cc: @valsson

cc: @gtribello

makes signatures available in notebooks

I also added a function in order to avoid too many line changes
for intentation

The used modules were not detected correctly on travis probably due to
some settings for the cd option. This was harmless since the list of used
modules was not checked indeed.

required fixing some incorrect escape sequence in plumedcheck

closing files to avoid too many open files

Fixes #493