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Just of the conclusion.
We finally approached the issue the following way: using the ISDK Skeleton, we implemented a function to save markup files on an external repository and forward its file information to an external server. Pretty standard stuff.
To perform the automatic loading, the applet and server generate standard events that we listen, so we chain a load markup file after loading a file. We use a single string with information about the file and the markup file(s) we want to open.