When we use JAR files such as DocX4J for exporting from XPages we need to store these within the git repositories so that the developer can add them to their /jvm/lib folder when building the XPage application. If the correct jars are not present the build fails.
The files are stored in a /jar folder away from the /notes folder where the Noes design elements are. We also use a /documentation folder for user guides etc..
When you add these jar or zip files to the repo they do not appear in SourceTree. In my case all that appeared was the /jars/readme.txt file.
The project specific .gitignore file was blank but the default settings in git are to ignore all compiled files and all zipped files. Given that we store documentation and artwork files int eh repo the .zip would also a problem for us.
You need to modify the global .gitignore file as shown below. The project specific .gitignore file is additive tot he global settings and does not replace them.