Fixes #2 - Update .gitignore and bootstrap.sh (No clobber config.h.in)

Updated .gitignore to ignore most of the autotools crap, if not all of it.

Additionally, updated bootstrap.sh so that autoheader is not called (The default
config.h is full of crap and not wanted)

Lastly, acx_pthread.m4 updated to no longer use deprecated macros
Fixes #2 - Reverted acx_pthread.m4, no longer call autoheader

On ubuntu (autoconf 2.68, automake 1.12.4, the new, non-deprecated autoconf LANG
macros would not work correctly, PTHREAD_LIBS/PTHREAD_CFLAGS were not being set
correctly.

I'm sure that this macro is workable with non-deprecated stuff, but I was not
able to make a workable solution.

I've reverted it to get past the linker errors encountered.
Fixes #2 - Use --add-missing rather than -a, remove -Wno-extra-portability
Merge pull request #2 from caitp/issue-2

[repo] config.h.in shouldn't be gitignored