// get changes
Iterator<DiffEntry> diff = command(DiffTree.class).setOldTree(parentTreeId)
.setNewTree(commitToApply.getTreeId()).setReportTrees(true).call();
// see if there are conflicts
MergeScenarioReport report = command(ReportCommitConflictsOp.class).setCommit(
commitToApply).call();
if (report.getConflicts().isEmpty()) {
// stage changes
index().stage(getProgressListener(), diff, 0);
// write new tree
ObjectId newTreeId = command(WriteTree2.class).call();
long timestamp = platform.currentTimeMillis();
// Create new commit
CommitBuilder builder = new CommitBuilder(commitToApply);
builder.setParentIds(Arrays.asList(rebaseHead));
builder.setTreeId(newTreeId);
builder.setCommitterTimestamp(timestamp);
builder.setCommitterTimeZoneOffset(platform.timeZoneOffset(timestamp));
RevCommit newCommit = builder.build();
repository.objectDatabase().put(newCommit);
rebaseHead = newCommit.getId();
command(UpdateRef.class).setName(currentBranch).setNewValue(rebaseHead).call();
command(UpdateSymRef.class).setName(Ref.HEAD).setNewValue(currentBranch).call();
workingTree().updateWorkHead(newTreeId);
index().updateStageHead(newTreeId);
} else {
Iterator<DiffEntry> unconflicted = report.getUnconflicted().iterator();
// stage unconflicted changes
index().stage(getProgressListener(), unconflicted, 0);
workingTree().updateWorkHead(index().getTree().getId());
// mark conflicted elements
command(ConflictsWriteOp.class).setConflicts(report.getConflicts()).call();
// created exception message
StringBuilder msg = new StringBuilder();
msg.append("error: could not apply ");
msg.append(commitToApply.getId().toString().substring(0, 7));
msg.append(" " + commitToApply.getMessage() + "\n");
for (Conflict conflict : report.getConflicts()) {
msg.append("CONFLICT: conflict in " + conflict.getPath() + "\n");
}
File branchFile = new File(getRebaseFolder(), "branch");
try {