I found out that run/resourcepacks and src/main/resources/ serve different purposes.
Resourcepacks
In run/resourcepacks/ you can add assets for existing parts of the game. E.g. to overwrite the texture of the vanilla creepers:
run/resourcepacks/
└── myresources
├── assets
│  └── minecraft
│  └── textures
│  └── entity
│  └── creeper
│  └── creeper.png
├── pack.mcmeta
└── pack.png
7 directories, 3 files
The content of pack.mcmeta:
{
"pack": {
"description": "My resources",
"pack_format": 64
}
}
For the pack_format for your version of MC see:
https://minecraft.wiki/w/Tutorial:Creating_a_resource_pack#Pack_format
pack.png is optional.
You do not have to zip the contents.
Resources
In src/main/resources you put the resources, i.e. client side assets, server side data, for your mod. E.g.:
src/main/resources/
├── META-INF
│  └── mods.toml
├── assets
│  └── myfirstmod
│  ├── items
│  │  └── banana.json
│  ├── lang
│  │  ├── de_de.json
│  │  └── en_us.json
│  ├── models
│  │  └── item
│  │  └── banana.json
│  └── textures
│  └── item
│  └── banana.png
├── data
│  └── myfirstmod
│  └── recipe
│  ├── my_first_shaped.json
│  └── my_first_shapeless.json
├── pack.mcmeta
└── pack.png
13 directories, 10 files
By
lmoellendorf ·