Update README.md
Update README.md

Added directions for mac directory structure
Merge branch 'development'

Conflicts:
	README.md
added warning in Readme
added begin/end free-response
added section about philosophy
fixed mis-spellings
trying to get this up-to-date
preambleinput is no more!

Long live input/masterinput
preamble input is now gone!
added variable label sep and several new environments
not sure what changed...
Changed free-response so that the "answer" shows.

Currently maxtrix answer does not do this... matrix answer may need to be a verbatim environment.
labels involving problems don't seem to work quite right...
fixed readme as per oscar's suggestions
made some changes - this may be totally correct
added headers for long documents
working on section numbering
section headings/numbers work
matrix-answer needs work