Fix recently broken ModuleBase.skipBytes method

Broken during incorrect merge of PR openpreserve#117. Each loop of the skip method
was skipping the same amount of bytes, not subtracting the amount already
skipped. Reverted to original pull request code then refactored.

Fixes openpreserve#71, fixes openpreserve#193.

jhove-core/src/main/java/edu/harvard/hul/ois/jhove/ModuleBase.java

@@ -1295,7 +1295,7 @@ public static float readFloat (DataInputStream stream, boolean endian,
     }
 
     public static double readDouble (RandomAccessFile file, boolean endian)
-        throws IOException 
+        throws IOException
     {
         double f = 0.0F;
         if (endian) {
@@ -1354,32 +1354,31 @@ public static double readDouble (DataInputStream stream, boolean endian,
         return f;
     }
 
-    /* Skip over some bytes.  */
-	public long skipBytes(DataInputStream stream, long bytesToSkip)
-            throws IOException
+    /** Skip over some bytes. Return number of bytes skipped. */
+    public long skipBytes(DataInputStream stream, long bytesToSkip)
+        throws IOException
     {
-	return skipBytes (stream, bytesToSkip, null);
+        return skipBytes(stream, bytesToSkip, null);
     }
 
-    /* Skip over some bytes.  */
-	public long skipBytes(DataInputStream stream, long bytesToSkip,
-			  ModuleBase counted) 
-            throws IOException
+    /** Skip over some bytes. Return number of bytes skipped. */
+    public long skipBytes(DataInputStream stream, long bytesToSkip,
+                          ModuleBase counted)
+        throws IOException
     {
-        long retVal = 0;
-        long bytesLeft = bytesToSkip;
-        while (bytesLeft > 0) {
-            long n = stream.skip(bytesToSkip);
-            bytesLeft -= n;
-            retVal += n;
-            if (counted != null) {
-                counted._nByte += n;
-            }
-            if (stream.available() == 0) {
-                break;
-            }
+        long totalBytesSkipped = 0;
+        while (bytesToSkip > 0) {
+            long bytesSkipped = stream.skip(bytesToSkip);
+            totalBytesSkipped += bytesSkipped;
+            bytesToSkip -= bytesSkipped;
+            // Cease skipping if end of stream reached before
+            // requested number of bytes have been skipped.
+            if (stream.available() == 0) break;
+        }
+        if (counted != null) {
+            counted._nByte += totalBytesSkipped;
         }
-        return retVal;
+        return totalBytesSkipped;
     }
 
     /**