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Overhaul our dependancy management
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Description

We should only use system python where we have to and then isolate stuff in venvs.

We should also consider adding proper on-system tracking of outdated dependencies.

The debian bundled pip is also a pain to update and old although when using system python we should consider using debian packages and puppet's require_package function. (This is only Flask).

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We also can note we don't need certbot etc anymore.