Draw a grey square if no exemplar exists
Use new jsmol tools
Remove old tools and outline new script
Add marks to summary map as well

The summary map needs to have marks when something is clicked. This add such
marks as well changes their opacity to be see through. Dots on them are not the
best idea, however, I don't have anything better right now.
Merge branch 'develop' into feature/rewrite-jmoltools
Remove show all button

It isn't really needed right now. I'll do it later if need be.
Handle clearing and highlighting rows

This roughly implements the clear button functionality as well as highlights the
correct rows in the table when needed. Right now the loading message is shown in
the jsmol window but not cleared. This will be cleared up later.
Only show status messages when during requests

We dont' need to display loading or done when we are not making requests. This
commit changes things to work that way. In this case we don't see loading when
we are clearning things.