Rename file causes renku to complain about deleted files forever

Describe the bug

Renaming a file causes renku to complain about deleted files forever.

To Reproduce

Step 1: run a workflow

Create a file src/python/limbo.py

import os

out_path = "data/out.txt"
print("Writing to {}".format(out_path))

with open(out_path, 'w') as f:
    f.write("Hello!\n")

os.makedirs('./.renku/tmp', exist_ok=True)
with open('./.renku/tmp/output.txt', 'w') as f:
    f.writelines([out_path])

Then run renku run python src/python/limbo.py

Step 2: Rename output file and update script

renku mv data/out.txt data/foo.txt

Update src/python/limbo.py to refer to new output path.

import os

out_path = "data/foo.txt"
print("Writing to {}".format(out_path))

with open(out_path, 'w') as f:
    f.write("Hello!\n")

os.makedirs('./.renku/tmp', exist_ok=True)
with open('./.renku/tmp/output.txt', 'w') as f:
    f.writelines([out_path])

Then git commit -m"Renamed output file"

Step 3: Stuck in limbo

How can you force renku to realize that the outputs are up to date? renku update does not help; renku run python src/python/limbo.py also does not help.

jovyan@jupyter-cramakri-limbo-2ddeceaee3:/work/limbo$ renku status
On branch master
All files were generated from the latest inputs.
Deleted files used to generate outputs:
  (use "git show <sha1>:<file>" to see the file content for the given revision)

        data/out.txt: b79ebd34

jovyan@jupyter-cramakri-limbo-2ddeceaee3:/work/limbo$ renku update
All files were generated from the latest inputs.
jovyan@jupyter-cramakri-limbo-2ddeceaee3:/work/limbo$ renku status
On branch master
All files were generated from the latest inputs.
Deleted files used to generate outputs:
  (use "git show <sha1>:<file>" to see the file content for the given revision)

        data/out.txt: b79ebd34

jovyan@jupyter-cramakri-limbo-2ddeceaee3:/work/limbo$ renku run python src/python/limbo.py 
Writing to data/foo.txt
Error: There are not any detected outputs in the repository.
  (use "git rm <file>..." to remove them first)

        src/python/limbo.py

Once you have removed files that should be used as outputs,
you can safely rerun the previous command.

Expected behavior Renku should recognize that a file was renamed and everything is fine and up to date, not complain about deleted files.

Desktop (please complete the following information):

renku version: 0.6.0

SwissDataScienceCenter / renku-python