Create README.md

Currently empty.
Updating README.md
Formatting README.
Added build instructions to README.
Merge branch 'master' into ReactionFactory
Adding real antioch.m4 since we don't have svn:externals anymore.
Common stuff for Doxygen since we don't have svn:externals anymore.
lcov and license header tools since we don't have svn:externals anymore.
Added .gitignore.
m4 files required for configure since we don't have svn:externals anymore.
Merge branch 'master' into ReactionFactory