Don't use deprecated Repository#getAllRefs in Repository

Also expose the potentially IOException thrown by RefDatabase#getRefs.
Hence the following methods now potentially throw IOException:
- Repository#getAllRefsByPeeledObjectId

Bug: 534731
Change-Id: Id6956ff112560e6314d4335238494708346f2338

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

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index 2d1aca8..e594e52 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -1161,12 +1161,14 @@ public Ref peel(Ref ref) {
 	 * Get a map with all objects referenced by a peeled ref.
 	 *
 	 * @return a map with all objects referenced by a peeled ref.
+	 * @throws IOException
 	 */
 	@NonNull
-	public Map<AnyObjectId, Set<Ref>> getAllRefsByPeeledObjectId() {
-		Map<String, Ref> allRefs = getAllRefs();
+	public Map<AnyObjectId, Set<Ref>> getAllRefsByPeeledObjectId()
+			throws IOException {
+		List<Ref> allRefs = getRefDatabase().getRefs();
 		Map<AnyObjectId, Set<Ref>> ret = new HashMap<>(allRefs.size());
-		for (Ref ref : allRefs.values()) {
+		for (Ref ref : allRefs) {
 			ref = peel(ref);
 			AnyObjectId target = ref.getPeeledObjectId();
 			if (target == null)

org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotWalk.java

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotWalk.java
index b4ccfe0..0582338 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revplot/PlotWalk.java
@@ -121,7 +121,7 @@ public RevCommit next() throws MissingObjectException,
 		return pc;
 	}
 
-	private Ref[] getRefs(AnyObjectId commitId) {
+	private Ref[] getRefs(AnyObjectId commitId) throws IOException {
 		if (reverseRefMap == null) {
 			reverseRefMap = repository.getAllRefsByPeeledObjectId();
 			for (Map.Entry<AnyObjectId, Set<Ref>> entry : additionalRefMap