>> 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.)

I do something similar to you, and the backup isn't the big issue (although I 
do have MANY locally compiled programs here).  C:\Users is backed up by the 
corporation, so I either have to duplicate the backup or do multiple recoveries 
from different backup systems to get it all back...that is why I prefer 
c:\cygwin\home

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.

>> 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%?

In our corporate environment, ALL programs (exe, dll, bat, shells and numerous 
others) on ALL PATHS must be on a corporate-enforced whitelist before they will 
run at all.  Typically even new versions must be whitelisted, although I've 
been able to negotiate a folder-and-workstation-specific blanket approval.  I'd 
like to suggest that we be sensitive to application whitelisting systems, as 
many corporations are moving in that direction (as it nearly eliminates virus 
problems altogether)....and yes, working in such an environment is a true PITA.

Also, in general I simply don't like mixing my corporate files (Office 
software, etc.) with my cygwin files.  They are unrelated and so I like to keep 
them separate.  Perhaps it is a personal preference, but it is an option I 
wouldn't want to lose....it would probably force me back to using the passwd 
file instead of the db.


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