Fix the INSTALL documentation

I accidentally muddled the compile/install documentation with a previous
commit. I didn't realize there was a separate INSTALL-FROM-GIT file and
mistakenly updated INSTALL. To remedy this I updated README.md to
include the compile from git instructions. README is the instructions
for the tarball source. Also, I updated the root Makefile so that README.md
will not end up in the `make dist` tarball.
Merge pull request #13 from lab11/configure-merge

Updated configure to check for more dependencies
Merge pull request #14 from lab11/install-fix

Fix the INSTALL documentation
Updaing configure files to automake 1.12+

.in files are deprecated, so are a couple of macros. Functionality
should be the same.