Replace StringUtils + Partially cleanup FileUtils + Fix unit test

.classpath

@@ -27,6 +27,7 @@
 	<classpathentry kind="lib" path="app/lib/jackson-module-mrbean-2.9.5.jar"/>
 	<classpathentry kind="lib" path="app/lib/jackson-annotations-2.9.5.jar"/>
 	<classpathentry kind="lib" path="app/lib/commons-compress-1.8.jar"/>
+	<classpathentry kind="lib" path="app/lib/commons-lang3-3.8.1.jar"/>
 	<classpathentry combineaccessrules="false" kind="src" path="/arduino-core"/>
 	<classpathentry kind="output" path="app/bin"/>
 </classpath>

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;
   }
 

app/test/cc/arduino/packages/uploaders/MergeSketchWithUploaderTest.java

@@ -35,18 +35,29 @@
 import processing.app.helpers.FileUtils;
 
 import java.io.File;
+import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.util.List;
 
 import static org.junit.Assert.assertEquals;
 
 public class MergeSketchWithUploaderTest {
 
   private File sketch;
+  private File bootloader;
 
   @Before
   public void setup() throws Exception {
-    File originalSketch = new File(MergeSketchWithUploaderTest.class.getResource("/sketch.hex").getFile());
+    File originalSketch = getResourceFile("/sketch.hex");
     sketch = new File(System.getProperty("java.io.tmpdir"), "sketch.hex");
     FileUtils.copyFile(originalSketch, sketch);
+    removeCariageReturns(sketch);
+
+    File originalBootloader = getResourceFile("/optiboot_atmega328.hex");
+    bootloader = new File(System.getProperty("java.io.tmpdir"), "optiboot_atmega328.hex");
+    FileUtils.copyFile(originalBootloader, bootloader);
+    removeCariageReturns(bootloader);
   }
 
   @After
@@ -57,11 +68,24 @@ public void removeTmpFile() {
   @Test
   public void shouldMergeWithOptiboot() throws Exception {
     assertEquals(11720, sketch.length());
+    assertEquals(1432, bootloader.length());
 
-    File bootloader = new File(MergeSketchWithUploaderTest.class.getResource("/optiboot_atmega328.hex").getFile());
+    File bootloader = getResourceFile("/optiboot_atmega328.hex");
     new MergeSketchWithBooloader().merge(sketch, bootloader);
     assertEquals(13140, sketch.length());
   }
 
+  private static File getResourceFile(String resourcePath) throws Exception {
+    return new File(URLDecoder.decode(
+        MergeSketchWithUploaderTest.class.getResource(resourcePath).getFile(), "UTF-8"));
+  }
 
+  private static void removeCariageReturns(File file) throws Exception {
+    List<String> lines = Files.readAllLines(file.toPath(), StandardCharsets.UTF_8);
+    StringBuilder contentBuilder = new StringBuilder();
+    for(String line : lines) {
+      contentBuilder.append(line).append('\n');
+    }
+    Files.write(file.toPath(), contentBuilder.toString().getBytes(StandardCharsets.UTF_8));
+  }
 }

arduino-core/.classpath

@@ -16,7 +16,7 @@
 	<classpathentry kind="lib" path="lib/bcprov-jdk15on-152.jar"/>
 	<classpathentry kind="lib" path="lib/commons-codec-1.7.jar"/>
 	<classpathentry kind="lib" path="lib/commons-compress-1.8.jar"/>
-	<classpathentry kind="lib" path="lib/commons-lang3-3.3.2.jar"/>
+	<classpathentry kind="lib" path="lib/commons-lang3-3.8.1.jar"/>
 	<classpathentry kind="lib" path="lib/jackson-annotations-2.9.5.jar"/>
 	<classpathentry kind="lib" path="lib/jackson-core-2.9.5.jar"/>
 	<classpathentry kind="lib" path="lib/jackson-databind-2.9.5.jar"/>

arduino-core/src/cc/arduino/packages/Uploader.java

@@ -37,35 +37,35 @@
 import processing.app.debug.MessageConsumer;
 import processing.app.debug.MessageSiphon;
 import processing.app.helpers.ProcessUtils;
-import processing.app.helpers.StringUtils;
 
 import java.io.File;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 import java.util.concurrent.TimeUnit;
 
+import org.apache.commons.lang3.StringUtils;
+
 import static processing.app.I18n.tr;
 
 public abstract class Uploader implements MessageConsumer {
 
-  private static final List<String> STRINGS_TO_SUPPRESS;
-  private static final List<String> AVRDUDE_PROBLEMS;
+  private static final String[] STRINGS_TO_SUPPRESS;
+  private static final String[] AVRDUDE_PROBLEMS;
 
   static {
-    STRINGS_TO_SUPPRESS = Arrays.asList("Connecting to programmer:",
+    STRINGS_TO_SUPPRESS = new String[] {"Connecting to programmer:",
             "Found programmer: Id = \"CATERIN\"; type = S",
             "Software Version = 1.0; No Hardware Version given.",
             "Programmer supports auto addr increment.",
             "Programmer supports buffered memory access with buffersize=128 bytes.",
-            "Programmer supports the following devices:", "Device code: 0x44");
+            "Programmer supports the following devices:", "Device code: 0x44"};
 
-    AVRDUDE_PROBLEMS = Arrays.asList("Programmer is not responding",
+    AVRDUDE_PROBLEMS = new String[] {"Programmer is not responding",
             "programmer is not responding",
             "protocol error", "avrdude: ser_open(): can't open device",
             "avrdude: ser_drain(): read error",
             "avrdude: ser_send(): write error",
-            "avrdude: error: buffered memory access not supported.");
+            "avrdude: error: buffered memory access not supported."};
   }
 
   protected final boolean verbose;
@@ -155,7 +155,7 @@ public String getFailureMessage() {
   @Override
   public void message(String s) {
     // selectively suppress a bunch of avrdude output for AVR109/Caterina that should already be quelled but isn't
-    if (!verbose && StringUtils.stringContainsOneOf(s, STRINGS_TO_SUPPRESS)) {
+    if (!verbose && StringUtils.containsAny(s, STRINGS_TO_SUPPRESS)) {
       s = "";
     }
 
@@ -175,7 +175,7 @@ public void message(String s) {
       error = tr("Device is not responding, check the right serial port is selected or RESET the board right before exporting");
       return;
     }
-    if (StringUtils.stringContainsOneOf(s, AVRDUDE_PROBLEMS)) {
+    if (StringUtils.containsAny(s, AVRDUDE_PROBLEMS)) {
       error = tr("Problem uploading to board.  See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.");
       return;
     }

arduino-core/src/cc/arduino/packages/discoverers/PluggableDiscovery.java

@@ -36,6 +36,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.commons.lang3.StringUtils;
+
 import com.fasterxml.jackson.annotation.JsonAutoDetect.Visibility;
 import com.fasterxml.jackson.annotation.PropertyAccessor;
 import com.fasterxml.jackson.core.JsonFactory;
@@ -48,7 +50,6 @@
 import cc.arduino.packages.BoardPort;
 import cc.arduino.packages.Discovery;
 import processing.app.PreferencesData;
-import processing.app.helpers.StringUtils;
 
 public class PluggableDiscovery implements Discovery {
 

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

@@ -29,19 +29,19 @@
 
 package cc.arduino.packages.uploaders;
 
-import processing.app.helpers.FileUtils;
-
 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/cc/arduino/packages/uploaders/SSHUploader.java

@@ -44,18 +44,23 @@
 import processing.app.helpers.PreferencesMap;
 import processing.app.helpers.PreferencesMapException;
 import processing.app.helpers.StringReplacer;
-import processing.app.helpers.StringUtils;
 
 import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.lang3.StringUtils;
 
 import static processing.app.I18n.tr;
 
 public class SSHUploader extends Uploader {
 
-  private static final List<String> FILES_NOT_TO_COPY = Arrays.asList(".DS_Store", ".Trash", "Thumbs.db", "__MACOSX");
+  private static final Set<String> FILES_NOT_TO_COPY =
+      Collections.unmodifiableSet(new HashSet<String>(Arrays.asList(".DS_Store", ".Trash", "Thumbs.db", "__MACOSX")));
 
   private final BoardPort port;
 
@@ -223,7 +228,7 @@ private void recursiveSCP(File from, SCP scp) throws IOException {
     }
 
     for (File file : files) {
-      if (!StringUtils.stringContainsOneOf(file.getName(), FILES_NOT_TO_COPY)) {
+      if (!FILES_NOT_TO_COPY.contains(file.getName())) {
         if (file.isDirectory() && file.canExecute()) {
           scp.startFolder(file.getName());
           recursiveSCP(file, scp);

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) {