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DarwinPorts maintains hard links to all files it installed in /opt/local below /opt/local/var/db/dports/software. As SD unrolls these while backing up, the clone may be significantly larger than the source. This could cause problems when restoring a drive that was nearly full before it failed.
At the moment I can't think of applications relying on changing file contents through hard linking (as opposed to the usual "unlink on overwrite").
To me it generally feels wrong that a "clone"'s filesystem should be differ from its source in such a fundamental way.
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