Polish tools module

[kysrpex]

• General polish and revision of tools (including semantic2dot)

• semantic2dot: allow plotting namespaces, sessions and individuals on the same graph

• semantic2dot: add IPython rendering

Note that find is meant to replace the CUDS selection mechanism. For example, imagine that you need to move individual freiburg and all the "contained" individuals (inhabitants, buildings, etc) in the mereotopological sense. Then first you get the list of individuals to move using individuals = find(freiburg, rel=city.encloses). After that, you add them to the new session using session.add(individuals).

[kysrpex]

@pablo-de-andres @yoavnash Just fixed the branch for proper readability during review.