Remove logic function layer (#17697)

## Remove logic function layer

Package.json and yarn.lock are now on the application entity, so the
logic function layer is no longer used except as a legacy source for the
1.17 backfill. This PR removes all layer usage outside of that migration
and keeps only the entity for backfill.

### Summary

- **Kept:** `LogicFunctionLayerEntity` and its table, only used by the
1.17 backfill command to read legacy layer data and backfill application
package files.
- **Removed:** All other layer logic: CRUD, cache, resolvers, services,
DTOs, and frontend types. Logic functions now depend only on the
application for package/dependency context.


### Why Dependencies instead of Source for package files

Package.json and yarn.lock are the application’s dependency set and are
stored under the application in **FileFolder.Dependencies**. The build
service and drivers now read them only from Dependencies; nothing is
written to Source for these files.

packages/twenty-server/src/engine/metadata-modules/flat-entity/constant/all-metadata-relations.constant.ts

@@ -267,7 +267,6 @@ export const ALL_METADATA_RELATIONS = {
     manyToOne: {
       workspace: null,
       application: null,
-      logicFunctionLayer: null,
     },
     oneToMany: {},
   },