How to remove ghost files from renku that were removed from git?

I have a weird problem in the following repo: Reproducible Data Science | Open Research | Renku
I re-organised it a while ago by moving files from one folder to another and then removing the empty folder. I assume that I did this using git mv instead of renku mv. I then kept updating the files in the new location using renku run, but now I realised that when I do renku status, renku still wants to update the non-existing files. I cannot run renku rm on them, as they don’t exist any more. Does anyone have an idea how I could clean up this mess? Thanks already!

You could try renku doctor and renku doctor --fix, but I’m not sure if it addresses this specific problem.

You could also renku workflow remove the workflows that used/created the deleted files, then they shouldn’t show up in renku status anymore

Thank you @ralf.grubenmann! I just found this again when I ran into a similar problem with another repo. renku doctor did not find any problems, so I had to run renku workflow ls to see all the workflows and then delete one-by-one those workflows that would create files I don’t need any more.

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