[Brian]

Every time data changes in the OmniFocus database, it gets written out to disk as an individual transaction file, stored in a folder that the finder knows to show to the user as if it were a single file. (Special folders like this are called "bundles"; it's a feature of Mac OS X.)

Practical example: adding an item to your OmniFocus database, changing it, and then deleting it all get written out to disk as three files, and those files stick around. When you delete the item, the previous two files are still on the disk.

On your hard drive, this makes a lot of sense - it's very speedy to write those small change files, if your computer goes kaboom we only lose the transaction file we're writing instead of the whole database, and other things that require more smarts than I possess to explain. Ken explained them elsewhere on the forums... someplace.

When it comes time to send your database to another machine, though, the file transfer spends time sending one of the transaction files, closing out that file, opening the next one, sending it, then closing it; repeat over and over again. (MP3 files are all one big stream of data - open the file, send all the bits, close the file.)

If you select File -> Rebuild Database, we'll collapse all those transactions down into one big 'State-of-the-Database' file, which will be faster to send over to the other machine.