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Weird %SystemDrive% directories


On my home machine, setup keeps creating subdirectory trees when installing certain packages, like:
/E/cygwin/%SystemDrive%/Dokumente und Einstellungen/towo/Anwendungsdaten/Microsoft/SystemCertificates/My/Certificates
/E/cygwin/%SystemDrive%/Dokumente und Einstellungen/towo/Anwendungsdaten/Microsoft/SystemCertificates/My/CRLs
/E/cygwin/%SystemDrive%/Dokumente und Einstellungen/towo/Anwendungsdaten/Microsoft/SystemCertificates/My/CTLs

(I had mentioned this before in a side note, http://www.cygwin.com/ml/cygwin-apps/2009-11/msg00041.html,
but didn't follow up so far because it's not really harmful.)

By the names, my guess was it's somehow related to access rights handling, maybe ACLs.
This is on a FAT drive (USB-connected) on Windows XP home.

I have now noticed that there are a few more directory trees of the same name and structure, in:
/lib (i.e. /E/cygwin/lib)
/bin
/usr/share/terminfo/* (in every subdirectory)
/... (one more, don't remember)

and this seems to correlate with those directories in which 
chmod is applied to some files during postinstall.

Does that give a clue on the cause?

------
Thomas


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