I read 

• Resource Packs
• Resources
• Tutorial:Creating a resource pack

As I understood I should place my resource pack files in:

src/main/resources/
├── META-INF
│   └── mods.toml
├── assets/
├── pack.mcmeta
└── pack.png

But in Minecraft, if I open Options > Resource Pack, I cannot find my resource pack.

However, if I zip the files above and put the zip into run/resourcepacks/MyFirstMod.zip, my resource pack shows up in Minecraft.

I assumed that ./gradlew build would take care of bundling my resource pack. Or am I supposed to zip the files and place them in run/resourcepacks manually? 

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

Edited October 31Oct 31 by lmoellendorf