Apple implemented Time Machine in a very peculiar way by most developers' reckoning to create an exact copy without duplicating every file. Using so-called hard links, which allows a single copy of data to appear multiple times in a folder hierarchy, Time Machine creates hidden folders that fully replicate a hard disk's file structure. A Time Machine backup comprises mostly hard links pointing to existing files or folders unchanged since the previous backup. Each hard link is counted by OS X as a separate file.
Dave notes that Time Machine also stores a sort of local backup on the startup drive to improve its performance in copying to a local drive or a remote one over the network. Most other backup software makes an initial copy of a file and then a "delta," or a kind of summary of differences, for every version stored thereafter.
And Spotlight contributes to the file count: for better indexing, Mac apps have reference files for each quantum of data, such as an email message, to match a result up with an item. On one machine, I have hundreds of thousands of metadata files associated with email messages. Combine Spotlight and Time Machine, and you can see where the file count comes from. I don't use Time Machine and have nearly 1.8 million files on my MacBook Air.
Dave has consoling words, though:
I wouldn't worry about it too much — let the system handle its files, and don't be too concerned about the count. As long as your drive isn't mysteriously filling up, you're good.
Selective Time Machine
On the related subject of Time Machine, Larry Landen asks:
When I reinstall Mac OS X (to solve performance problems, or clear space) I have a restore option to migrate data from my Time Capsule, but it currently only gives me options to migrate entire user profiles, applications, and settings.
How may I pull only selected data (such as images, and iTunes media like music and movies, and documents) rather than an entire profile? I fear that restoring an entire profile may also restore any problems that made me want to reinstall OS X.
It's a sensible and reasonable question: if some kind of corrupted or inaccurate setting is causing system problems, aren't you just asking for trouble by bringing all your settings over? Likely no. With the except of specific applications having corrupted configuration files, a clean installation and a migration of settings generally seems to avoid causing identical problems in OS X. (Solving corrupt app settings varies, but often involves tossing a file or several from ~Library/Preferences/ with the advice of the software's maker.)
That's in part because the corruption or other setting issues you're having can result from missing or overwritten system files or configurations that aren't copied back as part of a Time Machine migration.
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