Add before-afterScript warning regarding containers

[Kibubu]

before and afterScript directives are not executed inside the specified process container by design.

This behavior is not intuitive and will be fixed with prolog and epilog directives once implemented #540

Added a warning for the time being

Signed-off-by: Kirill Bulert [email protected]

[bentsherman]

One correction, the beforeScript and afterScript aren't run in the same environment as nextflow, they are run in the task environment but outside the container. "Host environment" would be more accurate.

[pditommaso]

Thanks for this improvement to the docs. This is actually very useful. Just suggested a minor improvement

[Kibubu]

using note instead of warning is reasonable, I was just salty because my host's ~/.gitconfig got modified and I did not expect that at all.

[pditommaso]

Thanks