Update precompilation input deck to reflect updated collisions options.

[mrhardman]

Changes to the precompile_run.jl file to make sure collisions and geometric features are available in the moment_kinetics.so.

Also update some example files with the new timestepping options. Query whether or not the example input files still contain redundant flags.

[johnomotani]

The documentation-build failure has appeared since yesterday (the corresponding job ran fine on master yesterday). The CI runners have switched from julia-10.2 to julia-10.3 in that time, but I've just tested a clean install with julia-10.3 on my laptop and I can build the docs fine. Not sure what's going on here, might be worth just waiting a few days and re-running the job to see if it fixes itself.