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As discussed at http://www.netbeans.org/servlets/ReadMsg?msgId=735498&listName=nbdev the MDR btree storage would profit from using memory mapped file instead of random access one. By doing that all occurences of byte[] would be replaced by ByteBuffer and the MDRCache which keeps some Pages in memory could be deleted as that kind of caching would be handled by operating system itself. It is understood that btree storage is kind of code that nobody wants to touch and that is the reason this is just advice, but it is expected that it will become request for some future release.
I should clarify that the b-tree is a code that noone wants to touch at this point of time (not generally) such a short time before the feature freeze with low resources on the team and so many other tasks with a higher priority, with uncertain (performance) outcomes of such a rewrite. I am not sure why this is a defect. At this point it seems to me more like a hypothesis (RFE/TASK?).
Note: By using mmap instead of RandomAccessFile, you also save a file descriptor (at least on linux), so you won't run out of them on large number of opened projects (like nbbuild/misc).
We prototyped usage of java.nio by the b-tree and decided to not switch. See issue 50085 for more info.