Warning: This tutorial assumes you have the Justine patch installed for your Amnesia installation. Also, i'll only help others solve issues caused by this process 
only for the things i provided (exact) directions for. Note, also, this article should be considered a work-in-progress and may be updated if any issues arise.
Note: Although i provide this tutorial, i do not intend it to imply that everyone should consider making a full conversion simply because they can and have the resources. Changing entities and objects is not a proper justification for choosing to go with a full conversion. Proper justification would be for the sake of changing game mechanics, like night vision, sanity drain, oil drain, etc.
Due to the fact that a lot of full conversion mods out there have a complicated installation, making it difficult to keep your Amnesia installation clean, i have decided to teach people how to create a fully isolated full conversion mod where the user would only need to delete one folder to completely uninstall the full conversion mod. I find complicated installations for full conversions unacceptable for community-based full conversions, and wouldn't you prefer to have a fully isolated full conversion too?
First steps
Create a folder called 
test_mod under the 
redist folder (for retail edition) or the 
amnesia the dark descent folder (for Steam edition). This folder will contain everything our full conversion mod needs.
Inside the 
test_mod folder, create the following folders:
- config
 
- config/lang
 
- entities
 
- graphics
 
- maps
 
- main_menu
 
- static_objects
 
- textures
 
Configuration
Go into the 
config folder of Amnesia and copy over the following files to 
test_mod/config:
- default_main_settings.cfg
 
- game.cfg (use ptest_game.cfg for female voice)
 
- ptest_main_init.cfg
 
- ptest_menu.cfg
 
- base_english.lang
 
Under 
test_mod/config, rename the files so that they 
don't have the prefix "ptest_". Under 
test_mod/config/lang create the file 
english.lang or simply copy the one located at 
config/lang_ptest.
Be sure to also copy the 
resources.cfg file into the 
test_mod folder.
test_mod/config/main_init.cfg
Open the 
test_mod/config/main_init.cfg file for editing. Every attribute shown in there must remain there, or else the game may crash for failing to parse the configuration. All attributes should have a value, or else the game may crash.
Make sure that the values for the following attributes have a prefix of "test_mod/":
ConfigFiles:
- Resources
 
- Game
 
- Menu
 
- DefaultMainSettings
 
Directories:
- BaseLanguageFolder
 
- GameLanguageFolder
 
StartMap:
Make sure 
none of the attributes have "ptest_" or "_ptest" in their values. Be sure to also modify 
Variables::GameName, 
Directories::MainSaveFolder, 
StartMap::File and 
StartMap: os
os to match your story.
test_mod/config/menu.cfg
Make sure 
Main::BGScene has a value like "test_mod/main_menu/menu_bg.map". Make sure 
Main::MenuLogo points to something like "test_mod/graphics/menu_logo.png". Change the values if you choose to change the file names. The rest i'll leave up to you to modify (if you're courageous enough 

).
test_mod/config/default_main_settings.cfg
Add 
ShowPreMenu="false" to the 
Main element. Change 
FullScreen to "false", 
LimitFPS to "false" and 
VSync to "true".
test_mod/resources.cfg
Prefix the 
/main_menu, 
/commentary, 
/maps and 
/flashbacks directories with "/test_mod".
Make sure to 
add the following directories to the list:
- /test_mod/entities
 
- /test_mod/static_objects
 
- /test_mod/music
 
- /test_mod/sounds
 
- /test_mod/graphics
 
- /test_mod/textures
 
- /test_mod/gui
 
For any new directories just add them to the list as you go. Don't worry if the directories listed do not exist, as you can create them later.
Maps
test_mod/main_menu/menu_bg.map
This is the map used for the main menu (as you could guess). For the camera, just make sure to have a PlayerStart area with the name "CameraPos". The direction of the camera is towards the -Z of the local coordinates of the area (i.e. the small arrows of the area).
StartMap::File and StartMap::Folder
Obviously, the starting map when the player starts a new game. It should be obvious how to set this up for those who are used to creating custom stories.
System-dependent scripts
Batch file (Windows)
test_mod.bat (can be named differently, but must end with .bat). 
Needs to be placed in your full conversion's folder.
cd /d ..
Amnesia.exe test_mod/config/main_init.cfg
 (can be named differently; doesn't need to end with .sh). 
Needs to be placed in your full conversion's folder.
#!/bin/bash
FCNAME="test_mod"
# 64-bit operating systems
if [ "$(uname -m)" = "x86_64" ]; then
    ../Amnesia.bin64 "$FCNAME/config/main_init.cfg"
# 32-bit operating systems
else
    ../Amnesia.bin "$FCNAME/config/main_init.cfg"
fi
 (can be named differently but should end with .scpt). Could probably be placed anywhere; however, i have no idea (i don't own a Mac).
do shell script "open /Applications/Amnesia.app --args test_mod/config/main_init.cfg"
Everything else i'm going to leave up to you.
Note: If you don't have Steam or a redist folder, simply assume the directory where all the important files and folders of Amnesia are located in.
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