replaced Algorythm and made it way faster

.idea/workspace.xml

@@ -10,7 +10,9 @@
   </component>
   <component name="ChangeListManager">
     <list default="true" id="9b57ac51-c870-474b-9dfd-64a5fc490635" name="Changes" comment="Fix MD">
-      <change beforePath="$PROJECT_DIR$/README.md" beforeDir="false" afterPath="$PROJECT_DIR$/README.md" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/src/Main.java" beforeDir="false" afterPath="$PROJECT_DIR$/src/Main.java" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/src/ThreadedCompare.java" beforeDir="false" afterPath="$PROJECT_DIR$/src/ThreadedCompare.java" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -72,7 +74,7 @@
     <configuration name="Main" type="Application" factoryName="Application" temporary="true" nameIsGenerated="true">
       <option name="MAIN_CLASS_NAME" value="Main" />
       <module name="Sherly" />
-      <option name="PROGRAM_PARAMETERS" value="-f $USER_HOME$/Pictures/ -p -h" />
+      <option name="PROGRAM_PARAMETERS" value="-f $USER_HOME$/.local/share/Steam -p" />
       <method v="2">
         <option name="Make" enabled="true" />
       </method>
@@ -260,7 +262,14 @@
       <option name="project" value="LOCAL" />
       <updated>1679508433400</updated>
     </task>
-    <option name="localTasksCounter" value="25" />
+    <task id="LOCAL-00025" summary="Fix MD">
+      <created>1679508468115</created>
+      <option name="number" value="00025" />
+      <option name="presentableId" value="LOCAL-00025" />
+      <option name="project" value="LOCAL" />
+      <updated>1679508468115</updated>
+    </task>
+    <option name="localTasksCounter" value="26" />
     <servers />
   </component>
   <component name="Vcs.Log.Tabs.Properties">

src/Main.java

@@ -121,7 +121,8 @@ public class Main {
 
             //sectionedList gives the thread their Assigned Part of Files and allFiles are all the Files
 
-            ThreadedCompare threadedCompare = new ThreadedCompare(sectionedList, allFiles);
+
+            ThreadedCompare threadedCompare = new ThreadedCompare(sectionedList);
             threadedCompare.start();
 
         }
@@ -136,6 +137,13 @@ public class Main {
             }
 
         }
+        ArrayList toRemove = new ArrayList<String>();
+        for (String md5: fileMap.keySet()) {
+            if (Main.fileMap.get(md5).size() == 1) {
+                toRemove.add(md5);
+            }
+        }
+        fileMap.keySet().removeAll(toRemove);
 
         //now everything is finished and the Filemap (hashmap with all Dups) can be printed out in a nice view
         //System.out.println(fileMap);

src/ThreadedCompare.java

@@ -4,55 +4,49 @@ import java.nio.file.Path;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 public class ThreadedCompare extends Thread {
     private final List<Path> pathsToCompareTo;
-    private final List<Path> pathsToBeCompared;
+    //private HashMap<String, List<Path>> threadFileMap = new HashMap<>();
-    public ThreadedCompare (List<Path> pathsToBeCompared, List<Path> pathsToCompareTo) {
+
-        this.pathsToBeCompared = pathsToBeCompared;
+    public ThreadedCompare (List<Path> pathsToCompareTo) {
+
         this.pathsToCompareTo = pathsToCompareTo;
     }
     @Override
     public void run() {
 
-        //Compare every File
+        for (Path file : pathsToCompareTo) {
-        for (Path file1 : pathsToBeCompared) {
+            List<Path> fileArray = new ArrayList<>();
-            for (Path file2 : pathsToCompareTo) {
+            assert fileArray != null;
-                try {
+            fileArray.add(file);
-                    if (sameContent(file1, file2)) {
+            String MD5;
-                        List<Path> bothList = new ArrayList<>();
+            try {
-                        String md5 = getMD5Sum(file1.toFile());
+                MD5 = getMD5Sum(file.toFile());
-
+            } catch (IOException e) {
-                        bothList.add(file1);
+                throw new RuntimeException(e);
-                        bothList.add(file2);
-
-                        //here it is trying to add the values in the HashMap so everything is nice and clear
-                        Main.fileMap.putIfAbsent(md5, bothList);
-
-                        if (!bothList.isEmpty()) {
-
-                            Main.fileMap.get(md5).remove(file1);
-                            Main.fileMap.get(md5).remove(file2);
-                            Main.fileMap.get(md5).addAll(bothList);
-                        }
-
-
-                    }
-                } catch (IOException e) {
-                    throw new RuntimeException(e);
-                }
             }
-            //Update the Progress that can be found in The Main Class
+
-            Main.progress += 1;
+
+            if (Main.fileMap.containsKey(MD5)) {
+                fileArray.addAll(Main.fileMap.get(MD5));
+                Main.fileMap.put(MD5, fileArray);
+            } else {
+                Main.fileMap.put(MD5, fileArray);
+            }
+
+
+            Main.progress++;
         }
-        //Update the thread Completion Counter that can be found in the Main Class
+
-        Main.completedThreads += 1;
+        
-    }
+        Main.completedThreads++;
-    private boolean sameContent(Path file1, Path file2) throws IOException {
+
-        if (file1 != file2) {
+
-            return Files.mismatch(file1, file2) == -1;
+
-        }
+
-        return false;
+
     }
 
     //this is used to get the MD5 String of one of the files (one of them is just fine since they both have the same value)