I used the swagger codegen to generate jaxrs server side classes and also client side java classes.
This is the command I used to generate the classes
ja
The latest master of Swagger Codegen allows you to specify files not to be overwritten in .swagger-codegen-ignore (similar to .gitignore) during code generation.
Please pull the latest master of Swagger Codegen to give it a try.
UPDATE: On May 2018, about 50 top contributors and template creators of Swagger Codegen decided to fork Swagger Codegen to maintain a community-driven version called OpenAPI Generator. Please refer to the Q&A for more information.