diff --git a/app/src/processing/app/Base.java b/app/src/processing/app/Base.java
index 7db2bd2cd..965b37ba6 100644
--- a/app/src/processing/app/Base.java
+++ b/app/src/processing/app/Base.java
@@ -2406,14 +2406,6 @@ public class Base {
   }
 
 
-  /**
-   * Return an InputStream for a file inside the Processing lib folder.
-   */
-  static public InputStream getLibStream(String filename) throws IOException {
-    return BaseNoGui.getLibStream(filename);
-  }
-
-
   // ...................................................................
 
 
@@ -2431,17 +2423,22 @@ public class Base {
    */
   static public byte[] loadBytesRaw(File file) throws IOException {
     int size = (int) file.length();
-    FileInputStream input = new FileInputStream(file);
-    byte buffer[] = new byte[size];
-    int offset = 0;
-    int bytesRead;
-    while ((bytesRead = input.read(buffer, offset, size - offset)) != -1) {
-      offset += bytesRead;
-      if (bytesRead == 0) break;
+    FileInputStream input = null;
+    try {
+      input = new FileInputStream(file);
+      byte buffer[] = new byte[size];
+      int offset = 0;
+      int bytesRead;
+      while ((bytesRead = input.read(buffer, offset, size - offset)) != -1) {
+        offset += bytesRead;
+        if (bytesRead == 0) break;
+      }
+      return buffer;
+    } finally {
+      if (input != null) {
+        input.close();
+      }
     }
-    input.close();  // weren't properly being closed
-    input = null;
-    return buffer;
   }
 
 
@@ -2476,20 +2473,25 @@ public class Base {
 
   static public void copyFile(File sourceFile,
                               File targetFile) throws IOException {
-    InputStream from =
-            new BufferedInputStream(new FileInputStream(sourceFile));
-    OutputStream to =
-            new BufferedOutputStream(new FileOutputStream(targetFile));
-    byte[] buffer = new byte[16 * 1024];
-    int bytesRead;
-    while ((bytesRead = from.read(buffer)) != -1) {
-      to.write(buffer, 0, bytesRead);
+    InputStream from = null;
+    OutputStream to = null;
+    try {
+      from = new BufferedInputStream(new FileInputStream(sourceFile));
+      to = new BufferedOutputStream(new FileOutputStream(targetFile));
+      byte[] buffer = new byte[16 * 1024];
+      int bytesRead;
+      while ((bytesRead = from.read(buffer)) != -1) {
+        to.write(buffer, 0, bytesRead);
+      }
+      to.flush();
+    } finally {
+      if (from != null) {
+        from.close(); // ??
+      }
+      if (to != null) {
+        to.close(); // ??
+      }
     }
-    to.flush();
-    from.close(); // ??
-    from = null;
-    to.close(); // ??
-    to = null;
 
     targetFile.setLastModified(sourceFile.lastModified());
   }
diff --git a/app/src/processing/app/Theme.java b/app/src/processing/app/Theme.java
index 7f23d3c46..4100bdfc5 100644
--- a/app/src/processing/app/Theme.java
+++ b/app/src/processing/app/Theme.java
@@ -26,6 +26,7 @@ import static processing.app.I18n._;
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.SystemColor;
+import java.io.File;
 
 import processing.app.helpers.PreferencesHelper;
 import processing.app.helpers.PreferencesMap;
@@ -45,7 +46,7 @@ public class Theme {
 
   static protected void init() {
     try {
-      table.load(Base.getLibStream("theme/theme.txt"));
+      table.load(new File(BaseNoGui.getContentFile("lib"), "theme/theme.txt"));
     } catch (Exception te) {
       Base.showError(null, _("Could not read color theme settings.\n" +
                              "You'll need to reinstall Arduino."), te);
diff --git a/app/src/processing/app/UpdateCheck.java b/app/src/processing/app/UpdateCheck.java
index 5e063bc6c..ac8117cb2 100644
--- a/app/src/processing/app/UpdateCheck.java
+++ b/app/src/processing/app/UpdateCheck.java
@@ -22,16 +22,16 @@
 
 package processing.app;
 
+import processing.app.legacy.PApplet;
+
+import javax.swing.*;
 import java.io.BufferedReader;
-import java.io.InputStream;
+import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.net.URLEncoder;
 import java.util.Random;
 
-import javax.swing.JOptionPane;
-
-import processing.app.legacy.PApplet;
 import static processing.app.I18n._;
 
 
@@ -126,11 +126,16 @@ public class UpdateCheck implements Runnable {
   }
 
 
-  protected int readInt(String filename) throws Exception {
+  protected int readInt(String filename) throws IOException {
     URL url = new URL(filename);
-    InputStream stream = url.openStream();
-    InputStreamReader isr = new InputStreamReader(stream);
-    BufferedReader reader = new BufferedReader(isr);
-    return Integer.parseInt(reader.readLine());
+    BufferedReader reader = null;
+    try {
+      reader = new BufferedReader(new InputStreamReader(url.openStream()));
+      return Integer.parseInt(reader.readLine());
+    } finally {
+      if (reader != null) {
+        reader.close();
+      }
+    }
   }
 }
diff --git a/app/src/processing/app/syntax/PdeKeywords.java b/app/src/processing/app/syntax/PdeKeywords.java
index 865325da3..b221796a5 100644
--- a/app/src/processing/app/syntax/PdeKeywords.java
+++ b/app/src/processing/app/syntax/PdeKeywords.java
@@ -61,10 +61,10 @@ public class PdeKeywords extends CTokenMarker {
       try {
         keywordColoring = new KeywordMap(false);
         keywordToReference = new Hashtable();
-        getKeywords(Base.getLibStream("keywords.txt"));
+        getKeywords(new File(BaseNoGui.getContentFile("lib"), "keywords.txt"));
         for (ContributedLibrary lib : Base.getLibraries()) {
           File keywords = new File(lib.getInstalledFolder(), "keywords.txt");
-          if (keywords.exists()) getKeywords(new FileInputStream(keywords));
+          if (keywords.exists()) getKeywords(keywords);
         }
       } catch (Exception e) {
         Base.showError("Problem loading keywords",
@@ -76,51 +76,56 @@ public class PdeKeywords extends CTokenMarker {
     return keywordColoring;
   }
   
-  static private void getKeywords(InputStream input) throws Exception {
-    InputStreamReader isr = new InputStreamReader(input);
-    BufferedReader reader = new BufferedReader(isr);
+  static private void getKeywords(File input) throws IOException {
+    BufferedReader reader = null;
+    try {
+      reader = new BufferedReader(new InputStreamReader(new FileInputStream(input)));
 
-    String line = null;
-    while ((line = reader.readLine()) != null) {
-      //System.out.println("line is " + line);
-      // in case there's any garbage on the line
-      //if (line.trim().length() == 0) continue;
+      String line = null;
+      while ((line = reader.readLine()) != null) {
+        //System.out.println("line is " + line);
+        // in case there's any garbage on the line
+        //if (line.trim().length() == 0) continue;
 
-      String pieces[] = PApplet.split(line, '\t');
-      if (pieces.length >= 2) {
-        //int tab = line.indexOf('\t');
-        // any line with no tab is ignored
-        // meaning that a comment is any line without a tab
-        //if (tab == -1) continue;
+        String pieces[] = PApplet.split(line, '\t');
+        if (pieces.length >= 2) {
+          //int tab = line.indexOf('\t');
+          // any line with no tab is ignored
+          // meaning that a comment is any line without a tab
+          //if (tab == -1) continue;
 
-        String keyword = pieces[0].trim();
-        //String keyword = line.substring(0, tab).trim();
-        //String second = line.substring(tab + 1);
-        //tab = second.indexOf('\t');
-        //String coloring = second.substring(0, tab).trim();
-        //String htmlFilename = second.substring(tab + 1).trim();
-        String coloring = pieces[1].trim();
+          String keyword = pieces[0].trim();
+          //String keyword = line.substring(0, tab).trim();
+          //String second = line.substring(tab + 1);
+          //tab = second.indexOf('\t');
+          //String coloring = second.substring(0, tab).trim();
+          //String htmlFilename = second.substring(tab + 1).trim();
+          String coloring = pieces[1].trim();
 
-        if (coloring.length() > 0 && Character.isDigit(coloring.charAt(coloring.length() - 1))) {
-          // text will be KEYWORD or LITERAL
-          boolean isKey = (coloring.charAt(0) == 'K');
-          // KEYWORD1 -> 0, KEYWORD2 -> 1, etc
-          int num = coloring.charAt(coloring.length() - 1) - '1';
-          byte id = (byte)
-            ((isKey ? Token.KEYWORD1 : Token.LITERAL1) + num);
-          //System.out.println("got " + (isKey ? "keyword" : "literal") +
-          //                 (num+1) + " for " + keyword);
-          keywordColoring.add(keyword, id);
-        }
-        if (pieces.length >= 3) {
-          String htmlFilename = pieces[2].trim();
-          if (htmlFilename.length() > 0) {
-            keywordToReference.put(keyword, htmlFilename);
+          if (coloring.length() > 0 && Character.isDigit(coloring.charAt(coloring.length() - 1))) {
+            // text will be KEYWORD or LITERAL
+            boolean isKey = (coloring.charAt(0) == 'K');
+            // KEYWORD1 -> 0, KEYWORD2 -> 1, etc
+            int num = coloring.charAt(coloring.length() - 1) - '1';
+            byte id = (byte)
+                    ((isKey ? Token.KEYWORD1 : Token.LITERAL1) + num);
+            //System.out.println("got " + (isKey ? "keyword" : "literal") +
+            //                 (num+1) + " for " + keyword);
+            keywordColoring.add(keyword, id);
+          }
+          if (pieces.length >= 3) {
+            String htmlFilename = pieces[2].trim();
+            if (htmlFilename.length() > 0) {
+              keywordToReference.put(keyword, htmlFilename);
+            }
           }
         }
       }
+    } finally {
+      if (reader != null) {
+        reader.close();
+      }
     }
-    reader.close();
   }
 
 
diff --git a/arduino-core/src/cc/arduino/contributions/GPGDetachedSignatureVerifier.java b/arduino-core/src/cc/arduino/contributions/GPGDetachedSignatureVerifier.java
index 718cd3080..cd64d59e6 100644
--- a/arduino-core/src/cc/arduino/contributions/GPGDetachedSignatureVerifier.java
+++ b/arduino-core/src/cc/arduino/contributions/GPGDetachedSignatureVerifier.java
@@ -52,23 +52,41 @@ public class GPGDetachedSignatureVerifier {
   public boolean verify(File signedFile, File signature, File publicKey) throws IOException, PGPException {
     PGPPublicKey pgpPublicKey = readPublicKey(publicKey, keyId);
 
-    PGPObjectFactory pgpObjectFactory = new PGPObjectFactory(new FileInputStream(signature), new BcKeyFingerprintCalculator());
+    FileInputStream signatureInputStream = null;
+    FileInputStream signedFileInputStream = null;
+    try {
+      signatureInputStream = new FileInputStream(signature);
+      PGPObjectFactory pgpObjectFactory = new PGPObjectFactory(signatureInputStream, new BcKeyFingerprintCalculator());
 
-    PGPSignatureList pgpSignatureList = (PGPSignatureList) pgpObjectFactory.nextObject();
-    assert pgpSignatureList.size() == 1;
-    PGPSignature pgpSignature = pgpSignatureList.get(0);
+      PGPSignatureList pgpSignatureList = (PGPSignatureList) pgpObjectFactory.nextObject();
+      assert pgpSignatureList.size() == 1;
+      PGPSignature pgpSignature = pgpSignatureList.get(0);
 
-    pgpSignature.init(new BcPGPContentVerifierBuilderProvider(), pgpPublicKey);
-    pgpSignature.update(IOUtils.toByteArray(new FileInputStream(signedFile)));
+      pgpSignature.init(new BcPGPContentVerifierBuilderProvider(), pgpPublicKey);
+      signedFileInputStream = new FileInputStream(signedFile);
+      pgpSignature.update(IOUtils.toByteArray(signedFileInputStream));
 
-    return pgpSignature.verify();
+      return pgpSignature.verify();
+    } finally {
+      if (signatureInputStream != null) {
+        signatureInputStream.close();
+      }
+      if (signedFileInputStream != null) {
+        signedFileInputStream.close();
+      }
+    }
   }
 
   private PGPPublicKey readPublicKey(File file, String keyId) throws IOException, PGPException {
-    InputStream keyIn = new BufferedInputStream(new FileInputStream(file));
-    PGPPublicKey pubKey = readPublicKey(keyIn, keyId);
-    keyIn.close();
-    return pubKey;
+    InputStream keyIn = null;
+    try {
+      keyIn = new BufferedInputStream(new FileInputStream(file));
+      return readPublicKey(keyIn, keyId);
+    } finally {
+      if (keyIn != null) {
+        keyIn.close();
+      }
+    }
   }
 
   private PGPPublicKey readPublicKey(InputStream input, String keyId) throws IOException, PGPException {
diff --git a/arduino-core/src/cc/arduino/contributions/libraries/LibrariesIndexer.java b/arduino-core/src/cc/arduino/contributions/libraries/LibrariesIndexer.java
index 7493d0e08..c285ade68 100644
--- a/arduino-core/src/cc/arduino/contributions/libraries/LibrariesIndexer.java
+++ b/arduino-core/src/cc/arduino/contributions/libraries/LibrariesIndexer.java
@@ -70,17 +70,24 @@ public class LibrariesIndexer {
   }
 
   private void parseIndex(File indexFile) throws IOException {
-    InputStream indexIn = new FileInputStream(indexFile);
-    ObjectMapper mapper = new ObjectMapper();
-    mapper.registerModule(new MrBeanModule());
-    mapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
-    mapper.configure(DeserializationFeature.EAGER_DESERIALIZER_FETCH, true);
-    mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
-    index = mapper.readValue(indexIn, LibrariesIndex.class);
+    InputStream indexIn = null;
+    try {
+      indexIn = new FileInputStream(indexFile);
+      ObjectMapper mapper = new ObjectMapper();
+      mapper.registerModule(new MrBeanModule());
+      mapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
+      mapper.configure(DeserializationFeature.EAGER_DESERIALIZER_FETCH, true);
+      mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+      index = mapper.readValue(indexIn, LibrariesIndex.class);
 
-    for (ContributedLibrary library : index.getLibraries()) {
-      if (library.getCategory() == null || "".equals(library.getCategory())) {
-        library.setCategory("Uncategorized");
+      for (ContributedLibrary library : index.getLibraries()) {
+        if (library.getCategory() == null || "".equals(library.getCategory())) {
+          library.setCategory("Uncategorized");
+        }
+      }
+    } finally {
+      if (indexIn != null) {
+        indexIn.close();
       }
     }
   }
diff --git a/arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java b/arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java
index a9ae55db5..4abd4801a 100644
--- a/arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java
+++ b/arduino-core/src/cc/arduino/contributions/packages/ContributionInstaller.java
@@ -277,10 +277,12 @@ public class ContributionInstaller {
 
     // Replace old index with the updated one
     if (outputFile.exists()) {
-      outputFile.delete();
+      if (!outputFile.delete()) {
+        throw new Exception("An error occurred while updating platforms index! I can't delete file " + outputFile);
+      }
     }
     if (!tmpFile.renameTo(outputFile)) {
-      throw new Exception("An error occurred while updating platforms index!");
+      throw new Exception("An error occurred while updating platforms index! I can't rename file " + tmpFile);
     }
 
     return outputFile;
diff --git a/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java b/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java
index 4f1bff48c..fd26b7e68 100644
--- a/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java
+++ b/arduino-core/src/cc/arduino/contributions/packages/ContributionsIndexer.java
@@ -158,13 +158,20 @@ public class ContributionsIndexer {
   }
 
   private ContributionsIndex parseIndex(File indexFile) throws IOException {
-    InputStream indexIn = new FileInputStream(indexFile);
-    ObjectMapper mapper = new ObjectMapper();
-    mapper.registerModule(new MrBeanModule());
-    mapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
-    mapper.configure(DeserializationFeature.EAGER_DESERIALIZER_FETCH, true);
-    mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
-    return mapper.readValue(indexIn, ContributionsIndex.class);
+    InputStream inputStream = null;
+    try {
+      inputStream = new FileInputStream(indexFile);
+      ObjectMapper mapper = new ObjectMapper();
+      mapper.registerModule(new MrBeanModule());
+      mapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
+      mapper.configure(DeserializationFeature.EAGER_DESERIALIZER_FETCH, true);
+      mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+      return mapper.readValue(inputStream, ContributionsIndex.class);
+    } finally {
+      if (inputStream != null) {
+        inputStream.close();
+      }
+    }
   }
 
   public void syncWithFilesystem(File hardwareFolder) throws IOException {
diff --git a/arduino-core/src/cc/arduino/utils/ArchiveExtractor.java b/arduino-core/src/cc/arduino/utils/ArchiveExtractor.java
index 8e4ed800d..fe68fa870 100644
--- a/arduino-core/src/cc/arduino/utils/ArchiveExtractor.java
+++ b/arduino-core/src/cc/arduino/utils/ArchiveExtractor.java
@@ -91,19 +91,13 @@ public class ArchiveExtractor {
 
       // Create an ArchiveInputStream with the correct archiving algorithm
       if (archiveFile.getName().endsWith("tar.bz2")) {
-        InputStream fin = new FileInputStream(archiveFile);
-        fin = new BZip2CompressorInputStream(fin);
-        in = new TarArchiveInputStream(fin);
+        in = new TarArchiveInputStream(new BZip2CompressorInputStream(new FileInputStream(archiveFile)));
       } else if (archiveFile.getName().endsWith("zip")) {
-        InputStream fin = new FileInputStream(archiveFile);
-        in = new ZipArchiveInputStream(fin);
+        in = new ZipArchiveInputStream(new FileInputStream(archiveFile));
       } else if (archiveFile.getName().endsWith("tar.gz")) {
-        InputStream fin = new FileInputStream(archiveFile);
-        fin = new GzipCompressorInputStream(fin);
-        in = new TarArchiveInputStream(fin);
+        in = new TarArchiveInputStream(new GzipCompressorInputStream(new FileInputStream(archiveFile)));
       } else if (archiveFile.getName().endsWith("tar")) {
-        InputStream fin = new FileInputStream(archiveFile);
-        in = new TarArchiveInputStream(fin);
+        in = new TarArchiveInputStream(new FileInputStream(archiveFile));
       } else {
         throw new IOException("Archive format not supported.");
       }
@@ -276,8 +270,9 @@ public class ArchiveExtractor {
   }
 
   private static void copyStreamToFile(InputStream in, long size, File outputFile) throws IOException {
-    FileOutputStream fos = new FileOutputStream(outputFile);
+    FileOutputStream fos = null;
     try {
+      fos = new FileOutputStream(outputFile);
       // if size is not available, copy until EOF...
       if (size == -1) {
         byte buffer[] = new byte[4096];
@@ -299,7 +294,9 @@ public class ArchiveExtractor {
         size -= length;
       }
     } finally {
-      fos.close();
+      if (fos != null) {
+        fos.close();
+      }
     }
   }
 
diff --git a/arduino-core/src/cc/arduino/utils/FileHash.java b/arduino-core/src/cc/arduino/utils/FileHash.java
index 87dabe172..0ce8afd4c 100644
--- a/arduino-core/src/cc/arduino/utils/FileHash.java
+++ b/arduino-core/src/cc/arduino/utils/FileHash.java
@@ -40,19 +40,18 @@ public class FileHash {
    * Calculate a message digest of a file using the algorithm specified. The
    * result is a string containing the algorithm name followed by ":" and by the
    * resulting hash in hex.
-   * 
+   *
    * @param file
-   * @param algorithm
-   *          For example "SHA-256"
+   * @param algorithm For example "SHA-256"
    * @return The algorithm followed by ":" and the hash, for example:<br />
-   *         "SHA-256:ee6796513086080cca078cbb383f543c5e508b647a71c9d6f39b7bca41071883"
+   * "SHA-256:ee6796513086080cca078cbb383f543c5e508b647a71c9d6f39b7bca41071883"
    * @throws IOException
    * @throws NoSuchAlgorithmException
    */
-  public static String hash(File file, String algorithm) throws IOException,
-      NoSuchAlgorithmException {
-    FileInputStream in = new FileInputStream(file);
+  public static String hash(File file, String algorithm) throws IOException, NoSuchAlgorithmException {
+    FileInputStream in = null;
     try {
+      in = new FileInputStream(file);
       byte buff[] = new byte[10240];
       MessageDigest digest = MessageDigest.getInstance(algorithm);
       while (in.available() > 0) {
@@ -69,7 +68,9 @@ public class FileHash {
       }
       return algorithm + ":" + res;
     } finally {
-      in.close();
+      if (in != null) {
+        in.close();
+      }
     }
   }
 }
diff --git a/arduino-core/src/processing/app/BaseNoGui.java b/arduino-core/src/processing/app/BaseNoGui.java
index 01adce511..06e807fbe 100644
--- a/arduino-core/src/processing/app/BaseNoGui.java
+++ b/arduino-core/src/processing/app/BaseNoGui.java
@@ -233,13 +233,6 @@ public class BaseNoGui {
     return librariesFolders;
   }
 
-  /**
-   * Return an InputStream for a file inside the Processing lib folder.
-   */
-  static public InputStream getLibStream(String filename) throws IOException {
-    return new FileInputStream(new File(getContentFile("lib"), filename));
-  }
-
   static public Platform getPlatform() {
     return platform;
   }
@@ -624,13 +617,17 @@ public class BaseNoGui {
       if (defaultLibraryJsonFile.isFile()) {
         FileUtils.copyFile(defaultLibraryJsonFile, librariesIndexFile);
       } else {
+        FileOutputStream out = null;
         try {
           // Otherwise create an empty packages index
-          FileOutputStream out = new FileOutputStream(librariesIndexFile);
+          out = new FileOutputStream(librariesIndexFile);
           out.write("{ \"libraries\" : [ ] }".getBytes());
-          out.close();
         } catch (IOException e) {
           e.printStackTrace();
+        } finally {
+          if (out != null) {
+            out.close();
+          }
         }
       }
     }
diff --git a/arduino-core/src/processing/app/PreferencesData.java b/arduino-core/src/processing/app/PreferencesData.java
index b34629983..d6dc14679 100644
--- a/arduino-core/src/processing/app/PreferencesData.java
+++ b/arduino-core/src/processing/app/PreferencesData.java
@@ -45,7 +45,7 @@ public class PreferencesData {
     // start by loading the defaults, in case something
     // important was deleted from the user prefs
     try {
-      prefs.load(BaseNoGui.getLibStream(PREFS_FILE));
+      prefs.load(new File(BaseNoGui.getContentFile("lib"), PREFS_FILE));
     } catch (IOException e) {
       BaseNoGui.showError(null, _("Could not read default settings.\n" +
               "You'll need to reinstall Arduino."), e);
@@ -94,41 +94,6 @@ public class PreferencesData {
   }
 
 
-  static public String[] loadStrings(InputStream input) {
-    try {
-      BufferedReader reader =
-              new BufferedReader(new InputStreamReader(input, "UTF-8"));
-
-      String lines[] = new String[100];
-      int lineCount = 0;
-      String line = null;
-      while ((line = reader.readLine()) != null) {
-        if (lineCount == lines.length) {
-          String temp[] = new String[lineCount << 1];
-          System.arraycopy(lines, 0, temp, 0, lineCount);
-          lines = temp;
-        }
-        lines[lineCount++] = line;
-      }
-      reader.close();
-
-      if (lineCount == lines.length) {
-        return lines;
-      }
-
-      // resize array to appropriate amount for these lines
-      String output[] = new String[lineCount];
-      System.arraycopy(lines, 0, output, 0, lineCount);
-      return output;
-
-    } catch (IOException e) {
-      e.printStackTrace();
-      //throw new RuntimeException("Error inside loadStrings()");
-    }
-    return null;
-  }
-
-
   static protected void save() {
     if (!doSave)
       return;
@@ -139,19 +104,25 @@ public class PreferencesData {
     if (preferencesFile == null) return;
 
     // Fix for 0163 to properly use Unicode when writing preferences.txt
-    PrintWriter writer = PApplet.createWriter(preferencesFile);
+    PrintWriter writer = null;
+    try {
+      writer = PApplet.createWriter(preferencesFile);
 
-    String[] keys = prefs.keySet().toArray(new String[0]);
-    Arrays.sort(keys);
-    for (String key: keys) {
-      if (key.startsWith("runtime."))
-        continue;
-      writer.println(key + "=" + prefs.get(key));
+      String[] keys = prefs.keySet().toArray(new String[0]);
+      Arrays.sort(keys);
+      for (String key : keys) {
+        if (key.startsWith("runtime."))
+          continue;
+        writer.println(key + "=" + prefs.get(key));
+      }
+
+      writer.flush();
+    } finally {
+      if (writer != null) {
+        writer.close();
+      }
     }
 
-    writer.flush();
-    writer.close();
-
     try {
       BaseNoGui.getPlatform().fixPrefsFilePermissions(preferencesFile);
     } catch (Exception e) {
diff --git a/arduino-core/src/processing/app/debug/Compiler.java b/arduino-core/src/processing/app/debug/Compiler.java
index e1c2e2fb2..1bc0f9074 100644
--- a/arduino-core/src/processing/app/debug/Compiler.java
+++ b/arduino-core/src/processing/app/debug/Compiler.java
@@ -1210,12 +1210,12 @@ public class Compiler implements MessageConsumer {
     // 2. run preproc on that code using the sugg class name
     //    to create a single .java file and write to buildpath
 
+    FileOutputStream outputStream = null;
     try {
       // Output file
       File streamFile = new File(buildPath, sketch.getName() + ".cpp");
-      FileOutputStream outputStream = new FileOutputStream(streamFile);
+      outputStream = new FileOutputStream(streamFile);
       preprocessor.write(outputStream);
-      outputStream.close();
     } catch (FileNotFoundException fnfe) {
       fnfe.printStackTrace();
       String msg = _("Build folder disappeared or could not be written");
@@ -1230,6 +1230,14 @@ public class Compiler implements MessageConsumer {
       System.err.println(I18n.format(_("Uncaught exception type: {0}"), ex.getClass()));
       ex.printStackTrace();
       throw new RunnerException(ex.toString());
+    } finally {
+      if (outputStream != null) {
+        try {
+          outputStream.close();
+        } catch (IOException e) {
+          //noop
+        }
+      }
     }
 
     // grab the imports from the code just preproc'd
diff --git a/arduino-core/src/processing/app/helpers/PreferencesMap.java b/arduino-core/src/processing/app/helpers/PreferencesMap.java
index f26c2b122..185e1bee4 100644
--- a/arduino-core/src/processing/app/helpers/PreferencesMap.java
+++ b/arduino-core/src/processing/app/helpers/PreferencesMap.java
@@ -21,18 +21,14 @@
  */
 package processing.app.helpers;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
+import processing.app.legacy.PApplet;
+
+import java.io.*;
 import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.SortedSet;
 import java.util.TreeSet;
 
-import processing.app.legacy.PApplet;
-
 @SuppressWarnings("serial")
 public class PreferencesMap extends LinkedHashMap<String, String> {
 
@@ -71,7 +67,15 @@ public class PreferencesMap extends LinkedHashMap<String, String> {
    * @throws IOException
    */
   public void load(File file) throws IOException {
-    load(new FileInputStream(file));
+    FileInputStream fileInputStream = null;
+    try {
+      fileInputStream = new FileInputStream(file);
+      load(fileInputStream);
+    } finally {
+      if (fileInputStream != null) {
+        fileInputStream.close();
+      }
+    }
   }
 
   protected String processPlatformSuffix(String key, String suffix, boolean isCurrentPlatform) {
diff --git a/arduino-core/src/processing/app/legacy/PApplet.java b/arduino-core/src/processing/app/legacy/PApplet.java
index 59ca701e3..e89955263 100644
--- a/arduino-core/src/processing/app/legacy/PApplet.java
+++ b/arduino-core/src/processing/app/legacy/PApplet.java
@@ -266,9 +266,20 @@ public class PApplet {
   }
 
   static public String[] loadStrings(File file) {
-    InputStream is = createInput(file);
-    if (is != null) return loadStrings(is);
-    return null;
+    InputStream is = null;
+    try {
+      is = createInput(file);
+      if (is != null) return loadStrings(is);
+      return null;
+    } finally {
+      if (is != null) {
+        try {
+          is.close();
+        } catch (IOException e) {
+          // noop
+        }
+      }
+    }
   }
 
   static public String[] loadStrings(InputStream input) {
@@ -319,14 +330,29 @@ public class PApplet {
 
 
   static public void saveStrings(File file, String strings[]) {
-    saveStrings(createOutput(file), strings);
+    OutputStream outputStream = null;
+    try {
+      outputStream = createOutput(file);
+      saveStrings(outputStream, strings);
+    } finally {
+      if (outputStream != null) {
+        try {
+          outputStream.close();
+        } catch (IOException e) {
+          //noop
+        }
+      }
+    }
   }
 
 
   static public void saveStrings(OutputStream output, String strings[]) {
     PrintWriter writer = createWriter(output);
-    for (int i = 0; i < strings.length; i++) {
-      writer.println(strings[i]);
+    if (writer == null) {
+      return;
+    }
+    for (String string : strings) {
+      writer.println(string);
     }
     writer.flush();
     writer.close();