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These features are fully superseded by Config Profiles which provide: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/services/manifest_compiler.py

@@ -351,13 +351,12 @@ def compute_image_tag(tool_name: str, manifest: dict) -> str:
 
 
 def merge_with_config(
-    manifest: dict, tool_configs: list[dict], profile: dict | None = None
+    manifest: dict, profile: dict | None = None
 ) -> dict:
-    """Merge ToolConfig and ConfigProfile overrides into a manifest.
+    """Merge ConfigProfile overrides into a manifest.
 
     Args:
         manifest: Base manifest from tool definition.
-        tool_configs: List of ToolConfig records.
         profile: Resolved ConfigProfile (optional).
 
     Returns:
@@ -365,29 +364,9 @@ def merge_with_config(
     """
     result = deepcopy(manifest)
 
-    # Apply ToolConfigs
     extra_env: dict[str, str] = {}
     extra_volumes: list[dict] = []
 
-    for config in tool_configs:
-        if config.get("config_type") == "env":
-            extra_env[config["key"]] = config["value"]
-        elif config.get("config_type") == "file" and config.get("file_path"):
-            # Files are handled outside the manifest (written to instance dir)
-            pass
-        if config.get("port_override"):
-            result["default_port"] = config["port_override"]
-        if config.get("start_command"):
-            result["runtime"] = result.get("runtime", {})
-            result["runtime"]["command"] = config["start_command"].split()
-        if config.get("working_directory"):
-            result["runtime"] = result.get("runtime", {})
-            result["runtime"]["working_dir"] = config["working_directory"]
-        if config.get("environment_variables"):
-            extra_env.update(config["environment_variables"])
-        if config.get("volumes"):
-            extra_volumes.extend(config["volumes"])
-
     # Apply ConfigProfile
     if profile:
         if profile.get("environment_variables"):