Fix precedence of commandline options and yaml options

[mvdbeek]

commandline options should take precedence over options specied in yaml
file, but default values should be used if options are not set in yaml
file. Fixes #180

[natefoo]

This looks like an issue with bioblend?

[martenson]

Just hit this again. What is more confusing is that the docs describe the default (True) as related to skipping. Which seems to be just a confusing error.

--skip-install-resolver-dependencies, --skip_install_resolver_dependencies
Skip installing tool dependencies through resolver (e.g. conda). Will be ignored on galaxy releases older than 16.07. Can be overwritten on a per-tool basis in the tools file

Default: True

[martenson]

docs rebuild does not update it, our docs generation logic maybe cannot make sense of two args storing in the same var in this way

https://github.com/galaxyproject/ephemeris/blob/d60bea5485f89f592da77eb22b31b10a3eccc21e/src/ephemeris/shed_tools_args.py#L136C1-L152C10