update works properly

questions

-problems learning how to build tree
-line endings - possibly not the issue
-index not updating
-how should push and merge work
-
-empty index
 
 when conflict in comments warn user that someone doing something bad
 edit comments

src/main/java/command/CommandUpdate.java

@@ -54,7 +54,7 @@ public class CommandUpdate implements Command {
                 }
                 if (commitMessage != null) {
                     try {
-                        repo.writeIssue(issue, commitMessage);
+                        repo.updateIssues(issue, commitMessage);
                     } catch (IOException e) {
                         e.printStackTrace();
                     }

src/main/java/git/IssueRepo.java

@@ -7,18 +7,14 @@ import org.eclipse.jgit.api.MergeCommand;
 import org.eclipse.jgit.api.MergeResult;
 import org.eclipse.jgit.api.ResetCommand;
 import org.eclipse.jgit.api.errors.GitAPIException;
-import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.lib.*;
 import org.eclipse.jgit.merge.MergeStrategy;
 import org.eclipse.jgit.merge.Merger;
 import org.eclipse.jgit.revwalk.RevCommit;
-import org.eclipse.jgit.revwalk.RevTree;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.transport.PushResult;
 import org.eclipse.jgit.transport.RefSpec;
-import org.eclipse.jgit.treewalk.AbstractTreeIterator;
-import org.eclipse.jgit.treewalk.TreeWalk;
 
 import java.awt.*;
 import java.io.File;
@@ -199,7 +195,6 @@ public class IssueRepo {
         }
     }
 
-
     public void writeIssue(Issue issue, String commitMessage) throws IOException {
         RevCommit currentCommit = getCurrentCommit();
 
@@ -220,6 +215,27 @@ public class IssueRepo {
 
     }
 
+    public void updateIssues(Issue issue, String commitMessage) throws IOException {
+        RevCommit currentCommit = getCurrentCommit();
+
+        IssueTreeBuilder issueWriter = new IssueTreeBuilder(repository);
+        issueWriter.buildIssueTree(issue);
+
+        List<Issue> sortedIssues = getIssues();
+        sortedIssues.sort(Comparator.comparing(Issue::getOriginalHash));
+
+        int i = sortedIssues.indexOf(issue);
+        sortedIssues.remove(i);
+        sortedIssues.add(i, issue);
+
+        TreeFormatter repoTreeFormatter = new TreeFormatter();
+
+        getTree(sortedIssues, repoTreeFormatter, issueWriter);
+
+        ObjectId repoTree = oi.insert(Constants.OBJ_TREE, repoTreeFormatter.toByteArray());
+
+        commit(commitMessage, repoTree, currentCommit);
+    }
 
     public void deleteIssue(String hash) throws IOException {
         RevCommit currentCommit = getCurrentCommit();