I'm trying to use JavaConfig with my own annotations by implementing a MetadataReaderFactory, which translates my annotations into standard Spring.
Unfortunately the metadataReaderFactory argument gets ignored by checkConfigurationClassCandidate:
This sounds like a reasonable request. However, there may be additional changes necessary to support the kind of low-level customization you're attempting here. Since you're already pretty familiar with the changes necessary, I would suggest that you fork the framework on GitHub (http://github.com/cbeams/spring-framework) and try such a change yourself. If it's all you need, great -- if you need more, you can make changes as you go to accommodate.
Once you have stable support for your use case, you can then issue a pull request (along with test cases) and we can discuss it's viability as a general-purpose improvement to the framework.
By the way, you'll find everything you need to build the framework in the wiki attached to the GitHub project.
I so far managed to make it work by tweaking the beanfactory right before handing it over to ConfigurationClassPostProcessor. Solving it properly may be more involved.
Thanks for the github link I may give it a shot.