If you want to exclude the generated files (R, BuildConfig, etc.) then you can specify a custom scope for the JavaDoc generation. For this to correctly work you will need to:
- In the Project view on the left, select the root source directory to generate the docs for (e.g. "com" or "org")
- Open the JavaDoc generation dialog (Tools -> Generate JavaDoc...)
- Select "Custom scope" (it's the 5th radio button in my version) and select your module (e.g. "Module 'library'")
- Select your other properties such as output directory, method visibility, etc. and click "OK"
That's it. Your JavaDocs should be generated without the R or BuildConfig files included.