Removed refs to toc and map mods (amended#2)
Don't put lib in .gitignore
Working on moving out project data from sys config (check point)
Fix a few bugs in tools.py

There were several cases where terminal() was called, but now that those
functions have been moved to be methods of the Tools class,
self.terminal() should be called instead.
Various bugfixes

This commit fixes all the places where the PyDev plugin for Eclipse
could find mistakes, e.g. "undefined variable" errors. Usually they were
the cause of previous refactoring: such-and-such a function had been
renamed, or moved into class XYZ, but one or two cases of calling that
function hadn't been updated. Those should be fixed now.
Working on moving out project data from sys config (check point #2)
Working on moving out project data from sys config (check point #3)
Continue to get add group to work