[AN-385] Move listRuntimes over to new Sam permissions model - take 2

[LizBaldo]

Reverts #4823

JIRA ticket: https://broadworkbench.atlassian.net/browse/AN-385

This change was originally reverted, because it removed the ability to list deleted runtimes, which AOU RWB was making use of. See https://docs.google.com/document/d/1uivQxiSoFAyD7vpmFxes5037Dn1m0yx8VovsonylKYw/edit?tab=t.0#heading=h.mf724qma605n

Now that we confirmed that RWB can default to default settings instead of the user’s prior configurations, we can move forward with this PR again, with some added modifications to the swagger page to deprecate the isDeleted flag.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.62%. Comparing base (1a00c81) to head (8ebc867).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4827      +/-   ##
===========================================
- Coverage    74.77%   74.62%   -0.16%     
===========================================
  Files          166      166              
  Lines        14800    14690     -110     
  Branches      1112     1158      +46     
===========================================
- Hits         11067    10962     -105     
+ Misses        3733     3728       -5     

Files with missing lines	Coverage Δ
...orkbench/leonardo/db/RuntimeServiceDbQueries.scala	96.69% <100.00%> (+0.37%)	⬆️
...rkbench/leonardo/http/AppDependenciesBuilder.scala	97.87% <ø> (-0.02%)	⬇️
...h/leonardo/http/service/RuntimeServiceInterp.scala	91.73% <100.00%> (+0.19%)	⬆️
...leonardo/http/service/RuntimeV2ServiceInterp.scala	95.45% <100.00%> (-0.68%)	⬇️

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