Remove deprecated command in Poetry >2.0 causing error in CI

[wren]

The --remove-untracked flag was recently deprecated in Poetry 2.0. It is now causing errors in the CI pipelines because we used the flag. This PR removes the flag to allow the CI to proceed.

Example of failing pipeline: https://github.com/jrnl-org/jrnl/actions/runs/13353056619/job/37373472281?pr=1970

Checklist

• I have read the contributing doc.
• I have included a link to the relevant issue number.
• I have checked to ensure there aren't other open pull requests
  for the same issue.
• I have written new tests for these changes, as needed.