Working directory not clean in CI job (LFS files)

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Summary

Our build script checks that the working directory is clean using git status, it is failing due to LFS objects being marked as modified. It is only a small fraction of the objects.

Steps to reproduce

Not sure how to reproduce. See the job output where this happens. To make debugging easier we have git diff executing before the build script runs. When the build scrip fails it also outputs git status --porcelain

What is the current bug behavior?

A small fraction of LFS objects appear modified in the working directory when running a CI pipeline.

What is the expected correct behavior?

The CI should clone the repository and these files should be un-modified.