Values migration does not remove files

[j-zimnowoda]

Describe the bug: (a clear and concise description of what the bug is)

To Reproduce
Steps to reproduce the behavior:
Let's say you want to remove an Harbor app

1. In the values-changes.yaml file add new migration

  - version: 23
    deletions:
      - 'apps.harbor'

2. Run npm run migrate
3. Observe that thetests/fixtures/env/apps/harbor.yaml still exists and contains its values
4. Observe that thetests/fixtures/env/apps/secrets.harbor.yaml still exists and contains its values

Expected behavior: (a clear and concise description of what you expected to happen)
Corresponding files are deleted if the whole app is removed