refactor: remove Tool Configs and Config Folders

These features are fully superseded by Config Profiles which provide:
- Env vars, file mounts, port overrides, start commands, working dirs
- Git mounts, profile composition, cycle detection
- Default selection, project/tool-type scoping

Changes:
- Delete backend models: ToolConfig, ConfigFolder
- Delete backend APIs: tool_configs.py, config_folders.py
- Delete frontend API clients: tool_configs.ts, config_folders.ts
- Remove Tool Config fetching from start_instance, use ConfigProfile only
- Simplify merge_with_config to accept only profile (no tool_configs)
- Remove configs/folders tabs from Tool Workshop page
- Delete associated integration and unit tests
- Add Alembic migration to drop tool_configs and config_folders tables

Quality gates: backend tests 59 passed, frontend typecheck clean

apps/api/src/models/__init__.py

@@ -1,5 +1,4 @@
 from src.models.base import Base
-from src.models.config_folder import ConfigFolder
 from src.models.config_profile import ConfigProfile, ConfigProfileInclude
 from src.models.git_repository import GitRepository
 from src.models.project import Project
@@ -13,7 +12,6 @@ from src.models.user_config import UserConfig
 
 __all__ = [
     "Base",
-    "ConfigFolder",
     "ConfigProfile",
     "ConfigProfileInclude",
     "GitRepository",

apps/api/src/models/config_folder.py

@@ -1,31 +0,0 @@
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import Boolean, ForeignKey, JSON, String, Text
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.user import User
-
-
-class ConfigFolder(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    __tablename__ = "config_folders"
-
-    user_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(), ForeignKey("users.id", ondelete="CASCADE"), nullable=False
-    )
-    name: Mapped[str] = mapped_column(String(255), nullable=False)
-    description: Mapped[str | None] = mapped_column(Text, nullable=True)
-    mount_path: Mapped[str] = mapped_column(String(1024), nullable=False)
-    files: Mapped[dict] = mapped_column(
-        JSON, default=dict, nullable=False
-    )  # {"relative/path": "content", ...}
-    project_overrides: Mapped[dict | None] = mapped_column(
-        JSON, default=dict, nullable=True
-    )  # {"project_id": {"mount_path": "...", "files": {...}}}
-    is_active: Mapped[bool] = mapped_column(Boolean, default=True, nullable=False)
-
-    user: Mapped["User"] = relationship()

apps/api/src/models/tool_config.py

@@ -1,48 +0,0 @@
-import uuid
-from typing import TYPE_CHECKING
-
-from sqlalchemy import ForeignKey, JSON, String, Text
-from sqlalchemy import Uuid as UUID
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-
-from src.models.base import Base, TimestampMixin, UUIDPrimaryKeyMixin
-
-if TYPE_CHECKING:
-    from src.models.project import Project
-    from src.models.tool_type import ToolType
-    from src.models.user import User
-
-
-class ToolConfig(UUIDPrimaryKeyMixin, TimestampMixin, Base):
-    __tablename__ = "tool_configs"
-
-    user_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(), ForeignKey("users.id"), nullable=False
-    )
-    tool_type_id: Mapped[uuid.UUID] = mapped_column(
-        UUID(), ForeignKey("tool_types.id"), nullable=False
-    )
-    project_id: Mapped[uuid.UUID | None] = mapped_column(
-        UUID(), ForeignKey("projects.id"), nullable=True
-    )
-    key: Mapped[str] = mapped_column(String(255), nullable=False)
-    value: Mapped[str] = mapped_column(Text, nullable=False)
-    config_type: Mapped[str] = mapped_column(
-        String(20), nullable=False, default="env"
-    )  # "env" or "file"
-    file_path: Mapped[str | None] = mapped_column(
-        String(1024), nullable=True
-    )  # Only for file type
-    port_override: Mapped[int | None] = mapped_column(nullable=True)
-    start_command: Mapped[str | None] = mapped_column(Text, nullable=True)
-    working_directory: Mapped[str | None] = mapped_column(Text, nullable=True)
-    environment_variables: Mapped[dict | None] = mapped_column(
-        JSON, default=dict, nullable=True
-    )
-    volumes: Mapped[list[dict] | None] = mapped_column(
-        JSON, default=list, nullable=True
-    )
-
-    user: Mapped["User"] = relationship()
-    tool_type: Mapped["ToolType"] = relationship()
-    project: Mapped["Project | None"] = relationship()