Attempted fix for SRCDEST/PKGDEST parsing

- Do *not* overwrite the makepkg.conf in the chroot
- Source global makepkg configs for SRCDEST and PKGDEST

Original commit 4bc819a2
by Evangelos Foutras <foutrelis@gmail.com>

Signed-off-by: Aaron Griffin <aaronmgriffin@gmail.com>