Created a unit test that reproduces JENKINS-23179

src/test/java/hudson/plugins/git/AbstractGitTestCase.java

@@ -3,6 +3,8 @@
 import com.google.common.collect.Lists;
 import hudson.EnvVars;
 import hudson.FilePath;
+import hudson.matrix.MatrixBuild;
+import hudson.matrix.MatrixProject;
 import hudson.model.*;
 import hudson.plugins.git.extensions.GitSCMExtension;
 import hudson.plugins.git.extensions.impl.CleanBeforeCheckout;
@@ -187,6 +189,19 @@ protected FreeStyleBuild build(final FreeStyleProject project, final String pare
         }
         return build;
     }
+
+    protected MatrixBuild build(final MatrixProject project, final Result expectedResult, final String...expectedNewlyCommittedFiles) throws Exception {
+        final MatrixBuild build = project.scheduleBuild2(0, new Cause.UserCause()).get();
+        System.out.println(build.getLog());
+        for(final String expectedNewlyCommittedFile : expectedNewlyCommittedFiles) {
+            assertTrue(expectedNewlyCommittedFile + " file not found in workspace", build.getWorkspace().child(expectedNewlyCommittedFile).exists());
+        }
+        if(expectedResult != null) {
+            assertBuildStatus(expectedResult, build);
+        }
+        return build;
+    }
+
 
     protected EnvVars getEnvVars(FreeStyleProject project) {
         for (hudson.tasks.Builder b : project.getBuilders()) {

src/test/java/hudson/plugins/git/GitSCMTest.java

@@ -1,8 +1,13 @@
 package hudson.plugins.git;
 
 import com.google.common.collect.Lists;
+
 import hudson.EnvVars;
 import hudson.FilePath;
+import hudson.matrix.Axis;
+import hudson.matrix.AxisList;
+import hudson.matrix.MatrixBuild;
+import hudson.matrix.MatrixProject;
 import hudson.model.*;
 import hudson.plugins.git.GitSCM.BuildChooserContextImpl;
 import hudson.plugins.git.browser.GitRepositoryBrowser;
@@ -985,6 +990,51 @@ public void testMergeFailedWithSlave() throws Exception {
         assertFalse("scm polling should not detect any more changes after build", project.poll(listener).hasChanges());
     }
 
+
+    public void testMergeWithMatrixBuild() throws Exception {
+
+        MatrixProject project = createMatrixProject("xyz");
+        project.setAxes(new AxisList(new Axis("VAR","a","b")));
+
+        //FreeStyleProject project = setupSimpleProject("master");
+        //project.setAssignedLabel(createSlave().getSelfLabel());
+
+        GitSCM scm = new GitSCM(
+                createRemoteRepositories(),
+                Collections.singletonList(new BranchSpec("*")),
+                false, Collections.<SubmoduleConfig>emptyList(),
+                null, null,
+                Collections.<GitSCMExtension>emptyList());
+        scm.getExtensions().add(new PreBuildMerge(new UserMergeOptions("origin", "integration", null)));
+        project.setScm(scm);
+
+        // create initial commit and then run the build against it:
+        commit("commitFileBase", johnDoe, "Initial Commit");
+        testRepo.git.branch("integration");
+        build(project, Result.SUCCESS, "commitFileBase");
+
+
+        testRepo.git.checkout(null, "topic1");
+        final String commitFile1 = "commitFile1";
+        commit(commitFile1, johnDoe, "Commit number 1");
+        final MatrixBuild build1 = build(project, Result.SUCCESS, commitFile1);
+        assertTrue(build1.getWorkspace().child(commitFile1).exists());
+
+        assertFalse("scm polling should not detect any more changes after build", project.poll(listener).hasChanges());
+        // do what the GitPublisher would do
+        testRepo.git.deleteBranch("integration");
+        testRepo.git.checkout("topic1", "integration");
+
+        testRepo.git.checkout("master", "topic2");
+        final String commitFile2 = "commitFile2";
+        commit(commitFile2, johnDoe, "Commit number 2");
+        assertTrue("scm polling did not detect commit2 change", project.poll(listener).hasChanges());
+        final MatrixBuild build2 = build(project, Result.SUCCESS, commitFile2);
+        assertTrue(build2.getWorkspace().child(commitFile2).exists());
+        assertBuildStatusSuccess(build2);
+        assertFalse("scm polling should not detect any more changes after build", project.poll(listener).hasChanges());
+    }
+
     public void testEnvironmentVariableExpansion() throws Exception {
         FreeStyleProject project = createFreeStyleProject();
         project.setScm(new GitSCM("${CAT}"+testRepo.gitDir.getPath()));