So I take it that compiling other applications with fink install doesn't ever call anything specific in /usr/X11R6/ that could be broken by swapping the Apple and XonX X11 installs?
Actually, it could break things, and if you're going to switch back and forth between Apple X11 and XFree86 4.3 make sure you always build stuff ('fink install') while Apple X11 is enabled, or else your stuff won't run right. Apple's X11 is based on XFree86 4.2.1, and you can't run binaries built against 4.3 on 4.2.1.
:)
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