Run aclocal, autoconf, automake before configure.

This solves problems on Mac OS X, where `configure` fails
with complaints about versions of aclocal, autoconf, automake
that do not exist.

Tested on Mac OS X Mountain Lion, Homebrew 0.9.4, apple-gcc42.
Rerun aclocal, autoconf, automake to more recent versions.

$ rm missing
$ aclocal
$ autoconf
$ automake --add-missing
Add .gitignore.
Added flag in install_deps.sh to allow running autotools.