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Lua Config Directory Structure

Example Structure

    ~/.config/nvim
    |-- after/
    |  |-- plugin/
    |-- ftplugin/
    |-- lua/
    |  |-- myluamodule.lua
    |  |-- other_modules/
    |     |-- anothermodule.lua
    |     |-- init.lua
    |-- plugin/
    |-- syntax/
    |-- init.lua

~/.config/nvim/

~/.config/nvim/lua

The directory structure for lua files: 

    ~/.config/nvim
    |-- after/
    |-- lua/
    |  |-- myluamodule.lua
    |  |-- other_modules/
    |     |-- anothermodule.lua
    |     |-- init.lua
    |-- init.lua

Anything that goes in ~/.config/nvim/lua can be loaded with require Then the following Lua code will load myluamodule.lua: 

require("myluamodule")
Do not include the .lua extension.

Loading other modules in subdirectories (other_modules/anothermodule.lua) is done with / or .: 

require('other_modules/anothermodule')
-- or
require('other_modules.anothermodule')

Any directory that has an init.lua file can be required directly, without having to specify the name of the file: 

require('other_modules') -- loads other_modules/init.lua

So, this structure: 

    ~/.config/nvim
    |-- after/
    |-- ftplugin/
    |-- lua/
    |  |-- myluamodule.lua
    |  |-- kolkhis/
    |     |-- set.lua
    |     |-- remap.lua
    |     |-- init.lua
    |-- plugin/
    |-- syntax/
    |-- init.lua
If you have, in ~/.config/nvim/lua/kolkhis/init.lua: 
require('set')
require('remap')

You can require it in ~/.config/nvim/init.lua 

require('kolkhis') -- just the directory name, since there is an init.lua inside it
Then everything you required in lua/kolkhis/init.lua will be loaded.

~/.config/nvim/after/plugin/

Anything in this directory will be automatically loaded after everything else.

Run Config Files from a Different Location

Set the $NVIM_APPNAME variable to the location that you want nvim to look for config files.

export NVIM_APPNAME='/home/kolkhis/test-nvim-config'
The directory structure of this directory should be the same as $XDG_CONFIG_HOME/nvim, but will allow you to switch to a different configuration.
Useful for testing.