Programs can now build independently.
Remove trailing whitespace.
Simplify main CMakeLists.
Many improvements to the build and packaging system.  Abandoned CPack due to annoyances such as a five-year old bug.
Update scripts to use results directory.
Customizable log directory.
Minor submit script cleanup.
Major readme update, still a WIP.
Readme touchup.
Clean up and document submit script.
Fix typo.
Add note to readme.
Clean up and document CMakeLists.
Update license year.
Add note to readme.
Fix typo.
Update readme.
Merge branch 'master' into new_urqmd

Conflicts:
	lib/urqmd/CMakeLists.txt
	lib/urqmd/src/CMakeLists.txt