...So that people don't spend five hours figuring out what sprites to delete when they remove the "extra animations" plugin.
Basically, there's an idea in the programming world that people should seperate their own stuff into their own "namespaces".
If you go into Minecraft's .jar file, you'll see some .class files and a couple directories. One of these directories is "net". If you open this, you'll see "minecraft". Back up a little bit. If I'm trying to tell java something's in that "minecraft" folder in the jar, what do I ask it for? "net.minecraft.file.class". This is a namespace. "net" is a directory in the root of the archive, and "minecraft" is a subdirectory of the "net" dir.
You might notice, this is basically a backwards "minecraft.net". This is because it is - notch organized it like that to keep minecraft-specific, notch-made code in one place in the archive, as long as it wasn't so important it deserved to be in the "root" namespace, which would make it "file.class". Why it's net.minecraft instead of something like notch.game, is because it's a naming convention - people who do that level of organizing tend to use their domain names as their namespaces.
You see this in greasemonkey script and ruby scripts too. Where am I going with this? I personally spent five hours gutting sprites out of the "Resources" folder, so I'm asking people who make plugins to start doing something like "Resources/Wareya/LaserFade/bloat.png" instead.
TL;DR: PUT PLUGIN RESOURCES IN SPECIAL FOLDERS OR PEOPLE GET FRUSTRATED REMOVING STUFF