Kepler

(2) Fix for ImageJ so that preferences are stored in an area other than the installation space. This may require a change to ImageJ source code.

The issue here is that the preferences are saved relative to the ImageJ jar file, and the jar file is often stored in a real-only area. Solving problem (1) will not solve this problem. A good solution if (1) is solved by downloading added modules in a local area would be to perhaps isolate ImageJ to its own module. Alternatively, the code of ImageJ could be changed to handle saving preferences differently, but this would cause maintenance issues.