Merge pull request #11 from marcvinyals/tests

Add tests for neq
a stub of the tool to apply substitutions to dimacs formulas
The CNF object do not store comments between clauses anymore.

This simplifies the code and  make some formula manipulation even more
streamlined.
Now the code can do clause transformation and parsing of a dimacs file
directly in the compressed format of clauses.
Tool that transform dimacs formula from the command line
Fix a line in the command line help.
Removing the obsolete dimacsshuffle
Working on the cnfgen documentation.
Work on documentation
PHP, Tseitin and Ordering principle
Graph ordering principle
Pebbling formulas
Documentation for the kclique formula.
Documentation on the Ramsey formulas
Few changes to README.org
License file
Networkx is is documented as a requirements.
Small fix in docstring
Merge remote-tracking branch 'massimo/master' into master2

Conflicts:
	kth2dimacs.py
	reshuffle.py