Well  I'm glad we followed Mr. S. Holmes dictum which I'll paraphrase... 
eliminate the impossible and what remains, even if it seems improbable, 
must hold.

BTW - you may want to look at  mmclone.  Personally, I find the doc and 
terminology confusing, but mmclone was designed to efficiently store 
copies and near-copies of large (virtual machine) images.  Uses 
copy-on-write strategy, similar to GPFS snapshots, but at a file by file 
granularity.

BBTW - we fixed directories - they can now be huge (up to about 2^30 
files) and automagically, efficiently grow and shrink in size.  Also small 
directories can be stored efficiently in the inode.  The last major 
improvement was just a few years ago.  Before that they could be huge, but 
would never shrink. 



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