Deal with deleted content in a provider registry

[matuskalas]

Related to PR #594

• [ ] Validation of IDs as part of CI in TE
• [ ] Bio.tools, OEB, BIII, etc. PRs deleting old records! Work needed in those resources to keep track of deletions!
• [ ] TE CI should purge empty directories
• [ ] I would also love if TE CI maintains a log / TSV / dashboard that would show deleted records (maybe also added and updated)