[DOCS] updates to the tools section.
Merge pull request #82 from roryk/master

Added iPython interaction, speeded up merging/loading steps.
[DOCS] loading with LSF and SGE.  Cheers to @roryk and @chapmanb.
stash
merge conflicts
minor doc tweak
Update tools.rst

typo
Swapped ipython loading to use the piping command.

Also some code cleanup. Moving comments to appropriate place.
Removal of unused functions.
Added PBS support.