Overhaul the pipeline configuration logic by collapsing all dynamic
configuration options, both for analyses and pipes into a single
dictionary. Change all the interfaces so that there is no longer
distinction between the configuration of an analysis and of pipes.
Expose these options to the command line via `--{name}-configuration`
options for each pipe/analysis that is applicable to the command-line
invocation.
Add categories in the pipeline, allow an artifact to have a category
specified which allows it to be shown or hidden by default. Adapt the
CLI tools to hide artifacts of the category that don't
`show_by_default=True`.
Fix the code that handles setting the `--format`, `--tar` and `--yaml`
command line options, which incorrectly wrote to the `format` kwargs
instead of the `container_format` one.
Add the functionality the the pipeline infrastructure and CLI to run
individual pipe and analyses as subcommands instead of in-process. This
allow better debuggability of individual pipes.
Giacomo Vercesi