How can I delete Time Machine files using the commandline
To work around "operation not permitted" errors, use the Time Machine Safety Net "bypass" program:
sudo /System/Library/Extensions/TMSafetyNet.kext/Contents/MacOS/bypass rm -rfv /Volumes/[disk]/Backups.backupdb/[path]
In 10.8 Mountain Lion, bypass moved into 'Helpers':
/System/Library/Extensions/TMSafetyNet.kext/Helpers/bypass
In 10.10 Yosemite, bypass moved here:
/System/Library/Extensions/TMSafetyNet.kext/Contents/Helpers/bypass
Beware when using this to delete specific snapshots: as Time Machine uses hard links, using rm -r on folders might also affect older and newer snapshots of the same machine. (See other answers referring to tmutil delete to safely delete a specific snapshot.) Using rm to delete all snapshots for a single machine is okay though. And so is using rm to delete a specific file, which will only remove that hard-linked file from the snapshot(s) you specify, assuming the file is not in a hard-linked directory as then you'd actually remove the file from all those hard-linked directories.
BLUF (bottom line up-front):
sudo tmutil delete snapshot-dir
Using sudo chmod -R -N folder to remove all ACLs from a folder hierarchy doesn't work on the files and folders in Time Machine's Backups.backupdb, because of the TM Safety Net mechanism and the criteria described in this 318 Tech Journal post (but possibly not exactly as described).
(Before learning this from looking up the Safety Net mentioned in Eric W's answer (which works), I had only tested on a folder cloned from a subfolder of a TM backup, and there chmod worked. But trying chmod on a folder in an actual TM backup gives the "Operation not permitted" error.)
Of possible use:
In Mac OS 10.7+, there's a tmutil command (which I haven't tried, since I'm still on Snow Leopard). It has a delete verb, which according to the description "can delete snapshots from backups that were not made by, or are not claimed by, the current machine" (where a "snapshot" is a dated folder representing a single incremental backup). It isn't clear to me if this means that it can't delete snapshots which are made by or claimed by the current machine.(?)
A warning about using the bypass command to remove an old backup: if the deleted backup has folders that are exactly the same in earlier or later backups, then files might be deleted from earlier or later backups as well!
Time Machine not only uses hard links for unchanged files, but also uses hard links for folders in which no files were added, changed or deleted at all. This results in something like:
/2014-11-06/folder/file1
/file2
/file3
/2014-11-13/folder/file1 = hard link to file /2014-11-06/folder/file1
/file2 (changed; new inode)
/file3 = hard link to file /2014-11-06/folder/file3
/2014-11-20/folder/ = hard link to folder /2014-11-13/folder/
/2014-11-27/folder/ = hard link to folder /2014-11-20/folder/
With the above, deleting any file from /2014-11-06/folder/ is fine, and only affects the backup for that date. The hard link reference counts are decreased, so the "inode" for file2 will be removed, but inodes for file1 and file3 will still have a reference count of 1 due to the later backups. Hence, rm -R /2014-11-06 is fine too.
However, removing any file from either /2014-11-13/folder/, /2014-11-20/folder/ or /2014-11-27/folder/ will effectively remove it from all those 3 folders.
The problem is that rm -R does not care about hard-linked folders. It just recurses into any hard-linked folder it finds, boldly deletes all its files, and then removes the empty folder.
So: when removing an old backup one should not recurse into a hard-linked folder and delete its contents. Instead, one should only remove the hard link for the folder itself. So, rather than rm -R use tmutil delete as explained in Arne's answer.
As an aside, it seems that the OS X unlink command cannot be used on folders: "only one argument, which must not be a directory, may be supplied". The OS X API can remove hard-linked folders, and so can GNU Coreutils, like installed using Homebrew.
Finally, to prove all of the above, a test-case (OSX 10.6.8):
sh-3.2# ls -lFa 2014-11*/Users/USERNAME/Library/Safari/TopSites.plist
-rw-r--r--@ 2 USERNAME staff 1551 10 30 2014 2014-11-06-012454/Users/USERNAME/Library/Safari/TopSites.plist
-rw-r--r--@ 2 USERNAME staff 1551 10 30 2014 2014-11-13-024438/Users/USERNAME/Library/Safari/TopSites.plist
-rw-r--r--@ 2 USERNAME staff 1551 10 30 2014 2014-11-20-014044/Users/USERNAME/Library/Safari/TopSites.plist
-rw-r--r--@ 2 USERNAME staff 1551 10 30 2014 2014-11-27-025033/Users/USERNAME/Library/Safari/TopSites.plist
Note that the number of links for each occurrence is 2 (second column). Let's remove the first occurrence:
sh-3.2# /System/Library/Extensions/TMSafetyNet.kext/Contents/MacOS/bypass unlink 2014-11-06-012454/Users/USERNAME/Library/Safari/TopSites.plist
sh-3.2# ls -lFa 2014-11*/Users/USERNAME/Library/Safari/TopSites.plist
-rw-r--r--@ 1 USERNAME staff 1551 10 30 2014 2014-11-13-024438/Users/USERNAME/Library/Safari/TopSites.plist
-rw-r--r--@ 1 USERNAME staff 1551 10 30 2014 2014-11-20-014044/Users/USERNAME/Library/Safari/TopSites.plist
-rw-r--r--@ 1 USERNAME staff 1551 10 30 2014 2014-11-27-025033/Users/USERNAME/Library/Safari/TopSites.plist
So, after unlinking one of the files, the number of links dropped to 1 for each occurrence, though the file is still shown 3 times. No problems yet. Remove the first occurrence again:
sh-3.2# /System/Library/Extensions/TMSafetyNet.kext/Contents/MacOS/bypass unlink 2014-11-13-024438/Users/USERNAME/Library/Safari/TopSites.plist
sh-3.2# ls -lFa 2014-11*/Users/USERNAME/Library/Safari/TopSites.plist
ls: 2014-11*/Users/USERNAME/Library/Safari/TopSites.plist: No such file or directory
Now all are gone. Apparently the file TopSites.plist was last changed 2014-11-06 and hard-linked on 2014-11-13 as then some other files were added, changed or removed in the Safari folder. Next, the contents of the Safari folder did not change in the subsequent two backups, so on 2014-11-20 and 2014-11-27 the Safari folder was hard-linked to the previous backup.
Indeed, the 4 folders only use 2 inodes (first column):
sh-3.2# ls -lFaid 2014-11*/Users/USERNAME/Library/Safari/
648651968 drwxr-xr-x@ 86 USERNAME staff 2924 9 10 16:06 2014-11-06-012454/Users/USERNAME/Library/Safari//
650804457 drwxr-xr-x@ 86 USERNAME staff 2924 9 10 16:07 2014-11-13-024438/Users/USERNAME/Library/Safari//
650804457 drwxr-xr-x@ 86 USERNAME staff 2924 9 10 16:07 2014-11-20-014044/Users/USERNAME/Library/Safari//
650804457 drwxr-xr-x@ 86 USERNAME staff 2924 9 10 16:07 2014-11-27-025033/Users/USERNAME/Library/Safari//