One of the biggest differences that I see is since plugins are based on the server side people can join without having to download and install anything to their game. For example you could play on a feed the beast server but would need to have all the server's mods loaded into your client first. Compare that to a factions server where anyone can join with an unmodded client and have access to the faction plugin.
I'm sure there is probably a more technical reason for why mods are not called plugins other than to just differentiate them though. Someone who knows more about coding would have to answer that.
",sans-serif">Mods vs Plugins, What's the difference?
As we know, normally mods are used in minecraft client to make the single player world more interesting, whereas plugins are used in server to make it more efficient and fun.
But when you take a closer look at plugins, they are made to modify the minecraft server, which works the similar way as a mod does to a minecraft client.
But again why does mod for server not called mod, but plugins?
From my own opinion it's purely just a disambiguation attempt, being able to distinguish between a mod and a plugin upon first glance. In software mod, plugin, add-on, add-in, etc are all interchangeable, in Minecraft a mod is any modification to the game, where a plugin is a specific kind of modification which only has to be installed on the server.
A mod typically has to be installed on both client and server, or only client (don't ask me why a client-only mod is a mod whilst a server-only mod is a plugin, I don't know). A plugin typically has to only be installed on the server and any client can connect to the server and work with the plugin just fine, no matter if you're running mods yourself, your client will work on a Bukkit server.
Because of this difference (mod being universal (client and server), plugin being strictly server-sided), a mod is much more flexible than a plugin. Where a mod can add new content, change existing content and piggyback on existing content, a plugin can only do the latter two (change and/or piggyback on existing content), it cannot add new content as you need code on the client to tell it how to render and the resources required, such as textures, models, sounds, etc. A plugin is only on the server, so it cannot do this.
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Author of the Clarity, Serenity, Sapphire & Halcyon shader packs for Minecraft: Java Edition.