Enable container-mapping tool by default

[sethRait]

Enables the container-mapping tool to run by default, along with the following changes:

• Deprecates the "includeTools" input, as "container-mapping" was the only possible value so it is now irrelevant.
• Deprecates the "command" input as the only two relevant values of "all" and "run" have the same effect.
• Small refactor and removal of unused code.