On Jun 22, 2016, at 12:40 PM, Zube <z...@stat.colostate.edu> wrote:
> 
> 1) putty will not execute.  Error is "Access is denied”.

Is it getting the +x permission for your user or one of its groups?  Windows 
requires this just as Unix does.

Post the getfacl and icalcs output for putty.exe if you think it’s correct.

> 2) Examining the permissions on putty.exe, the first thing that
> comes up is an error that reads:
> 
> "The permissions on putty.exe are incorrectly ordered, which may
> cause some entries to be ineffective.”

That’s Explorer saying that, not Cygwin, right?  Let Explorer fix it.

> The permissions are odd.

If it doesn’t need any Windows-specific permissions, you can strip all 
non-Cygwin/POSIX permissions:

   $ setfacl -kb putty.exe
   $ chmod +x putty.exe

Do it in that order.  (The second command may not work or may do strange things 
if you do it before stripping the non-POSIX permissions.)

If that still fails, setfacl -kb the directory you’re doing this in, but only 
if it’s a directory that only Cygwin uses.  Otherwise, you risk breaking some 
ACL Windows or a native Windows program depends on.

> If I use a browser to download the file or a different version of wget
> (e.g. https://eternallybored.org/misc/wget/) and drop putty.exe in
> the same directory, there are no issues.

Yes, Windows seems to set the +x permission the way some people use table salt.

> It also doesn't matter where
> the file is dropped.

Oh, that might not be true.  Windows’ permission inheritance model can result 
in the destination mattering.  What you mean to say is, you have yet to find a 
target directory where the results are different. :)

This may not be a wget problem.  cygwin1.dll is becoming more POSIX-compliant 
in its permission handling lately.
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