building cygwin: bug and question

[Marco Atzeri <marco_atzeri at yahoo dot it>]

Hi,

bug first:
I noticed that running "make clean" in the build directory
also remove

winsup/cygwin/tlsoffsets.h
winsup/cygwin/devices.cc

from the source directory.


Question:
building cygwin with a simple
configure; make; make install prefix=/installation_dir/usr

produce a directory structure

./usr
./usr/bin
./usr/etc
./usr/etc/defaults
./usr/etc/defaults/etc
./usr/i686-pc-cygwin
./usr/i686-pc-cygwin/bin
./usr/i686-pc-cygwin/include
./usr/i686-pc-cygwin/include/arpa
./usr/i686-pc-cygwin/include/asm
./usr/i686-pc-cygwin/include/attr
./usr/i686-pc-cygwin/include/bits
./usr/i686-pc-cygwin/include/cygwin
./usr/i686-pc-cygwin/include/machine
./usr/i686-pc-cygwin/include/mingw
./usr/i686-pc-cygwin/include/mingw/sys
./usr/i686-pc-cygwin/include/net
./usr/i686-pc-cygwin/include/netinet
./usr/i686-pc-cygwin/include/rpc
./usr/i686-pc-cygwin/include/sys
./usr/i686-pc-cygwin/include/w32api
./usr/i686-pc-cygwin/include/w32api/ddk
./usr/i686-pc-cygwin/include/w32api/gdiplus
./usr/i686-pc-cygwin/include/w32api/GL
./usr/i686-pc-cygwin/lib
./usr/i686-pc-cygwin/lib/mingw
./usr/i686-pc-cygwin/lib/w32api
./usr/i686-pc-cygwin/share
./usr/i686-pc-cygwin/share/doc
./usr/i686-pc-cygwin/share/doc/mingw-runtime
./usr/sbin
./usr/share
./usr/share/doc
./usr/share/doc/Cygwin
./usr/share/info
./usr/share/man
./usr/share/man/man2
./usr/share/man/man3
./usr/share/man/man5
./usr/share/man/man7
./usr/share/man/manmingw

different from cygwin snapshots and releases

./etc
./etc/defaults
./etc/defaults/etc
./usr
./usr/bin
./usr/include
./usr/include/arpa
./usr/include/asm
./usr/include/attr
./usr/include/bits
./usr/include/cygwin
./usr/include/machine
./usr/include/net
./usr/include/netinet
./usr/include/rpc
./usr/include/sys
./usr/lib
./usr/sbin
./usr/share
./usr/share/doc
./usr/share/doc/Cygwin

How should I configure ? 
I found nothing on the source documentation

Marco