Assuming the bundled version is an AVR bundle, force unpacking the default package if it's missing

arduino-core/src/cc/arduino/utils/ArchiveExtractor.java

@@ -69,6 +69,11 @@ public class ArchiveExtractor {
    * @throws IOException
    */
   public static void extract(File archiveFile, File destFolder, int stripPath) throws IOException {
+    extract(archiveFile, destFolder, stripPath, false);
+  }
+
+
+  public static void extract(File archiveFile, File destFolder, int stripPath, boolean overwrite) throws IOException {
 
     // Folders timestamps must be set at the end of archive extraction
     // (because creating a file in a folder alters the folder's timestamp)
@@ -193,14 +198,14 @@ public class ArchiveExtractor {
 
         // Safety check
         if (isDirectory) {
-          if (outputFile.isFile()) {
+          if (outputFile.isFile() && !overwrite) {
             throw new IOException("Can't create folder " + outputFile + ", a file with the same name exists!");
           }
         } else {
           // - isLink
           // - isSymLink
           // - anything else
-          if (outputFile.exists()) {
+          if (outputFile.exists() && !overwrite) {
             throw new IOException("Can't extract file " + outputFile + ", file already exists!");
           }
         }
@@ -233,6 +238,9 @@ public class ArchiveExtractor {
       }
 
       for (Map.Entry<File, File> entry : hardLinks.entrySet()) {
+        if (entry.getKey().exists() && overwrite) {
+          entry.getKey().delete();
+        }
         FileNativeUtils.link(entry.getValue(), entry.getKey());
         Integer mode = hardLinksMode.get(entry.getKey());
         if (mode != null) {
@@ -241,6 +249,9 @@ public class ArchiveExtractor {
       }
 
       for (Map.Entry<File, File> entry : symLinks.entrySet()) {
+        if (entry.getKey().exists() && overwrite) {
+          entry.getKey().delete();
+        }
         FileNativeUtils.symlink(entry.getValue(), entry.getKey());
         entry.getKey().setLastModified(symLinksModifiedTimes.get(entry.getKey()));
       }

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

@@ -578,11 +578,12 @@ public class BaseNoGui {
   static public void initPackages() throws Exception {
     indexer = new ContributionsIndexer(BaseNoGui.getSettingsFolder());
     File indexFile = indexer.getIndexFile();
-    if (!indexFile.isFile()) {
+    File avrCoreFolder = FileUtils.newFile(indexFile.getParentFile(), "packages", "arduino", "hardware", "avr");
+    if (!indexFile.isFile() || !(avrCoreFolder.exists() && avrCoreFolder.isDirectory())) {
       File distFile = findDefaultPackageFile();
       if (distFile != null) {
-        ArchiveExtractor.extract(distFile, BaseNoGui.getSettingsFolder(), 0);
-      } else {
+        ArchiveExtractor.extract(distFile, BaseNoGui.getSettingsFolder(), 0, true);
+      } else if (!indexFile.isFile()) {
         // Otherwise create an empty packages index
         FileOutputStream out = null;
         try {

arduino-core/src/processing/app/helpers/FileUtils.java

@@ -73,11 +73,13 @@ public class FileUtils {
   }
 
   public static void recursiveDelete(File file) {
-    if (file == null)
+    if (file == null) {
       return;
+    }
     if (file.isDirectory()) {
-      for (File current : file.listFiles())
+      for (File current : file.listFiles()) {
         recursiveDelete(current);
+      }
     }
     file.delete();
   }
@@ -254,5 +256,14 @@ public class FileUtils {
     return result;
   }
 
+  public static File newFile(File parent, String... parts) {
+    File result = parent;
+    for (String part : parts) {
+      result = new File(result, part);
+    }
+
+    return result;
+  }
+
 
 }