Add H5 event writer, random fixes

This was supposed to be adding an output format, but I got a bit distracted and did a few things

• Add a writer for EventInfo to HDF5.
  • Make this optional.
• Fix the metadata cache, was broken for a while.
  • Add a unit test that requires a second run with the cache enabled to finish in under 30 seconds.
• Some cleanup around the unit tests: consolidate common options.
• Rework how command line options are written to config flags and override configuration settings. Now command line options must be explicitly configured to override a configuration file option. If they do override a config file option, bool arguments must be explicit. If they don't the config option can't exist.
• Tell the argument parser to parse the yaml configuration file immediately, rather than forwarding the full path on to later code.