Deprecate _InternalCustomUpdater.update, _InternalCustomTuner.tune, and _InternalCustomWriter.write

[joaander]

Description

In a branch off trunk-minor, add deprecation warnings for:

• _InternalCustomUpdater.update.
• _InternalCustomTuner.tune.
• _InternalCustomWriter.write.
• HDF5Log.write.

After this branch is merged, remove these methods in a branch off trunk-major.

Motivation and context

These methods are not logically consistent with the operations model in hoomd. Simulation is responsible for calling the operation's action at the appropriate time during the simulation loop. See #1588 (comment) for additional context.