RFC: adding persist and remove methods back to the repository

[B4nan]

I went ahead with #3989 some time ago, but I keep thinking whether it was the right move. I still consider this a valid problem, but it feels like removing just the flush method could be enough. I also feel like not that many people were aware of the change by that time.

One argument for this I have is that technically, it's already possible to persist entities via a repository (em.create will call persist automatically).

So asking one more time, whether I should put those back as a last-minute change.

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The flush method will stay only on the EM level.