This shows how to allow to store Configuration objects outside of the main store file.
It extends the storage with a list of external files that is used to store coordinates of frames.
The current examples implementation can only use Configurations and not momenta. This is due to the fact that mdtraj (which I use to implement reading of external MD trajectories does not support velocities for reading, it can be used for writing I think). I presume to be compatible across several formats.

I am still looking for a way to read velocities for say .trr files. This problem is independent of the current implementation and will only make it accessible for the use with Gromacs, etc...

Implementation

The external way works the following.

1. Keep the internal way to store configurations and rename it to storage.intconf.
2. Create a new store storeage.extconf that only referenes an ExternalFile
3. Create a new store storage.mdfiles that keeps track of external files so that we do not have to store the file everytime we reuse the same file.
4. The storage.configuration will work exactly as before, if you do save normally. Hence it is completely backwards compatible and there is not problem with using cvs.
5. There is a new storage.configuration that replaces the old one and stores a reference to intconf and extconf. This allows to store a configuration internally or externally or both!
6. The are a few additional functions
   i. storage.configuraion.save_as_external(mdfile, frame) which stores a configuration which is already saved as a frame in an mdtraj readable file. This takes only the file and a frame.
   ii. storage.configuration.persist(idx) will copy (if necessary) the externally stored configuration to the internal store and references the internal for faster access. This means you can store everything in the main file if you wanted to.

This PR is based on PR #385 and #391.