added the todo comments with questions

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/batch2/DeleteExpungeSvcImpl.java

@@ -71,6 +71,7 @@ public class DeleteExpungeSvcImpl implements IDeleteExpungeSvc {
 	 */
 	private void clearHibernateSearchIndex(List<ResourcePersistentId> thePersistentIds) {
 		if (myFullTextSearchSvc != null) {
+			//TODO: Changing the class looks insignificant, since everything is then again converted from Long to Object, is there anything else that needs to be changed?
 			List<Object> objectIds = thePersistentIds.stream().map(id -> ((JpaPid) id).getId()).collect(Collectors.toList());
 			myFullTextSearchSvc.deleteIndexedDocumentsByTypeAndId(ResourceTable.class, objectIds);
 			ourLog.info("Cleared Hibernate Search indexes.");

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/cross/ResourceLookup.java

@@ -46,6 +46,7 @@ public class ResourceLookup implements IResourceLookup {
         return myDeletedAt;
     }
 
+	//TODO: Should I rename the method and change the returned type here? (ResourceHistoryTable and ResourceTable also have the same method)
 	@Override
 	public ResourcePersistentId getPersistentId() {
 		return new JpaPid(myResourcePid);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/index/IdHelperServiceTest.java

@@ -155,6 +155,7 @@ public class IdHelperServiceTest {
 	public void testResolveResourceIdentity_defaultFunctionality(){
 		RequestPartitionId partitionId = RequestPartitionId.fromPartitionIdAndName(1, "partition");
 		String resourceType = "Patient";
+		//TODO: I have changed the value here to long number but I'm not sure if it could be anything else
 		String resourceForcedId = "123L";
 
 		Object[] forcedIdView = new Object[4];

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/api/IMdmLink.java

@@ -26,14 +26,19 @@ import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import java.util.Date;
 
 public interface IMdmLink {
+	//TODO: Should I change the type of returned value in this method?
 	ResourcePersistentId getId();
 
+	//TODO: Should I change the type of parameter in this method?
 	IMdmLink setId(ResourcePersistentId theId);
 
+	//TODO: Should I change the type of returned value in this method?
 	ResourcePersistentId getGoldenResourcePersistenceId();
 
+	//TODO: Should I change the type of parameter in this method?
 	IMdmLink setGoldenResourcePersistenceId(ResourcePersistentId theGoldenResourcePid);
 
+	//TODO: Should I change the type of returned value in this method?
 	ResourcePersistentId getSourcePersistenceId();
 
 	IMdmLink setSourcePersistenceId(ResourcePersistentId theSourcePid);

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/model/MdmPidTuple.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 
 public class MdmPidTuple {
+	//TODO: Should I change the type of these fields and the methods where they are used?
 	private ResourcePersistentId myGoldenPid;
 	private ResourcePersistentId mySourcePid;
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/storage/TransactionDetails.java

@@ -54,6 +54,7 @@ import java.util.function.Supplier;
  */
 public class TransactionDetails {
 
+	// TODO: can't use JpaPid here since module doesn't have the dependency and I get Circular Dependency warning when I try to add it
 	public static final ResourcePersistentId NOT_FOUND = new ResourcePersistentId(-1L);
 
 	private final Date myTransactionDate;

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/export/models/ResourceIdList.java

@@ -27,6 +27,7 @@ import java.util.List;
 
 public class ResourceIdList extends BulkExportJobBase {
 
+	//TODO: I don't quite understand the connection between Id and JpaId. I found that Id uses String as inner value. Should I change it as well?
 	/**
 	 * List of Id objects for serialization
 	 */

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDao.java

@@ -177,6 +177,7 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 */
 	T read(IIdType theId);
 
+	//TODO: Should I modify this and similar methods?
 	/**
 	 * Read a resource by its internal PID
 	 * @throws ResourceNotFoundException If the ID is not known to the server

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/svc/IIdHelperService.java

@@ -52,6 +52,7 @@ public interface IIdHelperService {
 	 *
 	 * @param theOnlyForcedIds If <code>true</code>, resources which are not existing forced IDs will not be resolved
 	 */
+	//TODO: Should I change the type of returned value in all these methods?
 	@Nonnull
 	List<ResourcePersistentId> resolveResourcePersistentIdsWithCache(@Nonnull RequestPartitionId theRequestPartitionId, List<IIdType> theIds, boolean theOnlyForcedIds);
 

hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/api/pid/ResourcePidListBuilderTest.java

@@ -16,6 +16,7 @@ import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
 
+//TODO: Should I modify this class?
 class ResourcePidListBuilderTest {
 
 	public static final ResourcePersistentId PID_1 = new ResourcePersistentId(1L);