Hi,
For Papyrus, I tried to use the shared repo as much as possible for builds which only depend on milestones or releases (As they don't accumulate too quickly). That is mostly Papyrus-Master (Or Neon, ...). All other jobs had to use a private repo. In the case of Papyrus-RT, I guess there is no such build, since all of them depend on Papyrus.
Last time I checked (Couple of years ago...), mvn dependency:purge-local-repository only worked for Maven artifacts; not P2 artifacts. So it pretty much didn't work with Tycho. I didn't find a way to clean only "Papyrus Nightly bundles" from the repo, either. So ultimately, I either cleared the M2 repo before every build (Gerrit) or once every few weeks (Extra, Tests, ...)
Regarding the shared M2 repo, we don't have direct access to it, because it's not in a Workspace, so you need to run a shell script from an Hudson build to clear it (And as Christian mentioned, be careful not to delete settings and toolchains.xml - only the repo. I deleted everything once, and it didn't go well :) ). Same thing if you need to monitor disk usage of this repo; I don't think there is a tool for that (Beside shell scripts)
Then one has to monitor the "Disk usage" quite regularly to check if everything is still fine. On Papyrus, the reference disk usage for the workspace of a job depending on Papyrus is ~2-4 GB (That's Git + M2 dependencies + Latest build artifacts in target/ folders). So whenever a workspace reaches 6-10 GB, it typically indicates that clean up is required.
I didn't find the perfect solution to fully automate disk usage monitoring/clean-up, but I hope that these few leads at least help :)
Cheers,
Camille