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Let's be a bit more conservative here and actually fdatasync() the configurations we're generating. I'm seeing an issue at the moment where syslinux isn't finding the config sometimes, and while I don't think this is the issue, let's try it.
OSTree is a tool for managing bootable, immutable, versioned filesystem trees. While it takes over some of the roles of tradtional "package managers" like dpkg and rpm, it is not a package system; nor is it a tool for managing full disk images. Instead, it sits between those levels, offering a blend of the advantages (and disadvantages) of both.
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