let user specify if they want command to be run in shell-mode

[ericls]

This is a follow up to #1217 in v2.

In v2, things are easier because there's an explicit shell-mode. This makes this change easier to implement and won't cause backwards incompitable changes for existing configs.

Makes something like the following possible:

Without this option, scripts like this would fail for reason like:

bash: This: command not found

Would improve #808

closes #1217

[mbecker20]

Thanks will review

[ericls]

Thanks will review

Thanks for Komodo.
V2 has been fantastic!