[WIP] Implement trajectories as folders

[jhprinz]

Almost done. Explanation will come tomorrow...

• [x] much simpler creation of tasks
• [x] better parsing of tasks into scripts
• [x] Trajectories are now folders
• [x] fix run traj
• [x] fix extend
• [x] fix RPC
• [x] update examples

This also contains all of the other changes as well. We will then have full flexibility in the output files of a simulation

[jhprinz]

Well, this is done.

Trajectories are by default folders now. I have also simplified a lot of the API, so have a look at example notebooks 4 and 5 to see how this works.

This does not add capabilities to work with reduced trajectories, but makes this easy to add.

What is tricky with trajectories is to access a file in the traj folder. You can use

traj.file('myfile')

to get the location of this file, so instead of moving with

bash = 'mv %s %s' % (traj_file, target_file)
# new
bash = 'mv %s %s' % (traj.file('output.dcd')', target.file('traj.dcd'))

[jhprinz]

I checked all examples and it should work better. There are also some little bugfixes for the RPC calls.

[jhprinz]

If there are no objections I would merge this.

[franknoe]

Thanks, that looks good to me. Please go ahead.