What I'd like to do is have thin appliances that are managed with chef
or puppet (leaning to puppet). So what I'm thinking is to have one vm
client install with everything the automation system needs to run
(except creds) and network/hostname stuff - have another fs for that.
And a third fs for the actual installed package.

However, I an issue - I don't know how to make rules for which fs gets
updated. I'm thinking everything needs to overlay at the same point,
so directory writes might go to one fs or another - I think the base
should generally be ro, but the automation config and the 'thin' image
will both update /etc and I need some way of saying "this file gets
updated on fs, this file gets updated on another, and this file goes
to both". And then as I 'strace -e trace=stat64' or whatever and see
what the process touches, I'm going to want to copy it from one fs to
the other (kinda the same issue).

Is there some mechanism to do this?

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