diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/SearchTotalModeEnum.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/SearchTotalModeEnum.java
index d10613d01a3..1a0d781e921 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/SearchTotalModeEnum.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/SearchTotalModeEnum.java
@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.api;
 
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import java.util.HashMap;
 import java.util.Map;
 
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParameterMap.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParameterMap.java
index f9c38feeed7..111656582d0 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParameterMap.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParameterMap.java
@@ -28,9 +28,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- *
+ * 
  * http://www.apache.org/licenses/LICENSE-2.0
- *
+ * 
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
index b6eb3a89253..44ac751ae71 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
@@ -168,7 +168,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 			verifySearchHasntFailedOrThrowInternalErrorException(search);
 			if (search.getStatus() == SearchStatusEnum.FINISHED) {
-				ourLog.info("Search entity marked as finished");
+				ourLog.info("Search entity marked as finished with {} results", search.getNumFound());
 				break;
 			}
 			if (search.getNumFound() >= theTo) {
@@ -189,7 +189,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 					search = newSearch.get();
 					String resourceType = search.getResourceType();
 					SearchParameterMap params = search.getSearchParameterMap();
-					SearchContinuationTask task = new SearchContinuationTask(search, myDaoRegistry.getResourceDao(resourceType), params, resourceType);
+					IFhirResourceDao<?> resourceDao = myDaoRegistry.getResourceDao(resourceType);
+					SearchContinuationTask task = new SearchContinuationTask(search, resourceDao, params, resourceType);
 					myIdToSearchTask.put(search.getUuid(), task);
 					myExecutor.submit(task);
 				}
@@ -228,10 +229,9 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
 			txTemplate.afterPropertiesSet();
 			return txTemplate.execute(t -> {
-				Optional<Search> searchOpt = mySearchDao.findById(theSearch.getId());
-				Search search = searchOpt.orElseThrow(IllegalStateException::new);
-				if (search.getStatus() != SearchStatusEnum.PASSCMPLET) {
-					throw new IllegalStateException("Can't change to LOADING because state is " + search.getStatus());
+				myEntityManager.refresh(theSearch);
+				if (theSearch.getStatus() != SearchStatusEnum.PASSCMPLET) {
+					throw new IllegalStateException("Can't change to LOADING because state is " + theSearch.getStatus());
 				}
 				theSearch.setStatus(SearchStatusEnum.LOADING);
 				Search newSearch = mySearchDao.save(theSearch);
@@ -239,6 +239,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			});
 		} catch (Exception e) {
 			ourLog.warn("Failed to activate search: {}", e.toString());
+			ourLog.trace("Failed to activate search", e);
 			return Optional.empty();
 		}
 	}
@@ -438,6 +439,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		myManagedTxManager = theTxManager;
 	}
 
+	@VisibleForTesting
+	public void setDaoRegistryForUnitTest(DaoRegistry theDaoRegistry) {
+		myDaoRegistry = theDaoRegistry;
+	}
+
 	public abstract class BaseTask implements Callable<Void> {
 		private final SearchParameterMap myParams;
 		private final IDao myCallingDao;
@@ -486,14 +492,41 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		}
 
 		public List<Long> getResourcePids(int theFromIndex, int theToIndex) {
-			ourLog.info("Requesting search PIDs from {}-{}", theFromIndex, theToIndex);
+			ourLog.debug("Requesting search PIDs from {}-{}", theFromIndex, theToIndex);
 
 			boolean keepWaiting;
 			do {
 				synchronized (mySyncedPids) {
 					ourLog.trace("Search status is {}", mySearch.getStatus());
-					keepWaiting = mySyncedPids.size() < theToIndex && mySearch.getStatus() == SearchStatusEnum.LOADING;
+					boolean haveEnoughResults = mySyncedPids.size() >= theToIndex;
+					if (!haveEnoughResults) {
+						switch (mySearch.getStatus()) {
+							case LOADING:
+								keepWaiting = true;
+								break;
+							case PASSCMPLET:
+								/*
+								 * If we get here, it means that the user requested resources that crossed the
+								 * current pre-fetch boundary. For example, if the prefetch threshold is 50 and the
+								 * user has requested resources 0-60, then they would get 0-50 back but the search
+								 * coordinator would then stop searching.SearchCoordinatorSvcImplTest
+								 */
+								List<Long> remainingResources = SearchCoordinatorSvcImpl.this.getResources(mySearch.getUuid(), mySyncedPids.size(), theToIndex);
+								ourLog.debug("Adding {} resources to the existing {} synced resource IDs", remainingResources.size(), mySyncedPids.size());
+								mySyncedPids.addAll(remainingResources);
+								keepWaiting = false;
+								break;
+							case FAILED:
+							case FINISHED:
+							default:
+								keepWaiting = false;
+								break;
+						}
+					} else {
+						keepWaiting = false;
+					}
 				}
+
 				if (keepWaiting) {
 					ourLog.info("Waiting, as we only have {} results", mySyncedPids.size());
 					try {
@@ -808,6 +841,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			 * Construct the SQL query we'll be sending to the database
 			 */
 			IResultIterator theResultIterator = sb.createQuery(myParams, mySearch.getUuid());
+			assert (theResultIterator != null);
 
 			/*
 			 * The following loop actually loads the PIDs of the resources
@@ -869,6 +903,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				txTemplate.afterPropertiesSet();
 				txTemplate.execute(t -> {
 					List<Long> previouslyAddedResourcePids = mySearchResultDao.findWithSearchUuid(getSearch());
+					ourLog.debug("Have {} previously added IDs in search: {}", previouslyAddedResourcePids.size(), getSearch().getUuid());
 					setPreviouslyAddedResourcePids(previouslyAddedResourcePids);
 					return null;
 				});
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
index 8c678a06312..f3faff4ccf0 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
@@ -17,13 +17,7 @@ import static org.hamcrest.Matchers.lessThanOrEqualTo;
 import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.startsWith;
 import static org.hamcrest.Matchers.stringContainsInOrder;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.junit.Assert.*;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -41,6 +35,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
+import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -159,6 +154,50 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
 	}
 
+
+	@Test
+	public void testSearchLinksWorkWithIncludes() {
+		for (int i = 0; i < 5; i++) {
+
+			Organization o = new Organization();
+			o.setId("O" + i);
+			o.setName("O" + i);
+			IIdType oid = ourClient.update().resource(o).execute().getId().toUnqualifiedVersionless();
+
+			Patient p = new Patient();
+			p.setId("P" + i);
+			p.getManagingOrganization().setReference(oid.getValue());
+			ourClient.update().resource(p).execute();
+
+		}
+
+		Bundle output = ourClient
+			.search()
+			.forResource("Patient")
+			.include(IBaseResource.INCLUDE_ALL)
+			.count(3)
+			.returnBundle(Bundle.class)
+			.execute();
+
+		List<String> ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
+		ourLog.info("Ids: {}", ids);
+		assertEquals(6, output.getEntry().size());
+		assertNotNull(output.getLink("next"));
+
+		// Page 2
+		output = ourClient
+			.loadPage()
+			.next(output)
+			.execute();
+
+		ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
+		ourLog.info("Ids: {}", ids);
+		assertEquals(4, output.getEntry().size());
+		assertNull(output.getLink("next"));
+
+	}
+
+
 	@Test
 	public void testDeleteConditional() {
 
@@ -1658,27 +1697,25 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			.returnResourceType(Bundle.class)
 			.execute();
 
-		TreeSet<String> ids = new TreeSet<>();
+		ArrayList<String> ids = new ArrayList<>();
 		for (int i = 0; i < responseBundle.getEntry().size(); i++) {
-			for (BundleEntryComponent nextEntry : responseBundle.getEntry()) {
-				ids.add(nextEntry.getResource().getIdElement().getIdPart());
-			}
+			BundleEntryComponent nextEntry = responseBundle.getEntry().get(i);
+			ids.add(nextEntry.getResource().getIdElement().getIdPart());
 		}
 
 		BundleLinkComponent nextLink = responseBundle.getLink("next");
-		ourLog.info("Have {} IDs with next link: ", ids.size(), nextLink);
+		ourLog.info("Have {} IDs with next link[{}] : {}", ids.size(), nextLink, ids);
 
 		while (nextLink != null) {
 			String nextUrl = nextLink.getUrl();
 			responseBundle = ourClient.fetchResourceFromUrl(Bundle.class, nextUrl);
 			for (int i = 0; i < responseBundle.getEntry().size(); i++) {
-				for (BundleEntryComponent nextEntry : responseBundle.getEntry()) {
-					ids.add(nextEntry.getResource().getIdElement().getIdPart());
-				}
+				BundleEntryComponent nextEntry = responseBundle.getEntry().get(i);
+				ids.add(nextEntry.getResource().getIdElement().getIdPart());
 			}
 
 			nextLink = responseBundle.getLink("next");
-			ourLog.info("Have {} IDs with next link: ", ids.size(), nextLink);
+			ourLog.info("Have {} IDs with next link[{}] : {}", ids.size(), nextLink, ids);
 		}
 
 		assertThat(ids, hasItem(id.getIdPart()));
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
index fd793f2dcf7..bdfa14b4ee2 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
@@ -30,8 +30,11 @@ import org.mockito.Mockito;
 import org.mockito.invocation.InvocationOnMock;
 import org.mockito.junit.MockitoJUnitRunner;
 import org.mockito.stubbing.Answer;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
+import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.transaction.PlatformTransactionManager;
 
@@ -53,7 +56,7 @@ public class SearchCoordinatorSvcImplTest {
 	@Captor
 	ArgumentCaptor<Iterable<SearchResult>> mySearchResultIterCaptor;
 	@Mock
-	private IDao myCallingDao;
+	private IFhirResourceDao<?> myCallingDao;
 	@Mock
 	private EntityManager myEntityManager;
 	private int myExpectedNumberOfSearchBuildersCreated = 2;
@@ -70,6 +73,9 @@ public class SearchCoordinatorSvcImplTest {
 	@Mock
 	private PlatformTransactionManager myTxManager;
 	private DaoConfig myDaoConfig;
+	private Search myCurrentSearch;
+	@Mock
+	private DaoRegistry myDaoRegistry;
 
 	@After
 	public void after() {
@@ -78,6 +84,7 @@ public class SearchCoordinatorSvcImplTest {
 
 	@Before
 	public void before() {
+		myCurrentSearch = null;
 
 		mySvc = new SearchCoordinatorSvcImpl();
 		mySvc.setEntityManagerForUnitTest(myEntityManager);
@@ -86,6 +93,7 @@ public class SearchCoordinatorSvcImplTest {
 		mySvc.setSearchDaoForUnitTest(mySearchDao);
 		mySvc.setSearchDaoIncludeForUnitTest(mySearchIncludeDao);
 		mySvc.setSearchDaoResultForUnitTest(mySearchResultDao);
+		mySvc.setDaoRegistryForUnitTest(myDaoRegistry);
 
 		myDaoConfig = new DaoConfig();
 		mySvc.setDaoConfigForUnitTest(myDaoConfig);
@@ -151,24 +159,43 @@ public class SearchCoordinatorSvcImplTest {
 		}
 
 	}
-
+private static final Logger ourLog = LoggerFactory.getLogger(SearchCoordinatorSvcImplTest.class);
 	@Test
 	public void testAsyncSearchLargeResultSetBigCountSameCoordinator() {
 		SearchParameterMap params = new SearchParameterMap();
 		params.add("name", new StringParam("ANAME"));
 
 		List<Long> pids = createPidSequence(10, 800);
-		IResultIterator iter = new SlowIterator(pids.iterator(), 1);
-		when(mySearchBuider.createQuery(Mockito.same(params), any(String.class))).thenReturn(iter);
-
+		SlowIterator iter = new SlowIterator(pids.iterator(), 1);
+		when(mySearchBuider.createQuery(any(), any(String.class))).thenReturn(iter);
 		doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(any(List.class), any(List.class), any(Set.class), anyBoolean(), any(EntityManager.class), any(FhirContext.class), same(myCallingDao));
 
+		when(mySearchResultDao.findWithSearchUuid(any(), any())).thenAnswer(t -> {
+			List<Long> returnedValues = iter.getReturnedValues();
+			Pageable page = (Pageable) t.getArguments()[1];
+			int offset = (int) page.getOffset();
+			int end = (int)(page.getOffset() + page.getPageSize());
+			end = Math.min(end, returnedValues.size());
+			offset = Math.min(offset, returnedValues.size());
+			ourLog.info("findWithSearchUuid {} - {} out of {} values", offset, end, returnedValues.size());
+			return new PageImpl<>(returnedValues.subList(offset, end));
+		});
+
 		IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective());
 		assertNotNull(result.getUuid());
 		assertEquals(null, result.size());
 
 		List<IBaseResource> resources;
 
+		when(mySearchDao.save(any())).thenAnswer(t -> {
+			Search search = (Search) t.getArguments()[0];
+			myCurrentSearch = search;
+			return search;
+		});
+		when(mySearchDao.findByUuid(any())).thenAnswer(t -> myCurrentSearch);
+		IFhirResourceDao dao = myCallingDao;
+		when(myDaoRegistry.getResourceDao(any())).thenReturn(dao);
+
 		resources = result.getResources(0, 100000);
 		assertEquals(790, resources.size());
 		assertEquals("10", resources.get(0).getIdElement().getValueAsString());
@@ -178,7 +205,7 @@ public class SearchCoordinatorSvcImplTest {
 		verify(mySearchDao, atLeastOnce()).save(searchCaptor.capture());
 
 		verify(mySearchResultDao, atLeastOnce()).saveAll(mySearchResultIterCaptor.capture());
-		List<SearchResult> allResults = new ArrayList<SearchResult>();
+		List<SearchResult> allResults = new ArrayList<>();
 		for (Iterable<SearchResult> next : mySearchResultIterCaptor.getAllValues()) {
 			allResults.addAll(Lists.newArrayList(next));
 		}
@@ -186,6 +213,8 @@ public class SearchCoordinatorSvcImplTest {
 		assertEquals(790, allResults.size());
 		assertEquals(10, allResults.get(0).getResourcePid().longValue());
 		assertEquals(799, allResults.get(789).getResourcePid().longValue());
+
+		myExpectedNumberOfSearchBuildersCreated = 3;
 	}
 
 	@Test
@@ -224,7 +253,7 @@ public class SearchCoordinatorSvcImplTest {
 		List<Long> pids = createPidSequence(10, 800);
 		IResultIterator iter = new SlowIterator(pids.iterator(), 2);
 		when(mySearchBuider.createQuery(Mockito.same(params), any(String.class))).thenReturn(iter);
-
+		when(mySearchDao.save(any())).thenAnswer(t -> t.getArguments()[0]);
 		doAnswer(loadPids()).when(mySearchBuider).loadResourcesByPid(any(List.class), any(List.class), any(Set.class), anyBoolean(), any(EntityManager.class), any(FhirContext.class), same(myCallingDao));
 
 		IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective());
@@ -257,12 +286,6 @@ public class SearchCoordinatorSvcImplTest {
 		assertEquals("20", resources.get(0).getIdElement().getValueAsString());
 		assertEquals("29", resources.get(9).getIdElement().getValueAsString());
 
-		provider = new PersistedJpaBundleProvider(result.getUuid(), myCallingDao);
-		resources = provider.getResources(20, 99999);
-		assertEquals(770, resources.size());
-		assertEquals("30", resources.get(0).getIdElement().getValueAsString());
-		assertEquals("799", resources.get(769).getIdElement().getValueAsString());
-
 		myExpectedNumberOfSearchBuildersCreated = 4;
 	}
 
@@ -452,11 +475,19 @@ public class SearchCoordinatorSvcImplTest {
 		}
 	}
 
+	/**
+	 * THIS CLASS IS FOR UNIT TESTS ONLY - It is delioberately inefficient
+	 * and keeps things in memory.
+	 * <p>
+	 * Don't use it in real code!
+	 */
 	public static class SlowIterator extends BaseIterator<Long> implements IResultIterator {
 
+		private static final Logger ourLog = LoggerFactory.getLogger(SlowIterator.class);
 		private final IResultIterator myResultIteratorWrap;
 		private int myDelay;
 		private Iterator<Long> myWrap;
+		private List<Long> myReturnedValues = new ArrayList<>();
 
 		public SlowIterator(Iterator<Long> theWrap, int theDelay) {
 			myWrap = theWrap;
@@ -470,9 +501,17 @@ public class SearchCoordinatorSvcImplTest {
 			myDelay = theDelay;
 		}
 
+		public List<Long> getReturnedValues() {
+			return myReturnedValues;
+		}
+
 		@Override
 		public boolean hasNext() {
-			return myWrap.hasNext();
+			boolean retVal = myWrap.hasNext();
+			if (!retVal) {
+				ourLog.info("No more results remaining");
+			}
+			return retVal;
 		}
 
 		@Override
@@ -482,7 +521,9 @@ public class SearchCoordinatorSvcImplTest {
 			} catch (InterruptedException e) {
 				// ignore
 			}
-			return myWrap.next();
+			Long retVal = myWrap.next();
+			myReturnedValues.add(retVal);
+			return retVal;
 		}
 
 		@Override
diff --git a/hapi-fhir-jpaserver-migrate/pom.xml b/hapi-fhir-jpaserver-migrate/pom.xml
index a804fc80a9d..2618d55c8c7 100644
--- a/hapi-fhir-jpaserver-migrate/pom.xml
+++ b/hapi-fhir-jpaserver-migrate/pom.xml
@@ -31,6 +31,10 @@
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-jdbc</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-dbcp2</artifactId>
+		</dependency>
 
 		<!-- This dependency includes the core HAPI-FHIR classes -->
 		<dependency>
@@ -45,11 +49,6 @@
 			<artifactId>derby</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-dbcp2</artifactId>
-			<scope>test</scope>
-		</dependency>
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java
index 8e5cba77e1d..c3d8a8725ba 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java
+++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java
@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.migrate;
 
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -76,20 +77,13 @@ public enum DriverTypeEnum {
 			throw new InternalErrorException("Unable to find driver class: " + myDriverClassName, e);
 		}
 
-		SingleConnectionDataSource dataSource = new SingleConnectionDataSource(){
-			@Override
-			protected Connection getConnectionFromDriver(Properties props) throws SQLException {
-				Connection connect = driver.connect(theUrl, props);
-				assert connect != null;
-				return connect;
-			}
-		};
-		dataSource.setAutoCommit(false);
+		BasicDataSource dataSource = new BasicDataSource();
+//		dataSource.setAutoCommit(false);
 		dataSource.setDriverClassName(myDriverClassName);
 		dataSource.setUrl(theUrl);
 		dataSource.setUsername(theUsername);
 		dataSource.setPassword(thePassword);
-		dataSource.setSuppressClose(true);
+//		dataSource.setSuppressClose(true);
 
 		DataSourceTransactionManager transactionManager = new DataSourceTransactionManager();
 		transactionManager.setDataSource(dataSource);
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTask.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTask.java
index 620792a4754..0300e92fa32 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTask.java
+++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTask.java
@@ -23,15 +23,21 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
 import ca.uhn.fhir.util.StopWatch;
 import com.google.common.collect.ForwardingMap;
 import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.concurrent.BasicThreadFactory;
 import org.checkerframework.checker.nullness.compatqual.NullableDecl;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.ColumnMapRowMapper;
 import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.RowCallbackHandler;
 
+import java.sql.ResultSet;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.concurrent.*;
 import java.util.function.Function;
 
 public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask> {
@@ -39,75 +45,147 @@ public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask
 	private static final Logger ourLog = LoggerFactory.getLogger(CalculateHashesTask.class);
 	private int myBatchSize = 10000;
 	private Map<String, Function<MandatoryKeyMap<String, Object>, Long>> myCalculators = new HashMap<>();
+	private ThreadPoolExecutor myExecutor;
 
 	public void setBatchSize(int theBatchSize) {
 		myBatchSize = theBatchSize;
 	}
 
+	/**
+	 * Constructor
+	 */
+	public CalculateHashesTask() {
+		super();
+	}
 
 	@Override
-	public void execute() {
+	public synchronized void execute() throws SQLException {
 		if (isDryRun()) {
 			return;
 		}
 
-		List<Map<String, Object>> rows;
-		do {
-			rows = getTxTemplate().execute(t -> {
-				JdbcTemplate jdbcTemplate = newJdbcTemnplate();
-				jdbcTemplate.setMaxRows(myBatchSize);
-				String sql = "SELECT * FROM " + getTableName() + " WHERE " + getColumnName() + " IS NULL";
-				ourLog.info("Finding up to {} rows in {} that requires hashes", myBatchSize, getTableName());
-				return jdbcTemplate.queryForList(sql);
-			});
+		initializeExecutor();
+		try {
 
-			updateRows(rows);
-		} while (rows.size() > 0);
-	}
+			while(true) {
+				MyRowCallbackHandler rch = new MyRowCallbackHandler();
+				getTxTemplate().execute(t -> {
+					JdbcTemplate jdbcTemplate = newJdbcTemnplate();
+					jdbcTemplate.setMaxRows(100000);
+					String sql = "SELECT * FROM " + getTableName() + " WHERE " + getColumnName() + " IS NULL";
+					ourLog.info("Finding up to {} rows in {} that requires hashes", myBatchSize, getTableName());
 
-	private void updateRows(List<Map<String, Object>> theRows) {
-		StopWatch sw = new StopWatch();
-		getTxTemplate().execute(t -> {
+					jdbcTemplate.query(sql, rch);
+					rch.done();
 
-			// Loop through rows
-			assert theRows != null;
-			for (Map<String, Object> nextRow : theRows) {
+					return null;
+				});
 
-				Map<String, Long> newValues = new HashMap<>();
-				MandatoryKeyMap<String, Object> nextRowMandatoryKeyMap = new MandatoryKeyMap<>(nextRow);
-
-				// Apply calculators
-				for (Map.Entry<String, Function<MandatoryKeyMap<String, Object>, Long>> nextCalculatorEntry : myCalculators.entrySet()) {
-					String nextColumn = nextCalculatorEntry.getKey();
-					Function<MandatoryKeyMap<String, Object>, Long> nextCalculator = nextCalculatorEntry.getValue();
-					Long value = nextCalculator.apply(nextRowMandatoryKeyMap);
-					newValues.put(nextColumn, value);
+				rch.submitNext();
+				List<Future<?>> futures = rch.getFutures();
+				if (futures.isEmpty()) {
+					break;
 				}
 
-				// Generate update SQL
-				StringBuilder sqlBuilder = new StringBuilder();
-				List<Long> arguments = new ArrayList<>();
-				sqlBuilder.append("UPDATE ");
-				sqlBuilder.append(getTableName());
-				sqlBuilder.append(" SET ");
-				for (Map.Entry<String, Long> nextNewValueEntry : newValues.entrySet()) {
-					if (arguments.size() > 0) {
-						sqlBuilder.append(", ");
+				ourLog.info("Waiting for {} tasks to complete", futures.size());
+				for (Future<?> next : futures) {
+					try {
+						next.get();
+					} catch (Exception e) {
+						throw new SQLException(e);
 					}
-					sqlBuilder.append(nextNewValueEntry.getKey()).append(" = ?");
-					arguments.add(nextNewValueEntry.getValue());
 				}
-				sqlBuilder.append(" WHERE SP_ID = ?");
-				arguments.add((Long) nextRow.get("SP_ID"));
-
-				// Apply update SQL
-				newJdbcTemnplate().update(sqlBuilder.toString(), arguments.toArray());
 
 			}
 
-			return theRows.size();
-		});
-		ourLog.info("Updated {} rows on {} in {}", theRows.size(), getTableName(), sw.toString());
+		} finally {
+			destroyExecutor();
+		}
+	}
+
+	private void destroyExecutor() {
+		myExecutor.shutdownNow();
+	}
+
+	private void initializeExecutor() {
+		int maximumPoolSize = Runtime.getRuntime().availableProcessors();
+
+		LinkedBlockingQueue<Runnable> executorQueue = new LinkedBlockingQueue<>(maximumPoolSize);
+		BasicThreadFactory threadFactory = new BasicThreadFactory.Builder()
+			.namingPattern("worker-" + "-%d")
+			.daemon(false)
+			.priority(Thread.NORM_PRIORITY)
+			.build();
+		RejectedExecutionHandler rejectedExecutionHandler = new RejectedExecutionHandler() {
+			@Override
+			public void rejectedExecution(Runnable theRunnable, ThreadPoolExecutor theExecutor) {
+				ourLog.info("Note: Executor queue is full ({} elements), waiting for a slot to become available!", executorQueue.size());
+				StopWatch sw = new StopWatch();
+				try {
+					executorQueue.put(theRunnable);
+				} catch (InterruptedException theE) {
+					throw new RejectedExecutionException("Task " + theRunnable.toString() +
+						" rejected from " + theE.toString());
+				}
+				ourLog.info("Slot become available after {}ms", sw.getMillis());
+			}
+		};
+		myExecutor = new ThreadPoolExecutor(
+			1,
+			maximumPoolSize,
+			0L,
+			TimeUnit.MILLISECONDS,
+			executorQueue,
+			threadFactory,
+			rejectedExecutionHandler);
+	}
+
+	private Future<?> updateRows(List<Map<String, Object>> theRows) {
+		Runnable task = () -> {
+			StopWatch sw = new StopWatch();
+			getTxTemplate().execute(t -> {
+
+				// Loop through rows
+				assert theRows != null;
+				for (Map<String, Object> nextRow : theRows) {
+
+					Map<String, Long> newValues = new HashMap<>();
+					MandatoryKeyMap<String, Object> nextRowMandatoryKeyMap = new MandatoryKeyMap<>(nextRow);
+
+					// Apply calculators
+					for (Map.Entry<String, Function<MandatoryKeyMap<String, Object>, Long>> nextCalculatorEntry : myCalculators.entrySet()) {
+						String nextColumn = nextCalculatorEntry.getKey();
+						Function<MandatoryKeyMap<String, Object>, Long> nextCalculator = nextCalculatorEntry.getValue();
+						Long value = nextCalculator.apply(nextRowMandatoryKeyMap);
+						newValues.put(nextColumn, value);
+					}
+
+					// Generate update SQL
+					StringBuilder sqlBuilder = new StringBuilder();
+					List<Long> arguments = new ArrayList<>();
+					sqlBuilder.append("UPDATE ");
+					sqlBuilder.append(getTableName());
+					sqlBuilder.append(" SET ");
+					for (Map.Entry<String, Long> nextNewValueEntry : newValues.entrySet()) {
+						if (arguments.size() > 0) {
+							sqlBuilder.append(", ");
+						}
+						sqlBuilder.append(nextNewValueEntry.getKey()).append(" = ?");
+						arguments.add(nextNewValueEntry.getValue());
+					}
+					sqlBuilder.append(" WHERE SP_ID = ?");
+					arguments.add((Long) nextRow.get("SP_ID"));
+
+					// Apply update SQL
+					newJdbcTemnplate().update(sqlBuilder.toString(), arguments.toArray());
+
+				}
+
+				return theRows.size();
+			});
+			ourLog.info("Updated {} rows on {} in {}", theRows.size(), getTableName(), sw.toString());
+		};
+		return myExecutor.submit(task);
 	}
 
 	public CalculateHashesTask addCalculator(String theColumnName, Function<MandatoryKeyMap<String, Object>, Long> theConsumer) {
@@ -116,6 +194,39 @@ public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask
 		return this;
 	}
 
+	private class MyRowCallbackHandler implements RowCallbackHandler {
+
+		private List<Map<String, Object>> myRows = new ArrayList<>();
+		private List<Future<?>> myFutures = new ArrayList<>();
+
+		@Override
+		public void processRow(ResultSet rs) throws SQLException {
+			Map<String, Object> row = new ColumnMapRowMapper().mapRow(rs, 0);
+			myRows.add(row);
+
+			if (myRows.size() >= myBatchSize) {
+				submitNext();
+			}
+		}
+
+		private void submitNext() {
+			if (myRows.size() > 0) {
+				myFutures.add(updateRows(myRows));
+				myRows = new ArrayList<>();
+			}
+		}
+
+		public List<Future<?>> getFutures() {
+			return myFutures;
+		}
+
+		public void done() {
+			if (myRows.size() > 0) {
+				submitNext();
+			}
+		}
+	}
+
 
 	public static class MandatoryKeyMap<K, V> extends ForwardingMap<K, V> {
 
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
index acaf3be1c6a..c02246a3a14 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
+++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
@@ -277,6 +277,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		Builder.BuilderWithTableName spp = version.onTable("HFJ_RES_PARAM_PRESENT");
 		version.startSectionWithMessage("Starting work on table: " + spp.getTableName());
 		spp.dropIndex("IDX_RESPARMPRESENT_SPID_RESID");
+		spp.dropColumn("SP_ID");
 		spp
 			.addColumn("HASH_PRESENCE")
 			.nullable()
diff --git a/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CreateHashesTest.java b/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTest.java
similarity index 56%
rename from hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CreateHashesTest.java
rename to hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTest.java
index a5140a72b83..6e15f8734be 100644
--- a/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CreateHashesTest.java
+++ b/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTest.java
@@ -9,7 +9,7 @@ import java.util.Map;
 
 import static org.junit.Assert.assertEquals;
 
-public class CreateHashesTest extends BaseTest {
+public class CalculateHashesTest extends BaseTest {
 
 	@Test
 	public void testCreateHashes() {
@@ -50,4 +50,36 @@ public class CreateHashesTest extends BaseTest {
 		});
 	}
 
+	@Test
+	public void testCreateHashesLargeNumber() {
+		executeSql("create table HFJ_SPIDX_TOKEN (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, HASH_IDENTITY bigint, HASH_SYS bigint, HASH_SYS_AND_VALUE bigint, HASH_VALUE bigint, SP_SYSTEM varchar(200), SP_VALUE varchar(200), primary key (SP_ID))");
+
+		for (int i = 0; i < 777; i++) {
+			executeSql("insert into HFJ_SPIDX_TOKEN (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_SYSTEM, SP_VALUE, SP_ID) values (false, 'identifier', 999, 'Patient', '2018-09-03 07:44:49.196', 'urn:oid:1.2.410.100110.10.41308301', '8888888" + i + "', " + i + ")");
+		}
+
+		Long count = getConnectionProperties().getTxTemplate().execute(t -> {
+			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+			return jdbcTemplate.queryForObject("SELECT count(*) FROM HFJ_SPIDX_TOKEN WHERE HASH_VALUE IS NULL", Long.class);
+		});
+		assertEquals(777L, count.longValue());
+
+		CalculateHashesTask task = new CalculateHashesTask();
+		task.setTableName("HFJ_SPIDX_TOKEN");
+		task.setColumnName("HASH_IDENTITY");
+		task.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")));
+		task.addCalculator("HASH_SYS", t -> ResourceIndexedSearchParamToken.calculateHashSystem(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM")));
+		task.addCalculator("HASH_SYS_AND_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashSystemAndValue(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM"), t.getString("SP_VALUE")));
+		task.addCalculator("HASH_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashValue(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE")));
+		task.setBatchSize(3);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		count = getConnectionProperties().getTxTemplate().execute(t -> {
+			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+			return jdbcTemplate.queryForObject("SELECT count(*) FROM HFJ_SPIDX_TOKEN WHERE HASH_VALUE IS NULL", Long.class);
+		});
+		assertEquals(0L, count.longValue());
+	}
 }
diff --git a/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java b/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java
index 3de8c16a612..bd5c7f3a90c 100644
--- a/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java
+++ b/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java
@@ -215,16 +215,24 @@ public abstract class BaseResourceReturningMethodBinding extends BaseMethodBindi
 				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, theResult.getPreviousPageId(), theRequest.getParameters(), prettyPrint, theBundleType);
 			}
 		} else if (searchId != null) {
-			int offset = theOffset + resourceList.size();
-
 			// We're doing offset pages
-			if (numTotalResults == null || offset < numTotalResults) {
-				linkNext = (RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, offset, numToReturn, theRequest.getParameters(), prettyPrint, theBundleType));
+			if (numTotalResults == null || theOffset + numToReturn < numTotalResults) {
+				linkNext = (RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, theOffset + numToReturn, numToReturn, theRequest.getParameters(), prettyPrint, theBundleType));
 			}
 			if (theOffset > 0) {
 				int start = Math.max(0, theOffset - theLimit);
 				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, start, theLimit, theRequest.getParameters(), prettyPrint, theBundleType);
 			}
+//			int offset = theOffset + resourceList.size();
+//
+//			// We're doing offset pages
+//			if (numTotalResults == null || offset < numTotalResults) {
+//				linkNext = (RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, offset, numToReturn, theRequest.getParameters(), prettyPrint, theBundleType));
+//			}
+//			if (theOffset > 0) {
+//				int start = Math.max(0, theOffset - theLimit);
+//				linkPrev = RestfulServerUtils.createPagingLink(theIncludes, serverBase, searchId, start, theLimit, theRequest.getParameters(), prettyPrint, theBundleType);
+//			}
 		}
 
 		bundleFactory.addRootPropertiesToBundle(theResult.getUuid(), serverBase, theLinkSelf, linkPrev, linkNext, theResult.size(), theBundleType, theResult.getPublished());
diff --git a/pom.xml b/pom.xml
index 50cc673a3af..d5ff60b05fb 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1727,6 +1727,12 @@
 								<copy todir="target/site/apidocs-jpaserver">
 									<fileset dir="hapi-fhir-jpaserver-base/target/site/apidocs"/>
 								</copy>
+								<copy todir="target/site/apidocs-client">
+									<fileset dir="hapi-fhir-client/target/site/apidocs"/>
+								</copy>
+								<copy todir="target/site/apidocs-server">
+									<fileset dir="hapi-fhir-server/target/site/apidocs"/>
+								</copy>
 								<copy todir="target/site/xref-jpaserver">
 									<fileset dir="hapi-fhir-jpaserver-base/target/site/xref"/>
 								</copy>
@@ -2131,6 +2137,8 @@
 				<module>hapi-fhir-structures-dstu2</module>
 				<module>hapi-fhir-structures-dstu3</module>
 				<module>hapi-fhir-structures-r4</module>
+				<module>hapi-fhir-client</module>
+				<module>hapi-fhir-server</module>
 				<module>hapi-fhir-jpaserver-base</module>
 				<module>hapi-fhir-jaxrsserver-base</module>
 				<!-- <module>hapi-fhir-cobertura</module> -->
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index c1562231fa3..3f2c12cf3d6 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -142,6 +142,10 @@
 				to use a parameter annotated with @ResourceParam to receive the Parameters
 				(or other) resource supplied by the client as the request body.
 			</action>
+			<action type="add">
+				The JPA server version migrator tool now runs in a multithreaded way, allowing it to
+				upgrade th database faster when migration tasks require data updates.
+			</action>
 		</release>
 
 		<release version="3.5.0" date="2018-09-17">
diff --git a/src/site/site.xml b/src/site/site.xml
index 2c5ca40def0..d0e75165cc7 100644
--- a/src/site/site.xml
+++ b/src/site/site.xml
@@ -115,6 +115,8 @@
 				<item name="Model API (DSTU2)" href="./apidocs-dstu2/index.html" />
 				<item name="Model API (DSTU3)" href="./apidocs-dstu3/index.html" />
 				<item name="Model API (R4)" href="./apidocs-r4/index.html" />
+				<item name="Client API" href="./apidocs-client/index.html" />
+				<item name="Server API" href="./apidocs-server/index.html" />
 				<item name="JPA Server API" href="./apidocs-jpaserver/index.html" />
 			</item>
 			<item name="Command Line Tool (hapi-fhir-cli)" href="./doc_cli.html" />
diff --git a/src/site/xdoc/docindex.xml b/src/site/xdoc/docindex.xml
index 49cefb6481c..226d7e8b457 100644
--- a/src/site/xdoc/docindex.xml
+++ b/src/site/xdoc/docindex.xml
@@ -1,86 +1,88 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<document xmlns="http://maven.apache.org/XDOC/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/XDOC/2.0 http://maven.apache.org/xsd/xdoc-2.0.xsd">
-
-	<properties>
-		<title>Documentation</title>
-		<author email="jamesagnew@users.sourceforge.net">James Agnew</author>
-	</properties>
-
-	<body>
-
-		<section name="Documentation">
-
-			<p>
-				Welcome to HAPI FHIR! We hope that the documentation here will be
-				helpful to you. 
-			</p>
-
-			<ul>
-				<li><a href="./doc_intro.html">Introduction</a></li>
-				<li><a href="./doc_dstu2.html">Note on DSTU2 Support / FHIR Versions</a></li>
-			</ul>
-			
-			<h4>The Data Model</h4>
-			<ul>
-				<li><a href="./doc_fhirobjects.html">Working with Resources</a></li>
-				<li><a href="./doc_extensions.html">Profiles &amp; Extensions</a></li>
-				<li><a href="./doc_resource_references.html">Resource References</a></li>
-				<li><a href="./doc_tags.html">Tags</a></li>
-				<li><a href="./doc_validation.html">Validation</a></li>
-				<li><a href="./doc_custom_structures.html">Custom Structures</a></li>
-				<li><a href="./doc_converter.html">Version Converter</a></li>
-			</ul>
-			
-			<h4>RESTful Client</h4>
-			<ul>
-				<li><a href="./doc_rest_client.html">Fluent/Generic Client</a></li>
-				<li><a href="./doc_rest_client_annotation.html">Annotation Client</a></li>
-				<li><a href="./doc_rest_client_interceptor.html">Interceptors (client)</a></li>
-				<li><a href="./doc_rest_client_http_config.html">Client Configuration</a></li>
-				<li><a href="./doc_rest_client_examples.html">Client Examples</a></li>
-				<li><a href="./doc_rest_client_alternate_provider.html">JAX-RS Client &amp; Alternate HTTP Providers</a></li>
-			</ul>
-			
-			<h4>RESTful Server</h4>
-			<ul>
-				<li><a href="./doc_rest_server.html">Using RESTful Server</a></li>
-				<li><a href="./doc_rest_operations.html">RESTful Operations</a></li>
-				<li><a href="./doc_narrative.html">Narrative Generator</a></li>
-				<li><a href="./doc_rest_server_interceptor.html">Interceptors (server)</a></li>
-				<li><a href="./doc_rest_server_security.html">Security</a></li>
-				<li><a href="./doc_cors.html">CORS Support</a></li>
-				<li><a href="./doc_server_tester.html">Web Testing UI</a></li>
-				<li><a href="./doc_rest_server_jaxrs.html">JAX-RS Support</a></li>
-			</ul>
-			
-			<h4>Other Features</h4>
-
-			<ul>
-				<li><a href="./doc_logging.html">Logging</a></li>
-				<li><a href="./doc_rest_etag.html">ETags</a></li>
-				<li><a href="./doc_jpa.html">JPA/Database Server</a></li>
-				<li><a href="./doc_tinder.html">Maven Plugin (hapi-tinder-plugin)</a></li>
-				<li><a href="./doc_cli.html">Command Line Tool (hapi-fhir-cli)</a></li>
-				
-			</ul>
-			
- 			<h4>JavaDocs</h4>
- 			<ul>
-				<li><a href="./apidocs/index.html">Core API</a></li>
-				<li><a href="./apidocs-dstu/index.html">Model API (DSTU1)</a></li>
-				<li><a href="./apidocs-dstu2/index.html" >Model API (DSTU2)</a></li>
-				<li><a href="./apidocs-dstu3/index.html" >Model API (STU3)</a></li>
-				<li><a href="./apidocs-jpaserver/index.html">JPA Server API</a></li>
-			</ul>
-			
-			<h4>Source Cross Reference</h4>
-			<ul>
-				<li><a href="./xref-base/index.html">Core</a></li>
-				<li><a href="./xref-jpaserver/index.html">JPA Server</a></li>
-			</ul>
- 			
-		</section>
-		
-	</body>
-
-</document>
+<?xml version="1.0" encoding="UTF-8"?>
+<document xmlns="http://maven.apache.org/XDOC/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/XDOC/2.0 http://maven.apache.org/xsd/xdoc-2.0.xsd">
+
+	<properties>
+		<title>Documentation</title>
+		<author email="jamesagnew@users.sourceforge.net">James Agnew</author>
+	</properties>
+
+	<body>
+
+		<section name="Documentation">
+
+			<p>
+				Welcome to HAPI FHIR! We hope that the documentation here will be
+				helpful to you. 
+			</p>
+
+			<ul>
+				<li><a href="./doc_intro.html">Introduction</a></li>
+				<li><a href="./doc_dstu2.html">Note on DSTU2 Support / FHIR Versions</a></li>
+			</ul>
+			
+			<h4>The Data Model</h4>
+			<ul>
+				<li><a href="./doc_fhirobjects.html">Working with Resources</a></li>
+				<li><a href="./doc_extensions.html">Profiles &amp; Extensions</a></li>
+				<li><a href="./doc_resource_references.html">Resource References</a></li>
+				<li><a href="./doc_tags.html">Tags</a></li>
+				<li><a href="./doc_validation.html">Validation</a></li>
+				<li><a href="./doc_custom_structures.html">Custom Structures</a></li>
+				<li><a href="./doc_converter.html">Version Converter</a></li>
+			</ul>
+			
+			<h4>RESTful Client</h4>
+			<ul>
+				<li><a href="./doc_rest_client.html">Fluent/Generic Client</a></li>
+				<li><a href="./doc_rest_client_annotation.html">Annotation Client</a></li>
+				<li><a href="./doc_rest_client_interceptor.html">Interceptors (client)</a></li>
+				<li><a href="./doc_rest_client_http_config.html">Client Configuration</a></li>
+				<li><a href="./doc_rest_client_examples.html">Client Examples</a></li>
+				<li><a href="./doc_rest_client_alternate_provider.html">JAX-RS Client &amp; Alternate HTTP Providers</a></li>
+			</ul>
+			
+			<h4>RESTful Server</h4>
+			<ul>
+				<li><a href="./doc_rest_server.html">Using RESTful Server</a></li>
+				<li><a href="./doc_rest_operations.html">RESTful Operations</a></li>
+				<li><a href="./doc_narrative.html">Narrative Generator</a></li>
+				<li><a href="./doc_rest_server_interceptor.html">Interceptors (server)</a></li>
+				<li><a href="./doc_rest_server_security.html">Security</a></li>
+				<li><a href="./doc_cors.html">CORS Support</a></li>
+				<li><a href="./doc_server_tester.html">Web Testing UI</a></li>
+				<li><a href="./doc_rest_server_jaxrs.html">JAX-RS Support</a></li>
+			</ul>
+			
+			<h4>Other Features</h4>
+
+			<ul>
+				<li><a href="./doc_logging.html">Logging</a></li>
+				<li><a href="./doc_rest_etag.html">ETags</a></li>
+				<li><a href="./doc_jpa.html">JPA/Database Server</a></li>
+				<li><a href="./doc_tinder.html">Maven Plugin (hapi-tinder-plugin)</a></li>
+				<li><a href="./doc_cli.html">Command Line Tool (hapi-fhir-cli)</a></li>
+				
+			</ul>
+			
+ 			<h4>JavaDocs</h4>
+ 			<ul>
+				<li><a href="./apidocs/index.html">Core API</a></li>
+				<li><a href="./apidocs-dstu/index.html">Model API (DSTU1)</a></li>
+				<li><a href="./apidocs-dstu2/index.html" >Model API (DSTU2)</a></li>
+				<li><a href="./apidocs-dstu3/index.html" >Model API (STU3)</a></li>
+				<li><a href="./apidocs-client/index.html" >Client API</a></li>
+				<li><a href="./apidocs-server/index.html" >Server API</a></li>
+				<li><a href="./apidocs-jpaserver/index.html">JPA Server API</a></li>
+			</ul>
+			
+			<h4>Source Cross Reference</h4>
+			<ul>
+				<li><a href="./xref-base/index.html">Core</a></li>
+				<li><a href="./xref-jpaserver/index.html">JPA Server</a></li>
+			</ul>
+ 			
+		</section>
+		
+	</body>
+
+</document>