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In the Linux FSS, they talk about /,/usr,/usr/local like this: * / is for programs that are required to boot the system to its normal multi-user mode. Nominally, these would be statically-linked programs to remove a dependence on the shared library system being operational. * /usr is for other standard user-level programs installed with the OS (or official packages) and is normally built with shared libraries. * /usr/local is for programs that are installed only on that machine (i.e. not part of the "standard" package). I recall that there is a minimum set of "expected" commands in /bin (like ls, cp, sh, etc) but since cygwin isn't involved in booting most of its software belongs in /usr. /usr/local should never be touched (except maybe to set up an empty directory structure) by the standard installer.
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