An important file somehow became completely corrupted; and I had backed it up without knowing it was corrupted, so the backup was useless. I ran photorec, looking for a deleted version to restore from. I found most or all of what I needed, but to my surprise, I also found close to ten thousand deleted files of various types. Why do I have a very large number of deleted files? I thought Linux filesystems didn't leave very many deleted files, if any, and didn't need defragging.

When a file is deleted, its data blocks and its metadata, often contained in a datastructure named "inode" (the name depends on the filesystem) are simply marked as unused. If they are not reused, they stay like this, and forensic tools like photorec find them.

How long have you had the drive and what, if anything, have you used it for prior to installing Linux. In theory, if you've had the drive 10 years and installed multiple OSs on it you may have "deleted" files still on it going back 10 years to the first OS install, for example.

This hard drive contains only Linux; I haven't used Windows in years. It might be a few years old.

What I was trying to say is that the files you found could have been created at any point during the life of the drive, since files are not actually deleted unless you use a "shredder". So unless you have wiped every sector of your drive there is no telling where the file headers found came from.

Fragmentation is when you have bits of current files scattered all over the place, with a lot of little gaps that are too small to use. The "files" detected by photorec are areas on the HD that contain bytes that were obviously once part of a file. From the point of the filing system, those bytes might as well be nulls: it knows nothing about them and will overwrite them automatically whenever it needs to. The problem with photorec is that it can't look for details of deleted files in the directories, as Linux completely removes them: it has to just hunt right through the HD, looking for any blocks of code on the off-chance that they might be files.

The moral is to always make alternate backups on different media: if my blue medium has a corrupted file, the pink one may well be OK.

Because you and your OS have apparently deleted/modified a large number of files, which is perfectly normal. Think of how many intermediate files get created/deleted from a simple system update, and multiply that by several years.

Linux, like OSX and Windows, does not clean up deleted files automatically. When a file is deleted, it's not actually wiped from the drive, the reference to it is simply removed and those blocks are free to be overwritten whenever the space is needed. If the blocks are never overwritten, then the file never actually disappears from the drive platters, and you can recover it at an time with a tool like photorec.

What you're seeing has nothing to do with fragmentation.

inodes: the Dewey Decimal System of the Linux world.