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/tool_dependencies.py

@@ -0,0 +1,59 @@
+from pydantic import BaseModel, ConfigDict, Field
+
+from core.skill.entities.skill_metadata import ToolReference
+from core.tools.entities.tool_entities import ToolProviderType
+
+
+class ToolDependency(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+    type: ToolProviderType
+    provider: str
+    tool_name: str
+
+
+class ToolDependencies(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+    dependencies: list[ToolDependency] = Field(default_factory=list)
+    references: list[ToolReference] = Field(default_factory=list)
+
+    def is_empty(self) -> bool:
+        return not self.dependencies and not self.references
+
+    def filter(self, tools: list[tuple[str, str]]) -> "ToolDependencies":
+        tool_names = {f"{provider}.{tool_name}" for provider, tool_name in tools}
+        return ToolDependencies(
+            dependencies=[
+                dependency
+                for dependency in self.dependencies
+                if f"{dependency.provider}.{dependency.tool_name}" in tool_names
+            ],
+            references=[
+                reference
+                for reference in self.references
+                if f"{reference.provider}.{reference.tool_name}" in tool_names
+            ],
+        )
+
+    def merge(self, other: "ToolDependencies") -> "ToolDependencies":
+        dep_map: dict[str, ToolDependency] = {}
+        for dep in self.dependencies:
+            key = f"{dep.provider}.{dep.tool_name}"
+            dep_map[key] = dep
+        for dep in other.dependencies:
+            key = f"{dep.provider}.{dep.tool_name}"
+            if key not in dep_map:
+                dep_map[key] = dep
+
+        ref_map: dict[str, ToolReference] = {}
+        for ref in self.references:
+            ref_map[ref.uuid] = ref
+        for ref in other.references:
+            if ref.uuid not in ref_map:
+                ref_map[ref.uuid] = ref
+
+        return ToolDependencies(
+            dependencies=list(dep_map.values()),
+            references=list(ref_map.values()),
+        )