I wrote and contributed the forge module "magnolia-rest-queries" that adds a RESTful interface for executing JCR queries. After this latest swagger update my endpoint no longer appears in the REST Tools interface. I checked /.rest/swagger.json and it is also missing from there.

The module configures itself according to the documentation provided here: https://documentation.magnolia-cms.com/display/DOCS/REST+API#RESTAPI-Exposingyourownendpoints

It was working well in 5.4.x. It looks like the new Swagger re-organized things and now you're generating /.rest/swagger.json instead of /.rest/api-docs. I would guess that the code that generates swagger.json is failing to look in other module configurations for a /rest-endpoints/ node, but that is simply a guess.

RESTful requests to the endpoint do continue to work correctly.