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Drill >> mail # dev >> Directory cleanup & DRILL-165

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Directory cleanup & DRILL-165
I'd like to do DRILL-165 soon.  This has us cleaning up the directories and
moving the prototype directory down to the base directory.  This means all
patches merged post the move will need to be rebased.  There are a couple
of function patches outstanding but rebasing those shouldn't be very
difficult for the respective contributors.  Are there any patches
outstanding that people think should be merged before I do the directory
cleanup/move.  Note, my goal on this commit is to only moves so that Git
does the best possible job of managing a file's history.

Let me know your thoughts.