I'm creating and packaging a toolbox using the "matlab.addons.toolbox.packagetoolbox" methods in a CI system. Therefore, MATLAB runs headless (-nodisplay) in this environment. In this mode, the packaging tool does not correctly configure the "configuration.xml" file. Basically, it doesn't include the paths of the toolbox's files. However, when I do this directly from MATLAB with the desktop running it does provide these paths correctly in the "configuration.xml" file.
My guess is this is related to the jvm somehow.