During conception of my modding system I defined a few name conventions for simple things.
Mods can be downloaded from servers automatically on connection, such mods are placed within the servermods/ folder and named by their md5 hash. Mods can be force-reloaded ingame (can cause issues!) by using control-F12
The default content of the games (core) lives in the res/ folder and can serve as a basis for how you should organize your mods files. There aren't a lot of subsystems that enforce some directories for their assets, but it's good practice to mimic what the base content does.
The mod.txt file provides information about the mod such as author, name or description. An optional, 128×128 modicon.png file may be provided to serve as an illustration.
Tip to modders: You may want to provide server owners with a seperate set of jars to put in their general plugins/ folder to avoid bundling serverside files to end-users ( for security, intellectual property and file size )
All .jar files found within a mod will be analyzed, the game will look for a plugin.info to determine wether the .jar is a plugin or not. The game will also lists all .class files in the .jar and allow their use in custom objects. Any classes loaded from within a mod will be put onto the supervision of a SecurityManager and will have restricted access to io, net, etc for obvious security reasons.