Don't use deprecated Repository#getAllRefs in FileRepository

Also expose the potentially IOException thrown by RefDatabase#getRefs.
Hence the following methods now potentially throw IOException:
- AdvertiseRefsHook#advertiseRefs
- ReceivePack#setAdvertisedRefs
- Repository#getAdditionalHaves

Bug: 534731
Change-Id: I85bc6ce5815d40be5f80042c53f4663072d96be5

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/ReceivePackAdvertiseRefsHookTest.java

@@ -142,7 +142,7 @@ ReceivePack createReceivePack(Repository db) {
 				rp.setAdvertiseRefsHook(new AdvertiseRefsHook() {
 					@Override
 					public void advertiseRefs(ReceivePack rp2)
-							throws ServiceMayNotContinueException {
+							throws IOException {
 						rp.setAdvertisedRefs(rp.getRepository().getAllRefs(),
 								null);
 						new HidePrivateHook().advertiseRefs(rp);

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java

@@ -420,9 +420,11 @@ private File descriptionFile() {
 	 * advertise that it safely has that other repository's references, without
 	 * exposing any other details about the other repository. This may help a
 	 * client trying to push changes avoid pushing more than it needs to.
+	 *
+	 * @throws IOException
 	 */
 	@Override
-	public Set<ObjectId> getAdditionalHaves() {
+	public Set<ObjectId> getAdditionalHaves() throws IOException {
 		return getAdditionalHaves(null);
 	}
 
@@ -438,8 +440,11 @@ public Set<ObjectId> getAdditionalHaves() {
 	 *            Set of AlternateHandle Ids already seen
 	 *
 	 * @return unmodifiable collection of other known objects.
+	 * @throws IOException
+	 *             if getting refs hits an IO error
 	 */
-	private Set<ObjectId> getAdditionalHaves(Set<AlternateHandle.Id> skips) {
+	private Set<ObjectId> getAdditionalHaves(Set<AlternateHandle.Id> skips)
+			throws IOException {
 		HashSet<ObjectId> r = new HashSet<>();
 		skips = objectDatabase.addMe(skips);
 		for (AlternateHandle d : objectDatabase.myAlternates()) {
@@ -447,7 +452,7 @@ private Set<ObjectId> getAdditionalHaves(Set<AlternateHandle.Id> skips) {
 				FileRepository repo;
 
 				repo = ((AlternateRepository) d).repository;
-				for (Ref ref : repo.getAllRefs().values()) {
+				for (Ref ref : repo.getRefDatabase().getRefs()) {
 					if (ref.getObjectId() != null)
 						r.add(ref.getObjectId());
 					if (ref.getPeeledObjectId() != null)

org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java

@@ -1051,13 +1051,14 @@ public String getBranch() throws IOException {
 	 * <p>
 	 * When a repository borrows objects from another repository, it can
 	 * advertise that it safely has that other repository's references, without
-	 * exposing any other details about the other repository.  This may help
+	 * exposing any other details about the other repository. This may help a
-	 * a client trying to push changes avoid pushing more than it needs to.
+	 * client trying to push changes avoid pushing more than it needs to.
 	 *
 	 * @return unmodifiable collection of other known objects.
+	 * @throws IOException
 	 */
 	@NonNull
-	public Set<ObjectId> getAdditionalHaves() {
+	public Set<ObjectId> getAdditionalHaves() throws IOException {
 		return Collections.emptySet();
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/transport/AbstractAdvertiseRefsHook.java

@@ -42,6 +42,7 @@
 
 package org.eclipse.jgit.transport;
 
+import java.io.IOException;
 import java.util.Map;
 import java.util.Set;
 
@@ -65,10 +66,12 @@ public void advertiseRefs(UploadPack uploadPack)
 				uploadPack.getRepository(), uploadPack.getRevWalk()));
 	}
 
-	/** {@inheritDoc} */
+	/**
+	 * {@inheritDoc}
+	 */
 	@Override
 	public void advertiseRefs(ReceivePack receivePack)
-			throws ServiceMayNotContinueException {
+			throws IOException {
 		Map<String, Ref> refs = getAdvertisedRefs(receivePack.getRepository(),
 				receivePack.getRevWalk());
 		Set<ObjectId> haves = getAdvertisedHaves(receivePack.getRepository(),

org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHook.java

@@ -42,6 +42,8 @@
 
 package org.eclipse.jgit.transport;
 
+import java.io.IOException;
+
 /**
  * Hook to allow callers to take over advertising refs to the client.
  *
@@ -89,8 +91,9 @@ void advertiseRefs(UploadPack uploadPack)
 	 *            if necessary.
 	 * @throws org.eclipse.jgit.transport.ServiceMayNotContinueException
 	 *             abort; the message will be sent to the user.
+	 * @throws IOException
 	 * @since 5.6
 	 */
 	void advertiseRefs(ReceivePack receivePack)
-			throws ServiceMayNotContinueException;
+			throws ServiceMayNotContinueException, IOException;
 }

org.eclipse.jgit/src/org/eclipse/jgit/transport/AdvertiseRefsHookChain.java

@@ -10,6 +10,7 @@
 
 package org.eclipse.jgit.transport;
 
+import java.io.IOException;
 import java.util.List;
 
 /**
@@ -49,10 +50,12 @@ public static AdvertiseRefsHook newChain(List<? extends AdvertiseRefsHook> hooks
 		}
 	}
 
-	/** {@inheritDoc} */
+	/**
+	 * {@inheritDoc}
+	 */
 	@Override
 	public void advertiseRefs(ReceivePack rp)
-			throws ServiceMayNotContinueException {
+			throws IOException {
 		for (int i = 0; i < count; i++)
 			hooks[i].advertiseRefs(rp);
 	}

org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java

@@ -440,9 +440,10 @@ public Map<String, Ref> getAdvertisedRefs() {
 	 *            explicit set of additional haves to claim as advertised. If
 	 *            null, assumes the default set of additional haves from the
 	 *            repository.
+	 * @throws IOException
 	 */
 	public void setAdvertisedRefs(Map<String, Ref> allRefs,
-			Set<ObjectId> additionalHaves) {
+			Set<ObjectId> additionalHaves) throws IOException {
 		refs = allRefs != null ? allRefs : getAllRefs();
 		refs = refFilter.filter(refs);
 		advertisedHaves.clear();
@@ -1187,8 +1188,9 @@ protected void init(final InputStream input, final OutputStream output,
 	 * Get advertised refs, or the default if not explicitly advertised.
 	 *
 	 * @return advertised refs, or the default if not explicitly advertised.
+	 * @throws IOException
 	 */
-	private Map<String, Ref> getAdvertisedOrDefaultRefs() {
+	private Map<String, Ref> getAdvertisedOrDefaultRefs() throws IOException {
 		if (refs == null)
 			setAdvertisedRefs(null, null);
 		return refs;