Pass through flags to sub-commands

[CurtisL]

In a8cc4b9 I I introduced a hot-fix to hard-code --skip-plugins flags for many of the sub-commands.

We should consider what commands need to be spun up in a new thread vs what commands can run in the current command environment. In the top level wp project commands, pass through any flags to sub-commands running in a new thread where it makes sense. (--skip-wordpress wouldn't make sense in sub commands relating to core for example)

This way if there is the need to skip plugins, or skip themes, the main command will pass them through to the individual sub-commands.