I'm using Jooq code generation but I don't include all its java class in source control. That is when one of the developrts pull the code from get he has to run code generation to be up to date with the db schema But how to include it in the final jar?
There's no difference between that developer that has to run the code generation, and the build server producing the jar files that has to run code generation. Anyone building your application will need to generate code during the build if you do not want to check in your generated sources as a library.
Some more information on using jOOQ's code generator with version control can be found here.