Dear @jonsterling, this issue is likely caused by the recent modification of opam-repository to not carry extra-files anymore. See https://discuss.ocaml.org/t/ann-opam-repository-policy-change-checksums-no-md5-and-no-extra-files for further information.
You’re likely using a macOS system with opam < 2.1.6 and patch being not a GNU patch. (This results in files aren’t deleted, but only emptied, and kept around).
To recover, rm -rf ~/.opam/repo/default{,.tar.gz} && opam update default should bring your local opam-repository into a good shape.
EDIT: updated the instructions above with the remark by @kit-ty-kate in The compilation of ocaml.5.1.1 failed at "ocaml <...>/gen_ocaml_config.ml 5.1.1 ocaml" - #17 by kit-ty-kate