irmin: drop dead libraries flagged by monopam Dead_lib
Remove libraries that appeared in '(libraries ...)' clauses but had no
references in the surrounding source — caught by the new Dead_lib lint:
- bin/dune: drop atp-xrpc-server, base64
- lib/dune: drop bytesrw, logs
- lib/atproto/dune: drop nox-pds, fmt, bytesrw
- lib/git/dune: drop fmt, bytesrw
- lib/oci/dune: drop fmt
- test/bench/dune: drop nox-json
- test/mime/dune: drop nox-irmin (irmin_mime stanza only references
the sublib, not the umbrella)