Comment 27 for bug 1183322

Another option is to take a hard link of all the files. You can then back up the links. If the database renames a table, the link in the data directory will go away but the file will still be readable by the hard link made by xtrabackup. Xtrabackup can remove the hardlinks after completing the backup.

One danger is that if innobackupex dies, it won't clean up the hard links, so this option should probably only be used in the situation where the #tables would be > the limit.