Move from debug to release, since cl (VC++) does weird things with proxy objects for vectors

Resolves #43

Use README.md

also remove tree_cursor and other unused code since we don't use it

Finished first version of codebase guide. Changed format of some code comments so that doxygen recognizes them.

Added short text on the problem domain based on Prof. Stamatakis' introduction, a short description on how to use terraphast, and further structurization of the remaining README sections.