yarsync
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hard links don't work with ignore-existing
rsync key --ignore-existing seems to conflict with -H (hard links). Filed an issue for rsync, got no reply yet.
If this doesn't get fixed (or suggested how to fix that in yarsync), then ignoring existing files will not work. This is a nice security feature, it was introduced right before the 0.1 release.
At the moment, use --overwrite key during yarsync pull/push. Alternatively, use the hardlink executable afterwards (doesn't always work; in this case remove new commits and re-synchronize with --ignore-existing).
clone, commit and other commands work fine, because --ignore-existing is used only in pull/push.
Thanks for the workaround explanation.