Thanks for the quick response. The [Merge in existing file, keep manifest] option now works (and is very useful!). However, the [Create New] fails to do anything and the [Replace all] gives the following error:
java.io.FileNotFoundException: /Volumes/KINGSTON/learning-clausal-logic-copy.pdf (Directory not empty)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.j ava:179)
at java.io.FileOutputStream.<init>(FileOutputStream.j ava:70)
at iliadpdfscribblemerger.ScribbleMergeForm.copyFile( ScribbleMergeForm.java:701)
at iliadpdfscribblemerger.ScribbleMergeForm.btnMergeA ctionPerformed(ScribbleMergeForm.java:688)
Maybe you are not creating/deleting directories in a platform independent manner? I don't know much about how this works in Java...