Replace some FileUtils calls with direct methods

Not wrapping these calls in FileUtils methods makes the code cleaner and easier to understand (FileUtils is very poorly documented, whereas direct calls contain proper documentation).

Author: Pieter12345

app/src/processing/app/Base.java

@@ -1691,19 +1691,12 @@ public int compare(File file, File file2) {
     });
 
     boolean ifound = false;
-
     for (File subfolder : files) {
-      if (FileUtils.isSCCSOrHiddenFile(subfolder)) {
-        continue;
-      }
-
-      if (!subfolder.isDirectory()) continue;
-
-      if (addSketchesSubmenu(menu, subfolder.getName(), subfolder)) {
+      if (!FileUtils.isSCCSOrHiddenFile(subfolder) && subfolder.isDirectory()
+          && addSketchesSubmenu(menu, subfolder.getName(), subfolder)) {
         ifound = true;
       }
     }
-
     return ifound;
   }
 

arduino-core/src/cc/arduino/packages/uploaders/MergeSketchWithBooloader.java

@@ -34,14 +34,16 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 import java.util.List;
 
 public class MergeSketchWithBooloader {
 
   public void merge(File sketch, File bootloader) throws IOException {
-    List<String> mergedSketch = FileUtils.readFileToListOfStrings(sketch);
+    List<String> mergedSketch = Files.readAllLines(sketch.toPath(), StandardCharsets.UTF_8);
     mergedSketch.remove(mergedSketch.size() - 1);
-    mergedSketch.addAll(FileUtils.readFileToListOfStrings(bootloader));
+    mergedSketch.addAll(Files.readAllLines(bootloader.toPath(), StandardCharsets.UTF_8));
 
     FileWriter writer = null;
     try {

arduino-core/src/processing/app/BaseNoGui.java

@@ -485,8 +485,8 @@ static public void initPackages() throws Exception {
     } catch (JsonProcessingException | SignatureVerificationFailedException e) {
       File indexFile = indexer.getIndexFile(Constants.DEFAULT_INDEX_FILE_NAME);
       File indexSignatureFile = indexer.getIndexFile(Constants.DEFAULT_INDEX_FILE_NAME + ".sig");
-      FileUtils.deleteIfExists(indexFile);
-      FileUtils.deleteIfExists(indexSignatureFile);
+      indexFile.delete();
+      indexSignatureFile.delete();
       throw e;
     }
     indexer.syncWithFilesystem();
@@ -502,7 +502,7 @@ static public void initPackages() throws Exception {
       librariesIndexer.parseIndex();
     } catch (JsonProcessingException e) {
       File librariesIndexFile = librariesIndexer.getIndexFile();
-      FileUtils.deleteIfExists(librariesIndexFile);
+      librariesIndexFile.delete();
     }
 
     if (discoveryManager == null) {