It's not clear to me what a complete install of cygwin will do to things I've already installed either.
Nothing. Cygwin installs some files (completely within its own directory hierarchy), and adds something like 4 registry entries. See the Cygwin FAQ on uninstallation to see what Cygwin injects into your system. There's hardly anything, which is why uninstallation can be done by hand following a brief set of steps in the FAQ.
-- Keith
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