On Nov 11, 2014, at 5:47 AM, Habermann, David (D) <dahaberm...@dow.com> wrote:

> I also like having everything stored under one main directory (c:\cygwin) for 
> ease of backup

Why would you back up all of c:\cygwin?  Most of it is downloaded from the 
Internet, and this is easily reinstalled from your cached download.  (I’m 
assuming you keep setup.exe and its download tree on a network drive somewhere.)

My starting point for backup on Unix boxes is to exclude everything except 
/etc, /home and /usr/local.  Then maybe add a few choice things under /var.  
Everything else can be reinstalled.

Since I’m already cherry-picking what to back up, it doesn’t matter to me that 
/home might be somewhere physically different than /usr.

c:\Users should be part of your backups anyway.

> and ease of identification of all cygwin-involved files for our virus and our 
> application whitelisting systems.

Do you really have executables in $HOME/bin that won’t run unless whitelisted?  
Does your security software actually ban programs in %HOMEPATH%?

I can see the need to smack the AV with a clue-bat occasionally for some things 
under /usr, if only to address false positives.
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