I'm working on custom plugins migration and I'm facing a problem. My problem is also encountered and explained by somebody else in this thread : Kibana plugin development: Error when creating plugin in Kibana 8.6
The issue actually occured since Kibana 8.8. By reading the code, I found that a migration of kibana.json files was did into kibana.jsonc . The script that handle plugins optimization seems to ignore custom plugins based on a package-map.json file built at the bootstrap time. To build this file, the script use a git command excluding all paths under /plugins/ because of the gitignore.
May be I'm wrong but for me it seems to be a real issue or you have at least to update the plugin generator to generate a compatible plugin.