fix(server): embedding chunks primary key (#12416)

fix AI-131

<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit

- **Refactor**
  - Updated database schema to consolidate unique constraints into composite primary keys for embedding-related data, improving consistency.
  - Changed the relation in the Snapshot model to allow multiple embeddings.
  - Improved filtering logic for documents and snapshots based on embedding existence.
  - Reformatted SQL queries and schema attributes for improved readability; no changes to functionality.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

packages/backend/server/src/models/copilot-workspace.ts

@@ -47,7 +47,7 @@ export class CopilotWorkspaceConfigModel extends BaseModel {
         where: {
           workspaceId,
           embedding: {
-            is: null,
+            none: {},
           },
         },
         select: { id: true },