Over time a filesystem can become fragmented. To defrag a EXT4 filesystem use the tool e4defrag. It can be used while the filesystem is mounted. This should be run once in a while. Perhaps monthly via a cron job.
root@host:~# e4defrag
Usage : e4defrag [-v] file...| directory...| device...
: e4defrag -c file...| directory...| device...
root@host:~# e4defrag -c /mnt/<drive> # Will show fragmented files and provide a score
root@host:~# ls -1 /mnt | xargs -n1 e4defrag -v # Will defrag all EXT4 drives mounted in /mnt
Directories can, over time, become in need of reindexing, sorting, or compression. This helps with performance but isn't something that can really be done at runtime. The tool fsck.ext4 allows you to request directory optimization.
With the filesystem unmounted (booted into safemode or from a USB stick / CDROM):
# fsck.ext4 -f -D <device>
e2fsck 1.42.9 (4-Feb-2014)
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 3A: Optimizing directories
Pass 4: Checking reference counts
Pass 5: Checking group summary information
DriveLabel: ***** FILE SYSTEM WAS MODIFIED *****
DriveLabel: 1076/238496 files (0.0% non-contiguous), 205416408/244190645 blocks
This should be run after file defrag'ing.