[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 includeDeleted flag.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.59%. Comparing base (318fa57) to head (73f8f1a).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4827      +/-   ##
===========================================
- Coverage    74.77%   74.59%   -0.18%     
===========================================
  Files          166      166              
  Lines        14800    14609     -191     
  Branches      1112     1101      -11     
===========================================
- Hits         11067    10898     -169     
+ Misses        3733     3711      -22     

Files with missing lines	Coverage Δ
...ute/dsde/workbench/leonardo/dao/sam/SamUtils.scala	100.00% <100.00%> (ø)
...e/workbench/leonardo/db/DiskServiceDbQueries.scala	100.00% <100.00%> (ø)
...orkbench/leonardo/db/RuntimeServiceDbQueries.scala	96.69% <100.00%> (+0.37%)	⬆️
...rkbench/leonardo/http/AppDependenciesBuilder.scala	97.87% <100.00%> (-0.02%)	⬇️
...bench/leonardo/http/AzureDependenciesBuilder.scala	97.14% <ø> (-0.16%)	⬇️
...rkbench/leonardo/http/GcpDependenciesBuilder.scala	73.14% <ø> (-0.31%)	⬇️
...de/workbench/leonardo/http/api/RuntimeRoutes.scala	91.50% <ø> (+0.59%)	⬆️
...ench/leonardo/http/service/DiskServiceInterp.scala	95.27% <100.00%> (+3.51%)	⬆️
...ch/leonardo/http/service/DiskV2ServiceInterp.scala	97.22% <100.00%> (+4.76%)	⬆️
...ch/leonardo/http/service/LeoAppServiceInterp.scala	87.34% <ø> (-0.04%)	⬇️
... and 4 more

... and 1 file with indirect coverage changes

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[LizBaldo]

Testing is looking good on my BEE. Kicking the automation test again as ArgoCd has been a bit buggy today. Should be good for a final review.

[lucymcnatt]

Basic testing on BEE looked good