Why does my mod work on Windows but not Linux?

This is almost always caused by the case sensitivity difference between Windows and Linux:

• Windows is case-insensitive: beans.txt and BeAnS.tXt are equivalent.
• Linux is case-sensitive: beans.txt, Beans.txt, and beans.TXT are all different files.

For example when the game looks for "MasterBundle.dat" it will be found on Windows if the file is named "masterbundle.dat", but not found on Linux.