Originally posted by Bohemia Wiki:

Case sensitivity & Mods
Some mods such as CUP Terrains and @ALiVE will not function if there are capital letters in any of their file names. If you do not update your mods on a regular basis, you can just use the command
find . -depth -exec rename 's/(.*)\/([^\/]*)/$1\/\L$2/' {} \;
in the directory where your mods are located. This will recursively search the directory tree and make all the filenames lowercase.

If you regularly update your mods using, e.g. ArmA3Sync, you will find that this will redownload any files/folders that have changed case every time you run it. The solution to this is to use a package called "ciopfs" - Case Insensitive On Purpose Filesystem. You should first run the "find . -depth..." command mentioned above on your mod folder. Then, make an empty directory outside of the mods directory, e.g. mods_caseinsensitive. You then mount the directory with
ciopfs mods mods_caseinsensitive
and tell ArmA3Sync to synchronise in the mods_caseinsensitive directory. Once it has finished, you can unmount the directory with
fusermount -u mods_caseinsensitive
You should find that all of the files in the original mods directory are lowercase.