There is a very useful tool for finding and merging shared permanent storage, and its name is fdupes. There was a terrible occurrence in the software after version 1.51, however. They removed the -L argument because too many people were complaining about lost data. It sounds like user error to me, and so I continue to use this one. I have to build from source, since the newer versions do not have the -L option.
And so there you are. I recommend using it, even though this most useful feature has been deprecated and removed from the software. Perhaps there should be a fdupes-danger package in Debian?