Well, I made some modifications to the default files, by using the same package names in my mod as the default packages. It works fine when I launch MC through eclipse, but when I build my mod and put it in a normal minecraft environment, it doesn't work. Everything that isn't a net.minecraft package is loaded, and MC doesn't crash or fail. Any ideas?

Forge doesn't support modifing base classes. Plus the way you did it wouldn't work anyway. To do so you would need to decompile minecraft code edit it and then recompile it and use that as your jar file to launch minecraft, which wouldn't be compatible, what is it that you are trying to change?

Well it was my whole idea to modify the default minecraft experience. Essentially, it's adding a fourth difficulty to minecraft: Insane. And of course, I need to change attributes of mobs and AI etc. If forge doesn't support it, why does it work when I launch through eclipse?

Because that is the way java works. If forge supported it you would be able to modify the forge source directly leading to incompatibility between mods. You can change the AI of mobs in the way I suggested here

http://www.minecraftforge.net/forum/index.php/topic,40955.0.html

So how would I go about replacing the default mobs with replacements that have have what I want? I'm fairly new to modding (but not coding)

Well first you need to Subscribe to an event called LivingSpawnEvent here is a good tutorial on EventHandlers. You'll want to take the entity given by the event parameter and scroll through the tasks field and change the AI to it's corresponding alternative.

Well, the problem is that I am not only changing AI. I'm also changing their attributes and AI that can't be changed. (Such as the skeleton burning in daylight)

It is possible to change attributes as well

AttributeModifier modifierHealth = new AttributeModifier(((EntityMob)event.entity).getPersistentID(), ((EntityMob)event.entity).getPersistentID().toString() + "_Health", level * 4, 0);
		((EntityMob)event.entity).getEntityAttribute(SharedMonsterAttributes.maxHealth).applyModifier(modifierHealth);
		((EntityMob)event.entity).setHealth(((EntityMob)event.entity).getMaxHealth());

The reason that Skeletons and Zombies burn is because they are an instance of Undead, has nothing to do with AI. Though there is an AI that makes skeletons flee from the sunlight.

If you don't want skeletons to burn during daylight, you need to subscribe to the right event and replace the entity spawned with your own custom one.

What Draco18s said is the best way to do that. Although you could probably use LivingUpdateEvent to extinguish all entities with the EnumCreatureType UNDEAD if they are on fire (Note this is very lag intensive).

Ok, thanks guys. I'll look through some forge events and see how to do it tomorrow. Thanks!