I will Ondrej and other comment on the config/ change, I think it was necessary to keep them but not sure :)
About using pkg-config usage, does it work smoothly when one installs many versions of the respective library in separate directories? I do that a lot while testing various freetype versions f.e., installed in ~/usr and point configure to it.
i'm fairly certain that's incorrect. here's the files that i punted and where they come from:
config/config.guess: from the GNU config project; snapshots shipped with automake & libtool (this one dates to 2012-04-18)
config/config.sub: same as above
config/depcomp: comes from automake (1.11.x)
config/install-sh: comes from automake (1.11.x)
config/ltmain.sh: comes from libtool (2.4.2)
config/missing: comes from automake (1.11.x)
config/mkinstalldirs: comes from automake (1.11.x)
src/config.hin: generated from configure.ac by autoheader (from autoconf) and often changes based on various autotool related inputs as well as configure.ac
src/install-sh: actually unused (we get it from config/)
src/missing: same as above
src/mkinstalldirs: same as above
so on my system, while i might be running autoconf-2.69, i'm also running gnuconfig-2013.01.11 snapshot, automake-1.13.x, libtool-2.4.2, and gettext-0.18.2. so my local copies of files were constantly in flux as compared to what was checked into the git repo.