Proper way to configure a multi-version and multi-repo application Jenkins environment

I have some doubts about configuring a multi-version application Jenkins environment.

The application is separated in two Git repositories and two versions of each are developed simultaneously.

Sadly we still don't use a dependency management system.

Each repository has multiple Java projects and each Java project has a related Java project containing only JUnit tests.

What is the proper way to organize the build process?

There are currently one job per version and per repository that does git pull, one job per Java project that compiles and executes some verifications, one job per test project that executes Junit tests.

Considering that each Java project is a subdirectory of a repository, I didn't find a way to configure Git options properly in its Jenkins job (I could only pull entire repository).

Considering that each project has a lot of dependencies and there are more than 100 projects, it is very hard to maintain execution order configuration.