Add support for --bindir and remember the relative locations of bindir and libdir vs prefix (ie: sysroot)

Potential downsides:
 - right now adds a build dependency on `realpath`, which I'm not sure everyone has, to determine relative directories. It's possible we could substitute something else if this matters.

Upsides:
 - `--libdir` now avoids breaking things at runtime if it isn't in one of the expected locations
 - config diff between windows and everyone else is now confined to the configure script.
I think this came up for BSD-related platforms at some point, but I sadly don't recall the specifics. @brson, do you remember?