Fix support for multiple config files and README/install updates
format several files, delete script
Delete dox files

Dox files in doc directory are no longer needed as we have an extensive tutorial coming up soon.
Also, a test was not deleting a file.
added clean and uninstall make targets

added clean targets in all Makefiles
for tests/Makefile, replaced "rm -f obj/* bin/*" by "rm -rf obj bin"
added uninstall target in main Makefile