Refactor flat entity maps to be universal oriented (#17665)

# Introduction
In preparation of the workspace agnostic builder, we're migrating
`FlatEntityMaps` to be universal identifier oriented and based
As in the builder context there're won't be any ids at all
Please also note that the FlatEntity is a UniversalFlatEntity superset

From
```ts
import { type SyncableFlatEntity } from 'src/engine/metadata-modules/flat-entity/types/flat-entity-from.type';

export type FlatEntityMaps<T extends SyncableFlatEntity> = {
  byId: Partial<Record<string, T>>;
  idByUniversalIdentifier: Partial<Record<string, string>>;
  universalIdentifiersByApplicationId: Partial<Record<string, string[]>>;
};
```

To
```ts
export type FlatEntityMaps<
  T extends SyncableFlatEntity | UniversalSyncableFlatEntity,
> = {
  byUniversalIdentifier: Partial<Record<string, T>>;
  universalIdentifierById: Partial<Record<string, string>>;
  universalIdentifiersByApplicationId: Partial<Record<string, string[]>>; // this might make more sense to be migrated to universalIdentifiersByApplicationUniversalIdentifier but it's the main topic of this PR
};
```

## Low level maps tools
Had to refactor find | create | delete | replace | find-many | get-sub
tools ( through mutations and or throw equivalent )

packages/twenty-server/src/engine/metadata-modules/command-menu-item/command-menu-item.service.ts

@@ -38,7 +38,7 @@ export class CommandMenuItemService {
         },
       );
 
-    return Object.values(flatCommandMenuItemMaps.byId)
+    return Object.values(flatCommandMenuItemMaps.byUniversalIdentifier)
       .filter(isDefined)
       .sort((a, b) => a.label.localeCompare(b.label))
       .map(fromFlatCommandMenuItemToCommandMenuItemDto);
@@ -263,7 +263,7 @@ export class CommandMenuItemService {
         },
       );
 
-    return Object.values(flatCommandMenuItemMaps.byId)
+    return Object.values(flatCommandMenuItemMaps.byUniversalIdentifier)
       .filter(isDefined)
       .sort((a, b) => a.label.localeCompare(b.label));
   }
@@ -281,7 +281,7 @@ export class CommandMenuItemService {
       );
 
     const flatCommandMenuItem = Object.values(
-      flatCommandMenuItemMaps.byId,
+      flatCommandMenuItemMaps.byUniversalIdentifier,
     ).find(
       (item) => isDefined(item) && item.workflowVersionId === workflowVersionId,
     );