Cleaning up!

Moved things into lib and bin directories
More refactoring

Removed classes from the main "executables"
Finished dosurvey and populate

Updated the example file too
Refactored evolve
Updated docfiles
Fixing docs
Extended path length in ne2001
Removed dependence upon getpath!!!
Removed getpath reliance, updated compile instructions
More updates to make scripts/remove old makefiles
Merge branch 'refactoring' into develop

I've finished the major refactoring work on the code, seems to work ok --- therefore, committing to the develop branch