Update all notebooks and projects, add CI testing

[bdice]

This is a large PR that overhauls the entire signac-examples repo to bring it a little more up to date with signac's current structure. I sought out to enable CI testing for the notebooks and projects in this repo. However, the notebook syntax and project files were very out of date and inconsistent with modern Python / signac usage. For example, there were numerous references to the glotzerlab conda channel and a ton of Jupyter notebook "magic" syntax that is no longer valid, as well as example projects that still used operations.py and had an old-style project.py -- most of the code was not runnable and failed the flow-test script.

There is a still a lot of cleanup to do, specifically removing examples for features that we plan to deprecate and remove in signac 2.0, and modernizing specific projects (e.g. HOOMD, GROMACS, Quantum Espresso). Regardless, I think this is a good start.

I don't think it's worth the signac team's time to review the code changes in this PR in the form of a diff -- in spirit, the code is all the same. I am tagging @glotzerlab/signac-committers for awareness but not requesting reviewers. The diffs are massive because I applied some reformatting (the code style was super inconsistent) and all sorts of other miscellaneous improvements as well as adding the new CI scripts. I would be happy to give a short overview of this effort in a future dev meeting but I plan to merge this PR in its current state after a few days (to allow discussion), and perform all further changes incrementally.

I will also help rebase #14 and #15 over this set of changes. This PR supersedes #9 -- thanks again to @CryoZEUS for his initial efforts on getting this started!

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[csadorf]

@bdice Thank you for the effort. From my side it's fine to merge this without review, I trust your judgement.