Update manifest structure (#17547)

Move all sync entities in an `entities` key. Rename functions to
logicFunctions

```json
{
  application: {
    ...
  },
  entities: {
    objects: [],
    logicFunctions: [],
    ...
  }
}
```

packages/twenty-server/src/database/typeorm/core/migrations/common/1769685701443-updateColumnName.ts

@@ -0,0 +1,17 @@
+import { type MigrationInterface, type QueryRunner } from 'typeorm';
+
+export class UpdateColumnName1769685701443 implements MigrationInterface {
+  name = 'UpdateColumnName1769685701443';
+
+  public async up(queryRunner: QueryRunner): Promise<void> {
+    await queryRunner.query(
+      `ALTER TABLE "core"."application" RENAME COLUMN "defaultLogicFunctionRoleId" TO "defaultRoleId"`,
+    );
+  }
+
+  public async down(queryRunner: QueryRunner): Promise<void> {
+    await queryRunner.query(
+      `ALTER TABLE "core"."application" RENAME COLUMN "defaultRoleId" TO "defaultLogicFunctionRoleId"`,
+    );
+  }
+}