Tweaks to README and CITATION

Added some badges and moved some things around in README.
Run apt-get update in Travis

As suggested in https://github.com/travis-ci/travis-ci/issues/2124
Removed version badge and fix doi badge

It was lagging too much and not showing. Forgot the doi- string in doi
badge
Tweaks to bench mark code

Minor changes to the Makefile and remove the result kept. It's useless.
Added a simple Makefile to automate some tasks
Merge branch 'master' into speedup
Benchmarking more similar to topo correction
Merge branch 'master' into speedup