Cannot output to a non-empty directory under renku run

Describe the bug I have the following folder setup:

data/my-dataset/file1.txt
data/my-dataset/file2.txt

And I have a script script.py that takes data/my-dataset as an input and generates file1.txt, leaving file2.txt untouched.

When I execute renku run script.py data/my-dataset, I get an error

Error: The output directory "data/my-dataset" is not empty. 

Delete existing files before running the command:
  (use "git rm <file>..." to remove them first)

        data/my-dataset/file2.txt

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

Specifying the output explicitly as using --output or .renku/tmp/outputs.txt does not fix the problem. The repo is in a clean state, and the script does not touch data/my-dataset/file2.txt.

Link to project https://renkulab.io/projects/covid-19/covid-19-public-data

To Reproduce See description above.

Expected behavior

renku run should ignore files in the output directory unless they are modified by the execution
renku run should respect what is provided by the output argument

Screenshots and/or execution output If applicable, add screenshots and/or copy-pasted execution output to help explain your problem.

Run environment (please complete the following information):

renku-python: 0.10.2
Python version: 3.7.3
on renkulab
JupyterLab / Chrome

SwissDataScienceCenter / renku-python

Cannot output to a non-empty directory under renku run #1178