Update .gitignore and remove some generated files

Added all the files that were generated (for me, with this config) by
autogen.
Cherrypick .gitignore from branch 'problem-pt'

Conflicts:
	.gitignore
	config/configure.ac_scripts/user_drivers.dir_list
	config/configure.ac_scripts/user_drivers.dir_list.backup
Added fig2poly binary to gitignore