Fix documentation warnings #395
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I think some changes introduced in #350 resulted in various new documentation warnings being raised, possibly (but I don't think entirely) related to the version bump for sphinx, as I'm not sure why I didn't see them sooner.
This resolves two types of warning e.g.:
WARNING: py:class reference target not found: Dynamics [ref.class], requiring changes/updates to the nitpick ignore, as we have in the pastWARNING: duplicate object description of janus_core.calculations.phonons.Phonons.write_force_constants, other instance in apidoc/janus_core, use :no-index: for one of them. In most cases, these are class methods, which we already document slightly inconsistently, so for now I've just removed them. Other solutions are probably available (e.g. the suggestion from the warning)