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I know that cryfs[1] is resilient to at least the first of these, and possibly the second as well. I don't know if cryfs allows to modify the base directory while the filesystem is online, if it does then it might already be a better solution for syncthing, if you only care about Linux.
On the flip side syncthing could incorporate cryfs's base directory format instead of their home-grown one.
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The open source projects on this list are ordered by number of github stars.
The number of mentions indicates repo mentiontions in the last 12 Months or
since we started tracking (Dec 2020).
The latest post mention was on 2024-04-15.
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