Clean submodules.

src/de/uni_passau/fim/gitwrapper/Repository.java

 package de.uni_passau.fim.gitwrapper;
 
-import org.apache.commons.io.FileUtils;
-
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
 import java.time.Instant;
 import java.time.OffsetDateTime;
 import java.time.ZoneId;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.NoSuchElementException;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Scanner;
 import java.util.function.Function;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
 
+import org.apache.commons.io.FileUtils;
+
 import static de.uni_passau.fim.gitwrapper.Repository.ConflictMarker.CONFLICT_END;
 import static de.uni_passau.fim.gitwrapper.Repository.ConflictMarker.CONFLICT_MIDDLE;
 import static de.uni_passau.fim.gitwrapper.Repository.ConflictMarker.CONFLICT_START;
@@ -665,23 +674,48 @@ public class Repository {
      * @return {@code true} if the cleanup was successful
      */
     public boolean cleanup(String... retain) {
+        String[] strArr = new String[0];
         List<String> pars = new ArrayList<>(3 + retain.length * 2);
 
         pars.add("-x");
-        pars.add("-d");
         pars.add("-f");
+        pars.add("-d");
+        pars.add("-f"); // Apparently this cleans directories containing .git folders.
 
         for (String pattern : retain) {
             pars.add("-e");
             pars.add(pattern);
         }
 
-        Optional<ExecRes> clean = git.exec(dir, "clean", pars.toArray(new String[0]));
+        Optional<ExecRes> clean = git.exec(dir, "clean", pars.toArray(strArr));
         Optional<ExecRes> reset = clean.filter(ExecRes::succeeded) // this is '&&' in bash
                                        .flatMap(r -> git.exec(dir, "reset", "--hard"));
 
         if (!reset.isPresent() || !reset.get().succeeded()) {
-            LOG.warning("Failed to clean directory");
+            LOG.warning("Failed to clean " + this);
+            return false;
+        }
+
+        List<String> submoduleCleanPars = new ArrayList<>(8);
+        submoduleCleanPars.add("foreach");
+        submoduleCleanPars.add("--recursive");
+        submoduleCleanPars.add(git.getCmd());
+        submoduleCleanPars.add("clean");
+        submoduleCleanPars.addAll(pars.subList(0, 4));
+
+        List<String> submoduleResetPars = new ArrayList<>(5);
+        submoduleResetPars.add("foreach");
+        submoduleResetPars.add("--recursive");
+        submoduleResetPars.add(git.getCmd());
+        submoduleResetPars.add("reset");
+        submoduleResetPars.add("--hard");
+
+        Optional<ExecRes> cleanSub = git.exec(dir, "submodule", submoduleCleanPars.toArray(strArr));
+        Optional<ExecRes> resetSub = cleanSub.filter(ExecRes::succeeded) // this is '&&' in bash
+                                             .flatMap(r -> git.exec(dir, "submodule", submoduleResetPars.toArray(strArr)));
+
+        if (!resetSub.isPresent() || !resetSub.get().succeeded()) {
+            LOG.warning("Failed to clean submodules of " + this);
             return false;
         }