Program: 93562
Project: 93562
Buggy source:
@Override @Before public void setUp() throws Exception {
  super.setUp();
  resource1.getContents().add(createBasicModel(FILE1_SUFFIX));
  resource2.getContents().add(createBasicModel(FILE2_SUFFIX));
  makeCrossReference(resource1,resource2,CLASS1_NAME_PREFIX,CLASS1_NAME_PREFIX);
  makeCrossReference(resource2,resource1,CLASS2_NAME_PREFIX,CLASS2_NAME_PREFIX);
  save(resource1,resource2);
  commits[0]=repository.addAndCommit(project,"String_Node_Str",file1,file2);
  EPackage packFile2=(EPackage)findObject(resource2,PACKAGE_NAME_PREFIX);
  final EClass newClassFile2=createClass(packFile2,CLASS3_NAME_PREFIX + FILE2_SUFFIX);
  save(resource2);
  commits[1]=repository.addAndCommit(project,"String_Node_Str",file2);
  newClassFile2.setName(CLASS4_NAME_PREFIX + FILE2_SUFFIX);
  save(resource2);
  commits[2]=repository.addAndCommit(project,"String_Node_Str",file2);
  repository.createBranch(MASTER,BRANCH);
  packFile2.getEClassifiers().remove(newClassFile2);
  save(resource2);
  commits[3]=repository.addAndCommit(project,"String_Node_Str",file2);
  final EClass classBFile1=(EClass)findObject(resource1,CLASS2_NAME_PREFIX);
  final EClass classBFile2=(EClass)findObject(resource2,CLASS2_NAME_PREFIX);
  classBFile1.setName(CLASS3_NAME_PREFIX + FILE1_SUFFIX);
  classBFile2.setName(CLASS3_NAME_PREFIX + FILE2_SUFFIX);
  save(resource1,resource2);
  commits[4]=repository.addAndCommit(project,"String_Node_Str",file1,file2);
  repository.checkoutBranch(BRANCH);
  reload(resource1,resource2);
  final EClass classAFile1=(EClass)findObject(resource1,CLASS1_NAME_PREFIX);
  final EClass classAFile2=(EClass)findObject(resource2,CLASS1_NAME_PREFIX);
  classAFile1.setName(CLASS3_NAME_PREFIX + FILE1_SUFFIX);
  classAFile2.setName(CLASS3_NAME_PREFIX + FILE2_SUFFIX);
  save(resource1,resource2);
  commits[5]=repository.addAndCommit(project,"String_Node_Str",file1,file2);
  EcoreUtil.remove(findObject(resource2,CLASS4_NAME_PREFIX));
  save(resource2);
  commits[6]=repository.addAndCommit(project,"String_Node_Str",file2);
  masterTipSynonyms=new String[]{MASTER,commits[4].getName()};
  branchTipSynonyms=new String[]{BRANCH,commits[6].getName(),Constants.HEAD};
}

Fixed version (ground truth):
@Override @Before public void setUp() throws Exception {
  super.setUp();
  resource1.getContents().add(createBasicModel(FILE1_SUFFIX));
  resource2.getContents().add(createBasicModel(FILE2_SUFFIX));
  makeCrossReference(resource1,resource2,CLASS1_NAME_PREFIX,CLASS1_NAME_PREFIX);
  makeCrossReference(resource2,resource1,CLASS2_NAME_PREFIX,CLASS2_NAME_PREFIX);
  save(resource1,resource2);
  commits[0]=repository.addAndCommit(project,"String_Node_Str",file1,file2);
  EPackage packFile2=(EPackage)findObject(resource2,PACKAGE_NAME_PREFIX);
  final EClass newClassFile2=createClass(packFile2,CLASS3_NAME_PREFIX + FILE2_SUFFIX);
  save(resource2);
  commits[1]=repository.addAndCommit(project,"String_Node_Str",file2);
  newClassFile2.setName(CLASS4_NAME_PREFIX + FILE2_SUFFIX);
  save(resource2);
  commits[2]=repository.addAndCommit(project,"String_Node_Str",file2);
  repository.createBranch(MASTER,BRANCH);
  packFile2.getEClassifiers().remove(newClassFile2);
  save(resource2);
  commits[3]=repository.addAndCommit(project,"String_Node_Str",file2);
  final EClass classBFile1=(EClass)findObject(resource1,CLASS2_NAME_PREFIX);
  final EClass classBFile2=(EClass)findObject(resource2,CLASS2_NAME_PREFIX);
  classBFile1.setName(CLASS3_NAME_PREFIX + FILE1_SUFFIX);
  classBFile2.setName(CLASS3_NAME_PREFIX + FILE2_SUFFIX);
  save(resource1,resource2);
  commits[4]=repository.addAndCommit(project,"String_Node_Str",file1,file2);
  repository.checkoutBranch(BRANCH);
  reload(resource1,resource2);
  final EClass classAFile1=(EClass)findObject(resource1,CLASS1_NAME_PREFIX);
  final EClass classAFile2=(EClass)findObject(resource2,CLASS1_NAME_PREFIX);
  classAFile1.setName(CLASS3_NAME_PREFIX + FILE1_SUFFIX);
  classAFile2.setName(CLASS3_NAME_PREFIX + FILE2_SUFFIX);
  save(resource1,resource2);
  commits[5]=repository.addAndCommit(project,"String_Node_Str",file1,file2);
  EcoreUtil.remove(findObject(resource2,CLASS4_NAME_PREFIX));
  save(resource2);
  commits[6]=repository.addAndCommit(project,"String_Node_Str",file2);
  masterTipSynonyms=new String[]{MASTER,commits[4].getName()};
  branchTipSynonyms=new String[]{BRANCH,commits[6].getName()};
}