fix a series of issues with recent graph tool versions

[javispedro]

This series of patches fix some bugs (no new features):

• running setup.py install did not install the pmlab.log_ts module (which contains some functions to mine transition systems from logs).
• importing pmlab.* did not import the log_ts module nor many others
• cannot pickle TransitionSystem or PetriNet instances (and therefore cannot use e.g. python multiprocessing) because some maps were storing graph_tool Vertex objects. Fix by storing vertex indices, which do not change either.
• when writing a pnml file, ensure dummy transitions have no name; this will ensure they appear as silent transitions in many importers.