I had that problem at one point. I vaguely recall that I unmounted my home partition and fscked it at one point to find the fragmented inodes, then there was co

I had that problem at one point. I vaguely recall that I unmounted my home partition and fscked it at one point to find the fragmented inodes, then there was complicated magic to find the filenames that those inodes referred to, and then there was a script which copied them all to a tmpfs (i.e. into memory), deleted the original, and copied the copy back out. One of the goals of recent ext4 work was to get support for "online defragmentation" but I don't know to what extent it's automatic, what tools exist, et cetera. It sounds like pyfragtools also has attempted to solve this problem.