Update pre-commit config, remove duplicate keys, and add EndOfCheckPhase where needed

[homebysix]

This PR updates the versions of the hooks used by pre-commit in this repo.

• Note: the yamllint hook is complaining about numerous files in this repo, and may be too strict to be useful here. Consider adding a more lenient ruleset to the .yamllint.yaml file. I ignored these errors for now.

• Also note: the check-autopkg-recipes brings up these valid concerns, which I'm also ignoring for now:

  MiKTeX/MiKTeX-Win64.download.recipe.yaml: WARNING: Recommend converting from <!-- --> style comments to a Comment key.
  Oxygen/OxygenWebAuthor.download.recipe.yaml: identifier does not start with com.github.NickETH.
  Google/GoogleSync-Win64.build/zzTest_GoogleSyncMSI-Win64.download.recipe: identifier does not start with com.github.NickETH.
  Google/GoogleSync-Win64.build/zzTest_GoogleSyncMSI-Win64.download.recipe: WARNING: Recommend converting from <!-- --> style comments to a Comment key.
  SecureCRT/SecureCRT-Win64.BMS.recipe: identifier does not start with com.github.NickETH.
  SecureCRT/SecureCRT-Win64.BMS.recipe: WARNING: Recommend converting from <!-- --> style comments to a Comment key.
  Oracle/OracleInstantClient-Win64.build.recipe.yaml: Contains a download processor, but no EndOfCheckPhase processor.
  IrfanView/IrfanView-Win64.build.recipe.yaml: Contains a download processor, but no EndOfCheckPhase processor.
  Microsoft/MicrosoftWebView2EvergreenBootstrapper-Win64.BMS.recipe.yaml: identifier does not start with com.github.NickETH.
  Clarivate/Endnote-Win.build.recipe.yaml: Contains a download processor, but no EndOfCheckPhase processor.
  Oracle/OracleInstantClient-Win.build.recipe.yaml: Contains a download processor, but no EndOfCheckPhase processor.
  NotepadPlusPlus/NotepadPlusPlus-Win64.build.recipe.yaml: Contains a download processor, but no EndOfCheckPhase processor.
  

This PR also includes changes to EndOfCheckPhase positioning to align with AutoPkg conventions.