Remove data from linked items when removing data from indexset items

[glatterf42]

message_ix.Scenario.remove_set() expects that when an element from an IndexSet is removed, all corresponding keys from other optimization items (i.e. keys that contain this element from items linked the IndexSet) are also removed (because otherwise, the linked items would contain invalid data). This PR adds the functionality to provide the same behavior.

However, since I'm not a big of silently doing stuff in the background, our version of this comes with a flag to disable it. The default for this is True right now, i.e. to remove related data, but this is mainly because the function will for now mostly be called from message_ix, which needs this default. I'm happy to swap the default to False and have the shim layer request True every time it needs it if you think that's better.

The PR includes some preparatory cleanups and notes.

[codecov]

Codecov Report

Attention: Patch coverage is 95.28302% with 5 lines in your changes missing coverage. Please review.

Project coverage is 88.7%. Comparing base (73e7900) to head (1323f3d).

Files with missing lines	Patch %	Lines
ixmp4/data/api/optimization/equation.py	80.0%	1 Missing ⚠️
ixmp4/data/api/optimization/variable.py	80.0%	1 Missing ⚠️
ixmp4/data/db/optimization/equation/repository.py	94.1%	1 Missing ⚠️
ixmp4/data/db/optimization/indexset/repository.py	97.4%	1 Missing ⚠️
ixmp4/data/db/optimization/variable/repository.py	94.1%	1 Missing ⚠️

Additional details and impacted files

@@                             Coverage Diff                             @@
##           enh/handle-empty-optimization-data-addition    #171   +/-   ##
===========================================================================
  Coverage                                         88.6%   88.7%           
===========================================================================
  Files                                              223     223           
  Lines                                             8210    8284   +74     
===========================================================================
+ Hits                                              7282    7351   +69     
- Misses                                             928     933    +5     

Files with missing lines	Coverage Δ
ixmp4/core/optimization/equation.py	93.3% <100.0%> (ø)
ixmp4/core/optimization/indexset.py	91.9% <ø> (ø)
ixmp4/core/optimization/variable.py	93.4% <100.0%> (ø)
ixmp4/data/abstract/optimization/equation.py	97.1% <100.0%> (ø)
ixmp4/data/abstract/optimization/indexset.py	96.5% <ø> (ø)
ixmp4/data/abstract/optimization/variable.py	97.1% <100.0%> (ø)
ixmp4/data/api/optimization/indexset.py	97.8% <100.0%> (ø)
ixmp4/data/db/optimization/base.py	100.0% <100.0%> (ø)
ixmp4/data/db/optimization/equation/model.py	100.0% <ø> (ø)
ixmp4/data/db/optimization/parameter/model.py	97.4% <100.0%> (ø)
... and 11 more

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