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1. The different files represent transactions, and this granularity (in some form) is necessary in order to reliably sync an arbitrary number of clients. (Having multiple files allows us to deal with many transactions without having to pass the data across the wire unless it's actually needed.) In normal operation, the number of files should not grow without bound if all registered clients are in fact regularly syncing.

2. Syncing via multiple methods is a far more complex proposition. It may happen at some point, but the current situation required much less complexity (for a problem that is already very complex) yet provided a great deal of flexibility. Please feel encouraged to send a request for more advanced functionality to the OmniFocus feedback address, if it would be of use to you.