The Mod I want to install is BuildCraft, so I am wondering how are you supposed to install Mods like that into a Bukkit Server?
This particular mod was designed for vanilla, offline Minecraft, so you aren't able to install it onto a Bukkit Server. However, had it been a Bukkit-compatible mod, you would download the files of the mod. Sometimes, you are provided with only a
.jar file (ex.
SomeBukkitMod.jar) – other times you are given a
.zip containing a
.jar and also a directory with the name of the mod containing preference files. Whichever you're given, put the files in the
/plugins directory of your Bukkit Server.
Despite this, it seems a Minecraft Forums user by the name of krnlyng has ported a few vanilla Minecraft server mods over to Bukkit, including BuildCraft. This thread is linked to from the official BuildCraft thread so I'm assuming it's reliable; at the time of writing, though, it's only compatible with 1.7.3.