can now save toutatis files correctly

toutatis distributions has a 7th line of zeros
now can read both correctly

if merging files with differing length of arrays, assume
that the shorter one lost all beam

close buffer in case trying to save file multiple times..

new function which saves the density data into a HDF5 file format
useful after e.g. combining multiple data..

seems number of header lines vary..

many more of the options are added

in dst and plt
also cosmetic changes (spaces, ordering)

dictionary return now excludes lost particles
this was essential for the twiss calculation apparently

calc_avg and calc_sigma had some errors, apologies

 - added more stuff for dictionary type behaviour
 - added save functionality (Thanks Ryoichi!)
in plt class:
 - more goodies added

some minor fixes

added template scripts for submitting tracewin
error study to condor