How to work with the ImageJA submodule

We have a modified ImageJ core that operates as Fiji's kernel. The source code is in a branch named 'master' in ImageJA repository.

Here is how to get fiji.git's ImageJA submodule to run Fiji:

First check out the submodule ImageJA in fiji/:

$ git submodule init modules/ImageJA
$ git submodule update modules/ImageJA

Note: make sure that you have _no_ trailing slash after "modules/ImageJA". In other words, "modules/ImageJA/" will _not_ work.

Note: If the update finds a new revision to advance to, it will _detach_ the HEAD. That means that you will not be on any branch.

Therefore, if you want to work on ImageJA's master branch, you need to create a local branch:

$ cd modules/ImageJA/
$ git checkout -b master origin/master

This only needs to be done once. You can now work with git pull, git add, git commit and git push to your heart's content.

If you update the ImageJA submodule with git submodule update modules/ImageJA on purpose or by accident, you will have to go back to the master branch before doing any work inside ImageJA:

$ cd modules/ImageJA/
$ git checkout master && git pull