For the same reasons as specified here, Builds directory for an agent should have just one checkout per repository - #8 by ccarpita-butterfly.
I think there’s a pretty valid case for this becoming properly supported by Buildkite in the hopes of making this value immutable as an environment variable. See also, https://github.com/buildkite/elastic-ci-stack-for-aws/issues/917#issuecomment-918592144.
Thanks @jl-applied for the suggestion! I believe you will receive an answer to the GH issue from product engineers. Feel free to post as much detail of your use case as possible.