Meaningful error message and keeping tmp file when mergeInfo fails

-- BCF2 is failing for some reason when merging tmp. files with parallel combine variants.  ThreadLocalOutputTracker no longer sets deleteOnExit on the tmp file, as this prevents debugging.  And it's unnecessary because each mergeInto was deleting files as appropriate
-- MergeInfo in VariantContextWriterStorage only deletes the intermediate output if an error occurs

public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java

@@ -119,7 +119,7 @@ public class ThreadLocalOutputTracker extends OutputTracker {
 
         try {
             tempFile = File.createTempFile( stub.getClass().getName(), null );
-            tempFile.deleteOnExit();
+            //tempFile.deleteOnExit();
         }
         catch( IOException ex ) {
             throw new UserException.BadTmpDir("Unable to create temporary file for stub: " + stub.getClass().getName() );

public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java

@@ -194,6 +194,9 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
             }
 
             source.close();
+            file.delete(); // this should be last to aid in debugging when the process fails
+        } catch (UserException e) {
+            throw new ReviewedStingException("BUG: intermediate file " + file + " is malformed, got error while reading", e);
         } catch (IOException e) {
             throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e);
         }