unit
+@pytest.mark.asyncio
+async def test_dismiss_all_affects_all_non_dismissed(
+    db_session: AsyncSession,
+    notification_service: NotificationService,
+    user_a: User,
+) -> None:
+    for i in range(4):
+        await notification_service.create_notification(
+            db_session,
+            user_a.id,
+            category="instance",
+            severity="info",
+            title=f"Notification {i}",
+        )
+
+    cleared = await notification_service.dismiss_all(db_session, user_a.id)
+
+    assert cleared == 4
+    items, total = await notification_service.list_notifications(db_session, user_a.id)
+    assert total == 0
+
+
+@pytest.mark.unit
+@pytest.mark.asyncio
+async def test_dismiss_all_affects_only_caller(
+    db_session: AsyncSession,
+    notification_service: NotificationService,
+    user_a: User,
+    user_b: User,
+) -> None:
+    for i in range(3):
+        await notification_service.create_notification(
+            db_session, user_a.id, category="instance", severity="info", title=f"A-{i}"
+        )
+    for i in range(2):
+        await notification_service.create_notification(
+            db_session, user_b.id, category="instance", severity="info", title=f"B-{i}"
+        )
+
+    cleared = await notification_service.dismiss_all(db_session, user_a.id)
+
+    assert cleared == 3
+    items_a, total_a = await notification_service.list_notifications(
+        db_session, user_a.id
+    )
+    items_b, total_b = await notification_service.list_notifications(
+        db_session, user_b.id
+    )
+    assert total_a == 0
+    assert total_b == 2
+
+
 @pytest.mark.unit
 @pytest.mark.asyncio
 async def test_mark_all_read_affects_only_caller(

apps/api/tests/unit/test_notifications_api_routes.py

@@ -0,0 +1,34 @@
+"""Unit tests for notification API route ordering."""
+
+from fastapi import FastAPI
+from fastapi.testclient import TestClient
+
+from src.api.notifications import router as notifications_router
+
+
+def test_delete_notifications_route_order() -> None:
+    """DELETE /notifications must match before DELETE /notifications/{id}.
+
+    FastAPI matches routes in declaration order. The bulk clear endpoint
+    (DELETE /notifications) must be registered before the single dismiss
+    endpoint (DELETE /notifications/{notification_id}) or the path
+    parameter route will intercept the bulk route.
+    """
+    app = FastAPI()
+    app.include_router(notifications_router)
+    client = TestClient(app)
+
+    # Verify the bulk delete route exists and returns the expected schema
+    # (it will 401 without auth, but that's fine — we just need to confirm
+    # routing doesn't hit the UUID-parameter route first)
+    response = client.delete("/notifications")
+    # Should get 401 (unauthenticated), NOT 422 (UUID parse error)
+    assert response.status_code == 401, (
+        f"Expected 401 (auth required), got {response.status_code}. "
+        f"Route order may be wrong — DELETE /notifications matched "
+        f"DELETE /notifications/{{notification_id}} instead."
+    )
+
+    # Verify the single dismiss route still works (also 401 without auth)
+    response = client.delete("/notifications/12345678-1234-1234-1234-123456789abc")
+    assert response.status_code == 401

apps/api/tests/unit/test_permission_fixer.py

@@ -64,6 +64,24 @@ class TestApplyMountPermissions:
             "find /home/user/.ssh -type f -exec chmod 0600" in file_mode_call[0][1][2]
         )
 
+    @patch("src.services.permission_fixer._run_in_container")
+    def test_skips_readonly_mount(self, mock_run) -> None:
+        mounts = [
+            {
+                "name": "ssh_keys",
+                "target": "/home/user/.ssh",
+                "readonly": True,
+                "mode": "0700",
+                "file_mode": "0600",
+            },
+        ]
+        results = apply_mount_permissions("abc123", mounts)
+
+        assert len(results) == 1
+        assert results[0]["mount_name"] == "ssh_keys"
+        assert results[0]["success"] is True
+        mock_run.assert_not_called()
+
     @patch("src.services.permission_fixer._run_in_container")
     def test_skips_mount_with_no_policy(self, mock_run) -> None:
         mounts = [

apps/api/tests/unit/test_ssh_keys.py

@@ -13,7 +13,9 @@ class TestPrepareSshKeyFiles:
     """Tests for prepare_ssh_key_files."""
 
     @patch("src.services.ssh_keys._get_fernet")
-    def test_creates_files_with_default_permissions(self, mock_fernet, tmp_path) -> None:
+    def test_creates_files_with_default_permissions(
+        self, mock_fernet, tmp_path
+    ) -> None:
         mock_fernet.return_value.decrypt.return_value = b"private-key-content"
         ssh_key = MagicMock()
         ssh_key.private_key_encrypted = "enc"
@@ -35,9 +37,7 @@ class TestPrepareSshKeyFiles:
         ssh_key.public_key = "ssh-ed25519 AAA test@test"
 
         with patch("os.chown") as mock_chown:
-            ssh_dir = prepare_ssh_key_files(
-                str(tmp_path), ssh_key, uid=1001, gid=1001
-            )
+            ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key, uid=1001, gid=1001)
 
         # os.chown is called for the directory and each of the 3 files
         assert mock_chown.call_count == 4
@@ -56,8 +56,6 @@ class TestPrepareSshKeyFiles:
 
         with patch("os.chown", side_effect=PermissionError("not allowed")):
             # Should not raise
-            ssh_dir = prepare_ssh_key_files(
-                str(tmp_path), ssh_key, uid=1001, gid=1001
-            )
+            ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key, uid=1001, gid=1001)
 
         assert Path(ssh_dir).exists()

apps/api/tests/unit/test_tool_instances_legacy.py

@@ -411,8 +411,9 @@ class TestStartInstanceLegacyFallback:
     @patch("src.api.tool_instances.wait_for_container_running")
     @patch("src.api.tool_instances.execute_compose_command")
     @patch("src.api.tool_instances.get_container_id")
-    @patch("src.api.tool_instances.get_container_name")
     @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._ensure_container_name_in_compose")
+    @patch("src.api.tool_instances._ensure_web_bind_address")
     @patch("src.api.tool_instances._sanitize_compose_file")
     @patch("src.api.tool_instances._prepare_manifest_instance")
     @patch("src.api.tool_instances._get_user")
@@ -423,8 +424,9 @@ class TestStartInstanceLegacyFallback:
         mock_get_user,
         mock_prepare_manifest,
         mock_sanitize,
+        mock_ensure_web_bind,
+        mock_ensure_container_name,
         mock_connect_network,
-        mock_get_container_name,
         mock_get_container_id,
         mock_execute_compose,
         mock_wait_container,
@@ -440,7 +442,6 @@ class TestStartInstanceLegacyFallback:
         mock_get_project.return_value = AsyncMock()
         mock_execute_compose.return_value = (0, "started", "")
         mock_get_container_id.return_value = "abc123"
-        mock_get_container_name.return_value = "test-container"
         mock_connect_network.return_value = True
         mock_wait_container.return_value = {
             "success": True,
@@ -509,8 +510,9 @@ class TestStartInstanceLegacyFallback:
     @patch("src.api.tool_instances.wait_for_container_running")
     @patch("src.api.tool_instances.execute_compose_command")
     @patch("src.api.tool_instances.get_container_id")
-    @patch("src.api.tool_instances.get_container_name")
     @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._ensure_container_name_in_compose")
+    @patch("src.api.tool_instances._ensure_web_bind_address")
     @patch("src.api.tool_instances._sanitize_compose_file")
     @patch("src.api.tool_instances._prepare_manifest_instance")
     @patch("src.api.tool_instances._get_user")
@@ -521,8 +523,9 @@ class TestStartInstanceLegacyFallback:
         mock_get_user,
         mock_prepare_manifest,
         mock_sanitize,
+        mock_ensure_web_bind,
+        mock_ensure_container_name,
         mock_connect_network,
-        mock_get_container_name,
         mock_get_container_id,
         mock_execute_compose,
         mock_wait_container,
@@ -538,7 +541,6 @@ class TestStartInstanceLegacyFallback:
         mock_get_project.return_value = AsyncMock()
         mock_execute_compose.return_value = (0, "started", "")
         mock_get_container_id.return_value = "abc123"
-        mock_get_container_name.return_value = "test-container"
         mock_connect_network.return_value = True
         mock_wait_container.return_value = {
             "success": True,
@@ -606,8 +608,9 @@ class TestStartInstanceLegacyFallback:
     @patch("src.api.tool_instances.wait_for_container_running")
     @patch("src.api.tool_instances.execute_compose_command")
     @patch("src.api.tool_instances.get_container_id")
-    @patch("src.api.tool_instances.get_container_name")
     @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._ensure_container_name_in_compose")
+    @patch("src.api.tool_instances._ensure_web_bind_address")
     @patch("src.api.tool_instances._sanitize_compose_file")
     @patch("src.api.tool_instances._prepare_manifest_instance")
     @patch("src.api.tool_instances._get_user")
@@ -618,8 +621,9 @@ class TestStartInstanceLegacyFallback:
         mock_get_user,
         mock_prepare_manifest,
         mock_sanitize,
+        mock_ensure_web_bind,
+        mock_ensure_container_name,
         mock_connect_network,
-        mock_get_container_name,
         mock_get_container_id,
         mock_execute_compose,
         mock_wait_container,
@@ -635,7 +639,6 @@ class TestStartInstanceLegacyFallback:
         mock_get_project.return_value = AsyncMock()
         mock_execute_compose.return_value = (0, "started", "")
         mock_get_container_id.return_value = "abc123"
-        mock_get_container_name.return_value = "test-container"
         mock_connect_network.return_value = True
         mock_wait_container.return_value = {
             "success": True,
@@ -705,12 +708,14 @@ class TestStartInstanceSshPermissions:
     """SSH key mounts trigger permission fixes after container starts."""
 
     @patch("src.api.tool_instances.write_compose_file")
+    @patch("src.api.tool_instances.prepare_ssh_key_files")
     @patch("src.api.tool_instances.apply_ssh_permissions")
     @patch("src.api.tool_instances.wait_for_container_running")
     @patch("src.api.tool_instances.execute_compose_command")
     @patch("src.api.tool_instances.get_container_id")
-    @patch("src.api.tool_instances.get_container_name")
     @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._ensure_container_name_in_compose")
+    @patch("src.api.tool_instances._ensure_web_bind_address")
     @patch("src.api.tool_instances._sanitize_compose_file")
     @patch("src.api.tool_instances._get_user")
     @patch("src.api.tool_instances._get_owned_project")
@@ -719,12 +724,14 @@ class TestStartInstanceSshPermissions:
         mock_get_project,
         mock_get_user,
         mock_sanitize,
+        mock_ensure_web_bind,
+        mock_ensure_container_name,
         mock_connect_network,
-        mock_get_container_name,
         mock_get_container_id,
         mock_execute_compose,
         mock_wait_container,
         mock_apply_ssh,
+        mock_prepare_ssh,
         mock_write_compose,
         mock_session,
         fake_user_id,
@@ -743,7 +750,6 @@ class TestStartInstanceSshPermissions:
         mock_get_project.return_value = AsyncMock()
         mock_execute_compose.return_value = (0, "started", "")
         mock_get_container_id.return_value = "abc123"
-        mock_get_container_name.return_value = "test-container"
         mock_connect_network.return_value = True
         mock_wait_container.return_value = {
             "success": True,
@@ -836,12 +842,14 @@ class TestStartInstanceSshPermissions:
         assert result["status"] == "running"
         mock_apply_ssh.assert_called_once_with("abc123", "/home/user/.ssh", "user")
 
+    @patch("src.api.tool_instances.prepare_ssh_key_files")
     @patch("src.api.tool_instances.apply_ssh_permissions")
     @patch("src.api.tool_instances.wait_for_container_running")
     @patch("src.api.tool_instances.execute_compose_command")
     @patch("src.api.tool_instances.get_container_id")
-    @patch("src.api.tool_instances.get_container_name")
     @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._ensure_container_name_in_compose")
+    @patch("src.api.tool_instances._ensure_web_bind_address")
     @patch("src.api.tool_instances._sanitize_compose_file")
     @patch("src.api.tool_instances._get_user")
     @patch("src.api.tool_instances._get_owned_project")
@@ -850,12 +858,14 @@ class TestStartInstanceSshPermissions:
         mock_get_project,
         mock_get_user,
         mock_sanitize,
+        mock_ensure_web_bind,
+        mock_ensure_container_name,
         mock_connect_network,
-        mock_get_container_name,
         mock_get_container_id,
         mock_execute_compose,
         mock_wait_container,
         mock_apply_ssh,
+        mock_prepare_ssh,
         mock_session,
         fake_user_id,
         fake_project_id,
@@ -870,7 +880,6 @@ class TestStartInstanceSshPermissions:
         mock_get_project.return_value = AsyncMock()
         mock_execute_compose.return_value = (0, "started", "")
         mock_get_container_id.return_value = "abc123"
-        mock_get_container_name.return_value = "test-container"
         mock_connect_network.return_value = True
         mock_wait_container.return_value = {
             "success": True,
@@ -933,14 +942,15 @@ class TestStartInstanceSshPermissions:
         mock_session.get.side_effect = _get
 
         with patch("os.path.exists", return_value=True):
-            result = await start_instance(
-                project_id=fake_project_id,
-                repo_id=fake_repo_id,
-                instance_id=fake_instance_id,
-                data=None,
-                user_id=fake_user_id,
-                session=mock_session,
-            )
+            with patch("src.api.tool_instances._modify_compose_file"):
+                result = await start_instance(
+                    project_id=fake_project_id,
+                    repo_id=fake_repo_id,
+                    instance_id=fake_instance_id,
+                    data=None,
+                    user_id=fake_user_id,
+                    session=mock_session,
+                )
 
         assert result["status"] == "running"
         mock_apply_ssh.assert_called_once_with("abc123", "/root/.ssh", "root")
@@ -952,8 +962,9 @@ class TestStartInstanceManifestBranch:
     @patch("src.api.tool_instances.wait_for_container_running")
     @patch("src.api.tool_instances.execute_compose_command")
     @patch("src.api.tool_instances.get_container_id")
-    @patch("src.api.tool_instances.get_container_name")
     @patch("src.api.tool_instances.connect_container_to_network")
+    @patch("src.api.tool_instances._ensure_container_name_in_compose")
+    @patch("src.api.tool_instances._ensure_web_bind_address")
     @patch("src.api.tool_instances._sanitize_compose_file")
     @patch("src.api.tool_instances._prepare_manifest_instance")
     @patch("src.api.tool_instances.write_compose_file")
@@ -966,8 +977,9 @@ class TestStartInstanceManifestBranch:
         mock_write_compose,
         mock_prepare_manifest,
         mock_sanitize,
+        mock_ensure_web_bind,
+        mock_ensure_container_name,
         mock_connect_network,
-        mock_get_container_name,
         mock_get_container_id,
         mock_execute_compose,
         mock_wait_container,
@@ -987,7 +999,6 @@ class TestStartInstanceManifestBranch:
         mock_get_project.return_value = AsyncMock()
         mock_execute_compose.return_value = (0, "started", "")
         mock_get_container_id.return_value = "abc123"
-        mock_get_container_name.return_value = "test-container"
         mock_connect_network.return_value = True
         mock_wait_container.return_value = {
             "success": True,

apps/web/src/api/notifications.ts

@@ -30,6 +30,10 @@ export interface MarkAllReadResponse {
 	marked_count: number;
 }
 
+export interface ClearAllResponse {
+	cleared_count: number;
+}
+
 export const getNotifications = async (): Promise<NotificationListResponse> => {
 	const response =
 		await apiClient.get<NotificationListResponse>("/notifications");
@@ -62,3 +66,8 @@ export const markAllNotificationsRead = async (): Promise<number> => {
 export const dismissNotification = async (id: string): Promise<void> => {
 	await apiClient.delete(`/notifications/${id}`);
 };
+
+export const clearAllNotifications = async (): Promise<number> => {
+	const response = await apiClient.delete<ClearAllResponse>("/notifications");
+	return response.data.cleared_count;
+};

apps/web/src/components/create-session-form.tsx

@@ -171,7 +171,13 @@ export const CreateSessionForm = ({
       );
 
       setProgress("Starting container...");
-      await startInstance(projectId, repoId, instance.id);
+      await startInstance(
+        projectId,
+        repoId,
+        instance.id,
+        selectedConfigProfile || undefined,
+        selectedSshKeyIds.length > 0 ? selectedSshKeyIds : undefined
+      );
 
       // Reset form
       if (!fixedProjectId) setSelectedProject("");

apps/web/src/components/notification-center.test.tsx

@@ -9,6 +9,7 @@ vi.mock("../api/notifications", () => ({
 	markNotificationRead: vi.fn(),
 	markAllNotificationsRead: vi.fn(),
 	dismissNotification: vi.fn(),
+	clearAllNotifications: vi.fn(),
 }));
 
 import { getNotifications, getUnreadCount } from "../api/notifications";
@@ -146,6 +147,26 @@ describe("NotificationCenter", () => {
 		expect(vi.mocked(mockMarkAll)).toHaveBeenCalled();
 	});
 
+	it("calls clearAll on clear-all button click", async () => {
+		mockedGetNotifications.mockResolvedValue({
+			items: [makeNotification("1")],
+			total: 1,
+			limit: 20,
+			offset: 0,
+		});
+
+		render(<NotificationCenter />, { wrapper });
+		fireEvent.click(screen.getByRole("button", { name: /notifications/i }));
+
+		await vi.advanceTimersByTimeAsync(100);
+		fireEvent.click(screen.getByRole("button", { name: /clear all/i }));
+
+		const { clearAllNotifications: mockClearAll } = await import(
+			"../api/notifications"
+		);
+		expect(vi.mocked(mockClearAll)).toHaveBeenCalled();
+	});
+
 	it("refreshes list immediately on open", async () => {
 		render(<NotificationCenter />, { wrapper });
 		fireEvent.click(screen.getByRole("button", { name: /notifications/i }));

apps/web/src/components/notification-center.tsx

@@ -15,6 +15,7 @@ export function NotificationCenter({
 		unreadCount,
 		markRead,
 		markAllRead,
+		clearAll,
 		dismiss,
 		refreshList,
 		isDropdownOpen,
@@ -115,6 +116,15 @@ export function NotificationCenter({
 							>
 								Mark all as read
 							</button>
+							<button
+								type="button"
+								className="notification-clear-all"
+								onClick={() => {
+									void clearAll();
+								}}
+							>
+								Clear all
+							</button>
 						</div>
 					)}
 				</div>

apps/web/src/components/terminal.tsx

@@ -313,6 +313,96 @@ export const TerminalComponent = React.forwardRef<TerminalRef, TerminalProps>(
 			term.focus();
 			const ws = connectWebSocket();
 
+			// Mobile touch scroll.
+			// In normal mode xterm.js has a scrollable viewport; in alternate
+			// screen (tmux/vim) there is no scrollback and the only way to
+			// scroll is to send mouse-wheel protocol sequences to the
+			// application.  We detect which situation we're in by checking
+			// whether the viewport has scrollable height.
+			let touchCleanup: (() => void) | undefined;
+			if (isMobile) {
+				let startY = 0;
+				let startX = 0;
+				let isScrolling = false;
+
+				const onTouchStart = (e: TouchEvent) => {
+					if (e.touches.length === 1) {
+						startY = e.touches[0].clientY;
+						startX = e.touches[0].clientX;
+						isScrolling = false;
+					}
+				};
+				const onTouchMove = (e: TouchEvent) => {
+					if (e.touches.length !== 1) return;
+					const touch = e.touches[0];
+					const deltaY = startY - touch.clientY;
+					const deltaX = Math.abs(startX - touch.clientX);
+					if (!isScrolling) {
+						if (Math.abs(deltaY) > deltaX && Math.abs(deltaY) > 4) {
+							isScrolling = true;
+						}
+					}
+					if (isScrolling) {
+						e.preventDefault();
+						const viewport = container.querySelector(
+							".xterm-viewport",
+						) as HTMLElement | null;
+						if (!viewport) return;
+
+						// If the viewport is scrollable, scroll it directly.
+						// Otherwise we are in alternate screen (tmux/vim) and must
+						// send SGR 1006 mouse-wheel protocol data.
+						const hasScrollback =
+							viewport.scrollHeight > viewport.clientHeight;
+						if (hasScrollback) {
+							viewport.scrollTop += deltaY;
+						} else {
+							const ws = wsRef.current;
+							if (
+								ws?.readyState === WebSocket.OPEN &&
+								termRef.current
+							) {
+								// Use the cursor position as the wheel location so
+								// tmux knows which pane to scroll.
+								const buf = termRef.current.buffer.active;
+								const col = buf.cursorX + 1;
+								const row = buf.cursorY + 1;
+								// SGR 1006: 64 = wheel-up, 65 = wheel-down
+								const btn = deltaY > 0 ? 64 : 65;
+								ws.send(`\x1b[<${btn};${col};${row}M`);
+							}
+						}
+						startY = touch.clientY;
+					}
+				};
+				const onTouchEnd = () => {
+					isScrolling = false;
+				};
+
+				container.addEventListener("touchstart", onTouchStart, {
+					passive: true,
+					capture: true,
+				});
+				container.addEventListener("touchmove", onTouchMove, {
+					passive: false,
+					capture: true,
+				});
+				container.addEventListener("touchend", onTouchEnd, {
+					capture: true,
+				});
+				touchCleanup = () => {
+					container.removeEventListener("touchstart", onTouchStart, {
+						capture: true,
+					});
+					container.removeEventListener("touchmove", onTouchMove, {
+						capture: true,
+					});
+					container.removeEventListener("touchend", onTouchEnd, {
+						capture: true,
+					});
+				};
+			}
+
 			// Initial fit after layout settles (terminal must be opened first)
 			let fitAttempts = 0;
 			const doInitialFit = () => {
@@ -440,6 +530,7 @@ export const TerminalComponent = React.forwardRef<TerminalRef, TerminalProps>(
 					"visibilitychange",
 					handleVisibilityChange,
 				);
+				if (touchCleanup) touchCleanup();
 				if (ws) {
 					ws.close(1000, "Component unmounting");
 				}
@@ -568,7 +659,9 @@ export const TerminalComponent = React.forwardRef<TerminalRef, TerminalProps>(
 		};
 
 		return (
-			<div className={`terminal-wrapper ${isMobile ? "mobile" : ""} ${!showControls ? "no-controls" : ""}`}>
+			<div
+				className={`terminal-wrapper ${isMobile ? "mobile" : ""} ${!showControls ? "no-controls" : ""}`}
+			>
 				{showControls && (
 					<div className="terminal-header">
 						<div className="terminal-header-left">

apps/web/src/pages/terminal.tsx

@@ -5,10 +5,15 @@ import {
 	TerminalSessionTabs,
 	type TerminalSessionInfo,
 } from "../components/terminal-session-tabs";
+import { Icon } from "../components/icon";
+import { SpecialKeysStrip } from "../components/special-keys-strip";
+import { SpecialKeysPanel } from "../components/special-keys-panel";
 import { useMobileViewport } from "../hooks/use-mobile-viewport";
 import { useAutoHide } from "../hooks/use-auto-hide";
+import { useVirtualKeyboard } from "../hooks/use-virtual-keyboard";
 import { useTerminalSessions } from "../hooks/use-terminal-sessions";
 import type { TerminalSession } from "../api/terminal";
+import type { ModifierKey } from "../hooks/use-special-keys";
 
 const SESSIONS_TO_INFO = (sessions: TerminalSession[]): TerminalSessionInfo[] =>
 	sessions.map((s) => ({
@@ -39,7 +44,15 @@ export const TerminalPage: React.FC = () => {
 		Record<string, TerminalStatus>
 	>({});
 	const changeFontSizeRef = useRef<((delta: number) => void) | null>(null);
+	const sendDataRef = useRef<((data: string) => void) | null>(null);
+	const focusInputRef = useRef<(() => void) | null>(null);
 	const [showResetConfirm, setShowResetConfirm] = useState(false);
+	const [showSpecialKeysPanel, setShowSpecialKeysPanel] = useState(false);
+	const [activeModifier, setActiveModifier] = useState<ModifierKey | null>(
+		null,
+	);
+	const { isOpen: isKeyboardOpen, height: keyboardHeight } =
+		useVirtualKeyboard();
 
 	const {
 		sessions,
@@ -162,6 +175,47 @@ export const TerminalPage: React.FC = () => {
 		setActiveSessionId,
 	]);
 
+	// Keep screen awake while terminal is open
+	useEffect(() => {
+		let wakeLock: WakeLockSentinel | null = null;
+
+		const requestWakeLock = async () => {
+			try {
+				if ("wakeLock" in navigator) {
+					wakeLock = await navigator.wakeLock.request("screen");
+				}
+			} catch {
+				// Wake lock may be denied; silently ignore
+			}
+		};
+
+		void requestWakeLock();
+
+		const handleVisibilityChange = () => {
+			if (document.visibilityState === "visible") {
+				void requestWakeLock();
+			}
+		};
+
+		document.addEventListener("visibilitychange", handleVisibilityChange);
+		return () => {
+			document.removeEventListener("visibilitychange", handleVisibilityChange);
+			wakeLock?.release().catch(() => {});
+		};
+	}, []);
+
+	// Lock page scroll on mobile terminal so swipes scroll the terminal buffer,
+	// not the page.
+	useEffect(() => {
+		if (!isMobile) return;
+		document.documentElement.classList.add("terminal-page-open");
+		document.body.classList.add("terminal-page-open");
+		return () => {
+			document.documentElement.classList.remove("terminal-page-open");
+			document.body.classList.remove("terminal-page-open");
+		};
+	}, [isMobile]);
+
 	// Click outside terminal content/header to exit fullscreen
 	const handleFullscreenClick = useCallback(
 		(e: React.MouseEvent<HTMLElement>) => {
@@ -205,15 +259,17 @@ export const TerminalPage: React.FC = () => {
 
 	const handleTerminalReady = useCallback(
 		(
-			_sendData: (data: string) => void,
+			sendData: (data: string) => void,
 			status: TerminalStatus,
-			_focusInput: () => void,
+			focusInput: () => void,
 			changeFontSize: (delta: number) => void,
 		) => {
 			setTerminalStatuses((prev) => ({
 				...prev,
 				[activeSessionId ?? "default"]: status,
 			}));
+			sendDataRef.current = sendData;
+			focusInputRef.current = focusInput;
 			changeFontSizeRef.current = changeFontSize;
 		},
 		[activeSessionId],
@@ -223,6 +279,10 @@ export const TerminalPage: React.FC = () => {
 		changeFontSizeRef.current?.(delta);
 	}, []);
 
+	const handleSendKey = useCallback((data: string) => {
+		sendDataRef.current?.(data);
+	}, []);
+
 	const handleReset = useCallback(() => {
 		if (activeSessionId && terminalRefs.current[activeSessionId]) {
 			terminalRefs.current[activeSessionId].current?.reset();
@@ -241,45 +301,85 @@ export const TerminalPage: React.FC = () => {
 	const sessionInfos = SESSIONS_TO_INFO(sessions);
 
 	if (isMobile) {
+		const activeSession = sessions.find((s) => s.id === activeSessionId);
+		const status =
+			terminalStatuses[activeSessionId ?? "default"] ?? "connecting";
+
 		return (
 			<section
 				className={`terminal-page mobile ${isFullscreen ? "fullscreen" : ""}`}
 			>
+				{/* Overlay status bar — floats over terminal, never resizes it */}
 				<div
-					className={`terminal-page-header mobile-header ${headerAutoHide.isVisible ? "visible" : "hidden"}`}
-					onClick={() => headerAutoHide.show()}
+					className={`mobile-terminal-overlay ${headerAutoHide.isVisible ? "visible" : "hidden"}`}
+					onClick={(e) => e.stopPropagation()}
 				>
-					<button
-						className="secondary-button"
-						onClick={() => navigate(-1)}
-						type="button"
-					>
-						Back
-					</button>
-					<h1>Terminal</h1>
-					<button
-						className="secondary-button"
-						onClick={() => setIsFullscreen((p) => !p)}
-						type="button"
-					>
-						{isFullscreen ? "Exit" : "Fullscreen"}
-					</button>
+					<div className="mobile-terminal-toolbar">
+						<div className="mobile-terminal-toolbar-left">
+							<button
+								className="mobile-terminal-toolbtn"
+								onClick={() => navigate(-1)}
+								type="button"
+								aria-label="Back"
+							>
+								<Icon name="arrow-left" size="sm" />
+							</button>
+						</div>
+						<div className="mobile-terminal-toolbar-center">
+							<span className="mobile-terminal-title">
+								{activeSession?.name || "Terminal"}
+							</span>
+							<span
+								className={`mobile-terminal-status status-dot ${status}`}
+								aria-label={`Connection status: ${status}`}
+							/>
+						</div>
+						<div className="mobile-terminal-toolbar-right">
+							<button
+								className="mobile-terminal-toolbtn"
+								onClick={() => handleFontSizeChange(-1)}
+								type="button"
+								aria-label="Decrease font size"
+							>
+								<span style={{ fontSize: "0.75rem" }}>A-</span>
+							</button>
+							<button
+								className="mobile-terminal-toolbtn"
+								onClick={() => handleFontSizeChange(1)}
+								type="button"
+								aria-label="Increase font size"
+							>
+								<span style={{ fontSize: "1rem" }}>A+</span>
+							</button>
+							<button
+								className="mobile-terminal-toolbtn"
+								onClick={() => navigate(-1)}
+								type="button"
+								aria-label="Exit terminal"
+							>
+								<Icon name="close" size="sm" />
+							</button>
+						</div>
+					</div>
+					<div className="mobile-terminal-overlay-tabs">
+						<TerminalSessionTabs
+							sessions={sessionInfos}
+							activeSessionId={activeSessionId ?? ""}
+							onSelect={handleSelect}
+							onClose={handleClose}
+							onCreate={handleCreate}
+							onRename={handleRename}
+							isMobile={true}
+						/>
+					</div>
 				</div>
+
+				{/* Terminal content — always fills full viewport */}
 				<div
-					className={`mobile-tabs-container ${headerAutoHide.isVisible ? "visible" : "hidden"}`}
-					onClick={() => headerAutoHide.show()}
+					className="terminal-page-content mobile-full"
+					style={{ paddingBottom: isKeyboardOpen ? keyboardHeight : 0 }}
+					onClick={() => headerAutoHide.toggle()}
 				>
-					<TerminalSessionTabs
-						sessions={sessionInfos}
-						activeSessionId={activeSessionId ?? ""}
-						onSelect={handleSelect}
-						onClose={handleClose}
-						onCreate={handleCreate}
-						onRename={handleRename}
-						isMobile={true}
-					/>
-				</div>
-				<div className="terminal-page-content">
 					{error && <div className="terminal-error-banner">{error}</div>}
 					{sessions
 						.filter((session) => session.id === activeSessionId)
@@ -291,6 +391,9 @@ export const TerminalPage: React.FC = () => {
 									sessionId={session.id}
 									onClose={() => handleClose(session.id)}
 									isMobile={true}
+									showControls={false}
+									activeModifier={activeModifier}
+									onModifierChange={setActiveModifier}
 									onTerminalReady={handleTerminalReady}
 								/>
 							</div>
@@ -301,6 +404,24 @@ export const TerminalPage: React.FC = () => {
 						</div>
 					)}
 				</div>
+
+				<SpecialKeysStrip
+					onSend={handleSendKey}
+					isVisible={!showSpecialKeysPanel}
+					onMoreClick={() => setShowSpecialKeysPanel(true)}
+					onKeepFocus={() => focusInputRef.current?.()}
+					activeModifier={activeModifier}
+					onModifierChange={setActiveModifier}
+				/>
+
+				<SpecialKeysPanel
+					onSend={handleSendKey}
+					isOpen={showSpecialKeysPanel}
+					onClose={() => setShowSpecialKeysPanel(false)}
+					onKeepFocus={() => focusInputRef.current?.()}
+					activeModifier={activeModifier}
+					onModifierChange={setActiveModifier}
+				/>
 			</section>
 		);
 	}

apps/web/src/state/notifications.tsx

@@ -11,6 +11,7 @@ import {
 	markNotificationRead,
 	markAllNotificationsRead,
 	dismissNotification,
+	clearAllNotifications,
 } from "../api/notifications";
 import type { NotificationItem } from "../api/notifications";
 
@@ -21,6 +22,7 @@ export interface NotificationContextValue {
 	error: Error | null;
 	markRead: (id: string) => Promise<void>;
 	markAllRead: () => Promise<void>;
+	clearAll: () => Promise<void>;
 	dismiss: (id: string) => Promise<void>;
 	refreshList: () => Promise<void>;
 	isDropdownOpen: boolean;
@@ -265,6 +267,24 @@ export function NotificationProvider({
 		await fetchList();
 	}, [fetchList]);
 
+	const clearAll = useCallback(async () => {
+		const { notifications: currentNotifications } = stateRef.current;
+		const unreadInList = currentNotifications.filter(
+			(n) => n.read_at === null,
+		).length;
+
+		setNotifications([]);
+		setUnreadCount((c) => Math.max(0, c - unreadInList));
+		setError(null);
+
+		try {
+			await clearAllNotifications();
+		} catch (err) {
+			setNotifications(currentNotifications);
+			setError(err as Error);
+		}
+	}, []);
+
 	const value: NotificationContextValue = {
 		notifications,
 		unreadCount,
@@ -272,6 +292,7 @@ export function NotificationProvider({
 		error,
 		markRead,
 		markAllRead,
+		clearAll,
 		dismiss,
 		refreshList,
 		isDropdownOpen,

apps/web/src/styles.css

@@ -77,6 +77,11 @@ body {
 	color: var(--ink);
 }
 
+html.terminal-page-open,
+body.terminal-page-open {
+	overflow: hidden;
+}
+
 [data-theme="dark"] body {
 	background: radial-gradient(circle at top right, #2a2520, var(--bg));
 }
@@ -2950,42 +2955,148 @@ a.nav-item,
 	background: #cd3131;
 }
 
-/* Mobile auto-hide header and tabs */
-.terminal-page.mobile .terminal-page-header,
-.mobile-tabs-container {
+/* ============================================
+   Mobile Terminal Overlay
+   ============================================ */
+
+/* Mobile terminal page — no padding, terminal fills viewport */
+.terminal-page.mobile {
+	padding: 0;
+	gap: 0;
+	height: 100vh;
+	height: 100dvh;
+	position: relative;
+	overflow: hidden;
+}
+
+/* Overlay status bar — floats over terminal, never resizes it */
+.mobile-terminal-overlay {
+	position: absolute;
+	top: 0;
+	left: 0;
+	right: 0;
+	z-index: 100;
+	background: #2d2d2d;
+	border-bottom: 1px solid #3e3e3e;
 	transition:
 		transform 0.3s ease,
 		opacity 0.3s ease;
 }
 
-.terminal-page.mobile .terminal-page-header.hidden,
-.mobile-tabs-container.hidden {
+.mobile-terminal-overlay.hidden {
 	transform: translateY(-100%);
 	opacity: 0;
 	pointer-events: none;
 }
 
-.terminal-page.mobile .terminal-page-header.visible,
-.mobile-tabs-container.visible {
+.mobile-terminal-overlay.visible {
 	transform: translateY(0);
 	opacity: 1;
 }
 
+/* Toolbar row */
+.mobile-terminal-toolbar {
+	display: flex;
+	align-items: center;
+	justify-content: space-between;
+	padding: var(--space-2) var(--space-3);
+	gap: var(--space-2);
+}
+
+.mobile-terminal-toolbar-left,
+.mobile-terminal-toolbar-right {
+	display: flex;
+	align-items: center;
+	gap: var(--space-1);
+	flex: 0 0 auto;
+}
+
+.mobile-terminal-toolbar-center {
+	display: flex;
+	align-items: center;
+	gap: var(--space-2);
+	flex: 1;
+	justify-content: center;
+	min-width: 0;
+}
+
+.mobile-terminal-title {
+	font-size: 0.875rem;
+	font-weight: 500;
+	color: #d4d4d4;
+	white-space: nowrap;
+	overflow: hidden;
+	text-overflow: ellipsis;
+}
+
+.mobile-terminal-status {
+	width: 8px;
+	height: 8px;
+	border-radius: 50%;
+	background: #666;
+	flex-shrink: 0;
+}
+
+.mobile-terminal-status.connecting {
+	background: #f5f543;
+	animation: pulse 1.5s infinite;
+}
+
+.mobile-terminal-status.connected {
+	background: #0dbc79;
+}
+
+.mobile-terminal-status.disconnected,
+.mobile-terminal-status.error {
+	background: #cd3131;
+}
+
+.mobile-terminal-toolbtn {
+	display: flex;
+	align-items: center;
+	justify-content: center;
+	width: 36px;
+	height: 36px;
+	padding: 0;
+	background: transparent;
+	border: 1px solid #3e3e3e;
+	border-radius: 6px;
+	color: #d4d4d4;
+	cursor: pointer;
+	font-size: 0.875rem;
+	transition: background 0.2s ease;
+}
+
+.mobile-terminal-toolbtn:hover {
+	background: #3e3e3e;
+}
+
+/* Session tabs inside overlay */
+.mobile-terminal-overlay-tabs {
+	background: #1e1e1e;
+	border-top: 1px solid #3e3e3e;
+}
+
+.mobile-terminal-overlay-tabs .terminal-session-tabs {
+	background: #1e1e1e;
+	border-bottom: none;
+}
+
+/* Terminal content — always fills full viewport on mobile */
+.terminal-page-content.mobile-full {
+	flex: 1;
+	min-height: 0;
+	border: none;
+	border-radius: 0;
+	overflow: hidden;
+}
+
 /* Mobile fullscreen */
 @media (max-width: 767px) {
 	.terminal-page.fullscreen {
 		padding: 0;
 	}
 
-	.terminal-page.mobile .terminal-page-header {
-		padding: var(--space-2);
-		gap: var(--space-2);
-	}
-
-	.terminal-page.mobile .terminal-page-header h1 {
-		font-size: 1rem;
-	}
-
 	.terminal-session-tab-name {
 		max-width: 80px;
 	}
@@ -3597,6 +3708,7 @@ a.nav-item,
 	padding: 0;
 	overflow: hidden;
 	position: relative;
+	touch-action: none;
 }
 
 /* xterm.js manages its own sizing */
@@ -4602,10 +4714,12 @@ a:active,
 	padding: 0.75rem 1rem;
 	border-top: 1px solid var(--border);
 	flex-shrink: 0;
+	display: flex;
+	gap: 0.5rem;
 }
 
 .notification-mark-all {
-	width: 100%;
+	flex: 1;
 	padding: 0.5rem 0.75rem;
 	background: transparent;
 	border: 1px solid var(--border);
@@ -4623,6 +4737,25 @@ a:active,
 	border-color: var(--brand);
 }
 
+.notification-clear-all {
+	flex: 1;
+	padding: 0.5rem 0.75rem;
+	background: transparent;
+	border: 1px solid var(--border);
+	border-radius: 8px;
+	color: var(--muted);
+	font: inherit;
+	font-size: 0.85rem;
+	cursor: pointer;
+	transition: all 0.15s ease;
+}
+
+.notification-clear-all:hover {
+	background: var(--bg);
+	color: var(--danger);
+	border-color: var(--danger);
+}
+
 /* Notification Item */
 .notification-item {
 	display: flex;

docker-compose.traefik.yml

@@ -13,7 +13,11 @@ services:
     volumes:
       - postgres_data:/var/lib/postgresql/data
     healthcheck:
-      test: ["CMD-SHELL", "pg_isready -U ${POSTGRES_USER:-headquarter} -d ${POSTGRES_DB:-headquarter}"]
+      test:
+        [
+          "CMD-SHELL",
+          "pg_isready -U ${POSTGRES_USER:-headquarter} -d ${POSTGRES_DB:-headquarter}",
+        ]
       interval: 10s
       timeout: 5s
       retries: 5
@@ -92,7 +96,7 @@ services:
       AUTHENTIK_AUTHORIZE_URL: ${AUTHENTIK_AUTHORIZE_URL:-}
       AUTHENTIK_TOKEN_URL: ${AUTHENTIK_TOKEN_URL:-}
     volumes:
-      - repo_data:/data/repos
+      - /data/repos:/data/repos
       - /data/instances:/data/instances
       - avatar_uploads:/app/uploads
       - /var/run/docker.sock:/var/run/docker.sock
@@ -116,7 +120,6 @@ services:
 volumes:
   postgres_data:
   redis_data:
-  repo_data:
   avatar_uploads:
 
 networks:

docker-compose.yml

@@ -1,4 +1,4 @@
-version: '3.8'
+version: "3.8"
 
 services:
   # PostgreSQL Database
@@ -14,7 +14,11 @@ services:
     ports:
       - "5432:5432"
     healthcheck:
-      test: ["CMD-SHELL", "pg_isready -U ${POSTGRES_USER:-headquarter} -d ${POSTGRES_DB:-headquarter}"]
+      test:
+        [
+          "CMD-SHELL",
+          "pg_isready -U ${POSTGRES_USER:-headquarter} -d ${POSTGRES_DB:-headquarter}",
+        ]
       interval: 10s
       timeout: 5s
       retries: 5
@@ -57,7 +61,7 @@ services:
       REPO_BASE_PATH: /data/repos
       INSTANCE_BASE_PATH: /data/instances
     volumes:
-      - repo_data:/data/repos
+      - /data/repos:/data/repos
       - /data/instances:/data/instances
     ports:
       - "8000:8000"
@@ -91,7 +95,6 @@ services:
 volumes:
   postgres_data:
   redis_data:
-  repo_data:
 
 networks:
   backend: