So you are making changes to the open source project? Is that an open source project owned by someone else or is it yours? And that's why you have the open source project created in Eclipse.
What I would do is:
1) Store the source code for the open source project in Subversion (substitute your favorite version control system)
2) Modify the pom.xml for the open source artifact to differentiate it from the officially released one. A slightly different groupId, artfiactId or version will do.
3) Create a job in
Jenkins to build the open source project and place the result in a Nexus repository (you include a sources jar also if you need one)
4) Change the pom.xml for my projects to use the the coordinates defined in step "2"
Now when Jenkins builds your app, it uses your custom version of the open source artifact.
In fact, I have done the above for a few projects where we required modified open source. Note that we use a suite of tools (Subversion, Nexus, Maven, Jenkins) to define our build environment.