manually apply --sysroot to configuration

The previous chroot-based sysroot often broke due to glibc's delayed loading for much of its functionality when the sysroot did not contain compatible copies of the necessary libraries.

This approach instead manually prepends the sysroot to all configuration paths.

BREAKING CHANGE: targets to -U are no longer interpreted relative to sysroot

Signed-off-by: Andrew Gregory andrew.gregory.8@gmail.com