Use non-deprecated JGit methods to get references (jenkinsci#1191)

The JGit 7.0.0 upgrade reminded me that it is unwise to depend on
deprecated methods from JGit because they will eventually be removed.
Better to stop using the deprecated methods now and avoid problems in
the future.

Author: MarkEWaite

src/main/java/org/jenkinsci/plugins/gitclient/CliGitAPIImpl.java

@@ -3016,10 +3016,15 @@ public Set<Branch> getBranches() throws GitException, InterruptedException {
     @Override
     public Set<Branch> getRemoteBranches() throws GitException, InterruptedException {
         try (Repository db = getRepository()) {
-            Map<String, Ref> refs = db.getAllRefs();
+            List<Ref> refs;
+            try {
+                refs = db.getRefDatabase().getRefs();
+            } catch (IOException ioe) {
+                throw new GitException(ioe);
+            }
             Set<Branch> branches = new HashSet<>();
 
-            for (Ref candidate : refs.values()) {
+            for (Ref candidate : refs) {
                 if (candidate.getName().startsWith(Constants.R_REMOTES)) {
                     Branch buildBranch = new Branch(candidate);
                     if (!GitClient.quietRemoteBranches) {

src/main/java/org/jenkinsci/plugins/gitclient/JGitAPIImpl.java

@@ -2090,7 +2090,7 @@ public void prune(RemoteConfig repository) throws GitException {
 
             Set<String> branches = listRemoteBranches(remote);
 
-            for (Ref r : new ArrayList<>(gitRepo.getAllRefs().values())) {
+            for (Ref r : new ArrayList<>(gitRepo.getRefDatabase().getRefs())) {
                 if (r.getName().startsWith(prefix) && !branches.contains(r.getName())) {
                     // delete this ref
                     RefUpdate update = gitRepo.updateRef(r.getName());
@@ -2347,7 +2347,7 @@ public void execute() throws GitException {
                         out.add(c.copy());
 
                         if (all) {
-                            for (Ref r : repo.getAllRefs().values()) {
+                            for (Ref r : repo.getRefDatabase().getRefs()) {
                                 c = walk.parseCommit(r.getObjectId());
                                 out.add(c.copy());
                             }
@@ -2730,7 +2730,13 @@ public List<Branch> getBranchesContaining(String revspec, boolean allBranches)
     private List<Ref> getAllBranchRefs(boolean originBranches) throws GitException {
         List<Ref> branches = new ArrayList<>();
         try (Repository repo = getRepository()) {
-            for (Ref r : repo.getAllRefs().values()) {
+            List<Ref> refs;
+            try {
+                refs = repo.getRefDatabase().getRefs();
+            } catch (IOException ioe) {
+                throw new GitException(ioe);
+            }
+            for (Ref r : refs) {
                 final String branchName = r.getName();
                 if (branchName.startsWith(R_HEADS) || (originBranches && branchName.startsWith(R_REMOTES))) {
                     branches.add(r);
@@ -2799,7 +2805,7 @@ private void markAllRefs(RevWalk walk) throws GitException, IOException {
      */
     private void markRefs(RevWalk walk, Predicate<Ref> filter) throws GitException, IOException {
         try (Repository repo = getRepository()) {
-            for (Ref r : repo.getAllRefs().values()) {
+            for (Ref r : repo.getRefDatabase().getRefs()) {
                 if (filter.test(r)) {
                     RevCommit c = walk.parseCommit(r.getObjectId());
                     walk.markStart(c);
@@ -2919,7 +2925,7 @@ public String describe(String tip) throws GitException, InterruptedException {
             w.setRetainBody(false);
 
             Map<ObjectId, Ref> tags = new HashMap<>();
-            for (Ref r : repo.getTags().values()) {
+            for (Ref r : repo.getRefDatabase().getRefsByPrefix(R_TAGS)) {
                 ObjectId key = repo.getRefDatabase().peel(r).getPeeledObjectId();
                 if (key == null) {
                     key = r.getObjectId();