ModsClients mods are modifications to the client-side game. They can improve your gameplay, fix annoyances in the original game, or simply customize your game more to your preference.
The most popular Siege clientmod in use is NewMod. It is a clientside code and assets mod which updates JA with many important features (such as automatic map downloading), bugfixes (allowing unlimited custom maps) and optimizations. NewMod is compatible with most server mods including base, JA+ and base_entranced.
Back in 2013, Raven software released Jedi Academy's source code. As a result, it's now possible to modify the game engine (jamp.exe). Included above is a build containing fixes for the most crippling bugs in the original engine.
NewJK is an executable that replaces jamp.exe, which launches when you start your game. It contains many crash fixes and features for Jedi Academy (JA) that are not possible with the vanilla JA executable.
GameData\base folder, usually /steamapps/common/Jedi Academy/GameData/base/.