Is there a way to run the pipelines for running cleanup actions after a pull request is merged? The merge is never done through the UI but with plain git commands and a push to the main branch.
If the merge is local and then distributed to origin via git push, the pipeline you're looking for is in the branches section - it runs when the branch HEAD changes (which it does on push).
Depending on what you would like to find out / to do after merging the branch pipeline can take care of it.
However as the pull request never has been merged through the UI, the only data you can normally work with is the information in the git repository itself as that is shared with Bitbucket and available in the pipeline.
Alternatively you can make use of the Bitbucket API to gather information about open pull requests etc., again looking for git revisions might be a connection point here again.
Not saying there is anything wrong with merging local and pushing to Bitbucket, but I wonder a bit why a pull request is created in the UI if the merge is not done there or more specifically I have problems to give more concrete suggestions as I don't know anything about that cleanup you're talking about in your question.
If it's about closing those pull-requests, then I guess it's about declining the PR via the REST API.
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