I have a customised cgit server that the cgit indexer doesn't work on, but also only have a relatively small number of repositories to scan.
I think it should be possible to do something like this in the config JSON:
[
{ "GitURL": "http://git.server/repo-one", "Name": foo/repo-one"},
{ "GitURL": "http://git.server/repo-two", "Name": foo/repo-two"}
]