> Maybe it should only delete these files when you say “fossil set manifest 0”?

Thanks for the info.
I also looked up where this happens in the code (manifest_to_disk() in

One way to get around this automatic deletion (when creating a new
repo with files already in the work directory) is to use 'fossil open
--empty' flag, though such use is somewhat non-intuitive.

I wonder if before deleting the local manifest files we should test if
the repo is freshly created and is empty (How?).
This would at least give the user a chance to decide what to do about
these manifest files and the "manifest" setting.
Otherwise the manifest files just surprisingly disappear.

BTW, I discovered this behavior while trying to populate a new repo
with the contents of a downloaded current Fossil master tarball. It
would add all files without any warnings, then it would just fail to
build due to missing 'manifest.uuid' needed to gen the VERSION.h. Yet
the 'manifest.uuid' is included in the tarball.
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