Add allowed_directories to the filesystem config

[rumpl]

By default cagent adds the current working directory.

Note: The "add current working directory by default" is not great IMO, so please hold on merging this one. What I think would be best is:

if no allowed_directories defined, we add the current working directory
if allowed_directories is defined, we use that and don't add the CWD.

This would mean that we need to give a way for the user to also add the CWD to the list of allowed directories, so we need to use our scripiting engine for the user to be able to add ${env.PWD} for example.