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If you're familiar with git and GitHub, here's the short version of what you need to know. Once you fork and clone the jPOS code:
Don't develop on the master branch. Always create a development branch specific to the issue you're working on. Name it by issue # and description. For example, if you're working on Issue #359, an aspect naming fix, your development branch should be called 359-aspect-names. If you decide to work on another issue mid-stream, create a new branch for that issue--don't work on both in one branch.
Do not merge the upstream master with your development branch; rebase your branch on top of the upstream master.
A single development branch should represent changes related to a single issue. If you decide to work on another issue, create another branch.
Step-by-step (the short version)
Fork on GitHub (click Fork button)
Clone to computer ($ git clone firstname.lastname@example.org:~you~/jPOS.git)
Don't forget to cd into your repo: ($ cd jPOS/)
Set up remote upstream ($ git remote add upstream git://github.com/jpos/jPOS.git)
Create a branch for new issue ($ git checkout -b 100-new-feature, if you don't have a bug report no worries just skip the number)
Develop on issue branch. [Time passes, the main jPOS repository accumulates new commits]