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According to pobox@verysmall.org on 1/22/2006 2:13 PM:
It seems to me that the cygwin packages are installed in different
locations than the locations they would go if ./compile make make
install are performed on the source.
Yes, many packages default to an installation prefix of /usr/local if no
options were given to ./configure, while cygwin packages intentionally
override this with ./configure --prefix=/usr. This distinction is
recommended by the FHS (http://www.pathname.com/fhs/) so that you can
compile local updates of your favorite programs to /usr/local/bin without
overwriting the shipped system programs in /usr/bin. But if you use
setup.exe to grab the sources, every one of those src tarballs should come
with directions (and usually with a script) that tells you exactly which
options were passed to ./configure when building the official cygwin
release of that package.