Allow manually editing the versions.tsv file

There might be situations where we want to tweak the installed versions of packages. I propose that we should check to see if `versions.tsv` exists, and if it does skip the step where we generate it. Otherwise, we require a docker container to be specified and we generate it.

Locate the code that generates versions.tsv and the entry point that requires a Docker container, then read how package versions are currently collected. The change is done when an existing versions.tsv is preserved without requiring a container, while a missing file still requires the container and generates the file.

Written by the indexing model from the issue text.