Store executed versions of notebooks

[ketch]

Currently we are storing notebooks with all output removed. I think we should instead store fully-executed notebooks.

Advantages:

• Anyone viewing the notebook on github will see the output (including images and JSAnimations) without having to download and run the notebook
• Currently we keep a second copy of most notebooks, executed, as a gist. Duplication is evil! Even moreso for notebooks, since they are harder to diff. This will avoid it.
• We could include a watermark cell in each notebook, showing the version of Clawpack (and other libraries) that it was last executed with. This would be a nice solution to #55.

Disadvantages:

• Bigger files. But I don't think they'll be huge, and I think it's okay for an 'apps' repository to be fairly heavy.
• Output like images and animations may change and can't reasonably be diffed. Again, I think this is okay. Its only effect is to create large sections of unparseable stuff in the diffs, and I believe that's worth it.

[rjleveque]

This is an old issue, but I just came across it again and I would strongly advocate to keep output out of the commits. Some geoclaw notebooks with multiple animations are big and all that output changes when you rerun it so I think it's a mess to version control it, and hard to see when doing git diff whether anything changed in the inputs.

Recently I've been using the new notebooks/Makefile to create html versions and then this script to copy the desired ones to the gallery of notebooks