improve handling + construction of shell arguments

[kevinushey]

This PR does a few things:

1. Fixes the handling of potentially nested lists-of-lists when passed to a shell arguments builder,
2. Ensures that alternate format characters (e.g. %i) are handled,
3. Implicitly discards any inputs containing NULLs (making it easier to just pass through potentially missing arguments, cleaning up a few call sites)