'flux build kustomization' corrupts files when run concurrently

[rycli]

Describe the bug

When multiple instances of the flux build kustomization command are run concurrently, there is a chance of corruption due to the file writing of .original creation and related logic. This manifests as;

• kustomization.yaml files being modified/corrupted
• kustomization.yaml files being emptied
• kustomization.yaml.original files being left behind
• failing builds, due to the above

A similar build failure also occurs if the repository files/directories are read-only.

Steps to reproduce

Given that this is a timing-sensitive issue, I've created a set of small reproduction scripts at https://github.com/rycli/fluxcd-kustomize-build-bug-repro . See the README.txt for example output of the failures.

Expected behavior

One or more of the following:

• flux kustomize build does not write any files.
• flux only writes files when necessary (e.g., missing kustomization.yaml file)
• flux writes all of its files to a tempdir/the configured cache dir.

OS / Distro

macOS 26, Ubuntu 24

Flux version

v2.8.1

Additional context

While this doesn't happen on every execution, I'm consistently running into this issue when running Flux in CI/CD pipelines. I'm running a busy multi-tenant environment with very frequent automated checks; these issues end up showing up rather frequently.

Code of Conduct

• I agree to follow this project's Code of Conduct

[rycli]

Hello! Just to follow up on this, I took a little time to dig into this, and see if I could identify the root cause / a potential fix.

As mentioned above, it's clear this is caused by the writing of Kustomization files during the build process, specifically calls to https://github.com/fluxcd/pkg/blob/main/kustomize/kustomize_generator.go#L132

One solution I've tested successfully is to use the sigs.k8s.io/kustomize/kyaml/filesys package (already a dependency via kustomize) and its filesys.MakeFsInMemory() to move all the file processing to a virtual file system in memory.

A couple of patches that implement this proof-of-concept fix: https://github.com/rycli/fluxcd-kustomize-build-bug-repro/blob/main/patches/pkg-kustomize-generator.patch#L1

Hope this is something that might be fixed; happy to help if I can.

[stefanprodan]

Using MakeFsInMemory sounds like a good solution but it needs to be opt-in and only enabled in the CLI. The kustomize-controller build should keep writing files to disk.