refactor(skill): transition from artifact set to bundle structure

- Replaced SkillArtifactSet with SkillBundle across various components, enhancing the organization of skill dependencies and references.
- Updated SkillManager methods to load and save bundles instead of artifacts, improving clarity in asset management.
- Refactored SkillCompiler to compile skills into bundles, streamlining the dependency resolution process.
- Adjusted DifyCli and SandboxBashSession to utilize ToolDependencies, ensuring consistent handling of tool references.
- Introduced AssetReferences for better management of file dependencies within skill bundles.

api/core/skill/entities/asset_references.py

@@ -0,0 +1,9 @@
+from pydantic import BaseModel, ConfigDict, Field
+
+from core.skill.entities.skill_metadata import FileReference
+
+
+class AssetReferences(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+    references: list[FileReference] = Field(default_factory=list)