Recursive merge configs

[anders-kiaer]

User can now have a base configuration file, and also provide an optional configuration file which will be merged into the base configuration.

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Contributor checklist

• 🎉 This PR closes Some easy way of overriding or merging configurations? #142 and closes Let user define "base config" and optionally a config to merge to into base config. #168.
• 📜 I have broken down my PR into the following tasks:
  • Add a function that recusrively merges dictionaries down to leaves (then being non-dictionaries)
  • Change config parser of AHM and pred to support base and (optional) update config.
  • Add optional update config in commandline entrypoints.
  • Add unit test.
• 🤖 I have added tests, or extended existing tests, to cover any new features or bugs fixed in this PR.
• 📖 I have considered adding a new entry in CHANGELOG.md.
• 📚 I have considered updating the documentation (command line help is updated).

[wouterjdb]

LGTM 🚀