Cleanup stale submodule references

[pieterhijma]

The repository is in a strange state where BOLTSFC and pluginloader are represented as directories on the main page (without a referenced git commit), whereas Ondsel-Lens doesn't appear as a directory while having an entry in the .gitmodules file. I suspect .gitmodules and the other module administration has to be cleaned up to ensure that Github's internal .git/config file can list the correct repositories as submodules. This PR provides this cleanup.