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I use unison to synchronize the files, and meld for some occasional manual merges you may need.

Manual merging can be required for the meta files, as it can have some new feeds (by the machine who updates) and can have some marked as read (by the machine where the user marked posts as read).

The configuration line I use for unison for the manual merges is:

merge = Name meta -> meld CURRENT1 CURRENT2

For more details, please read the unison help on merging.