** This article was written upon the release of Complex item Sorter 1.9.  

DOWNLOAD THE INSTALLATION PDF ON THE FILES PAGE FOR CURRENT INSTALLATION GUIDELINES.

The focus of this document is only the installation of Complex Item Sorter 1.9 even though I recommend the entire FallUI suite.  CS 1.9 implements new feature and abilities which make future mod installation possible using only Mod Organizer 2.  Some mods previously require an .ini file manually installed into a CS folder and an INNR file installed in Mod organizer 2. 

Going forward only the MO2 installation will be required to install Mods.  Modders will be able to restructure INNRs into a Ruddy 88/CS convention using a one-line command in the <modname>.ini file.  Do NOT remove current INNR installations until a new file has been created to replace it.  Moving away from a separate INNR installation is not automatic.
 
The main Complex Item Sorter (CS) program does require a manual installation to function within xEdit. 

A successful FallUi CS build requires a proper foundation.  That foundation is covered in steps 1-5 of this article:
Installing the User Interface for a FallUI Complex Item Sorter Build

1. HUDFramework
- Required by Sim Settlements and other HUD mods
- - DEFUI Compatibility Patch NOT required
- - - Install with Mod Organizer 2.

2. DEF_UIIconlibs Rescaled and Fixed
- Install with Mod Organizer 2.

3. FallUI Inventory
- Check both Main FIles
- Check Optional File - MOD: Disable PipboyFX (unless you know for sureFallout4Custom.ini contains bPipboyDisableFX=1)

4. FallUI HUD
- Install with Mod Organizer 2.
- First time installation - check the top 3 options
- - ONLY use the MCM settings fix if you have MCM saving issues.  Read the
warning on that installer page.
- When updating - UNCHECK the MCM settings and only run the top 3 options.

5. Ruddy88's Simple Sorter INNR esp File
- Only get R88SimpleSorter_INNR in"Optional Files"
- This MUST get relocated to the end of the Load Order. 
- Only a couple specific INNR and the Complex Item Sorter output files follow the
R88 INNR file. 
** There is also an option for this in Complex Sorter options but I'm not using it as I require a couple INRR files after the R88SimpleSorter_INNR.esp in the Load Order.

CS 1.9 Preparation: If upgrading, rename the old Complex Item Sorter Folder:

• Install FO4Edit
• Install MXPF into your FO4Edit folder (Hosted on skyrim nexus, but the framework works flawless for FO4Edit)
• Copy the files from Complex Item Sorter to "...\F04Edit\Edit Scripts\"
  

New installation:

Folder explanations:

Plugins – M8r’s work – don’t touch it.
Rules (Default) - M8r’s work – don’t touch it.
Rules (Mods) – some default .ini files for configuring a few mods.  Just leave thisNEW folder and M8r’s default files alone. 
Rules (User) – ONLY used if you write your own files and want them to over-write any files in the MO2 \ Complex Sorter\ Rules
(Mods) folder.  This is the highest priority folder for mod.ini files.  I only have the default files here.

If this is a first-time installation of Complex Item Sorter, you are done. 

Take note that M8r has a ton of instruction and articles which are a great resource.  Refer to the "Quick Start" section for usage of the Complex Item Sorter script in xEdit:
M8r98a4f2's Complex Item Sorter
 
Continue to step 3 if you are a current CS user.
 
3.      Update mods which previously required manual installation of CS .ini files to FO4Edit\Edit Scripts\M8r Complex Item Sorter\Rules (Mods) folders.
·        Verify these mods are created to the Complex Sorter 1.9 standard.
·        Read the instruction on the mod’s page.
·        Install the mods into Mod Organizer 2.
·        The new format and installation of these files should be seamless to the end user.  However, there could be mods which require being moved in the MO2 Load Order.  READ THE MOD PAGE INSTRUCTIONS.

There are three new Mod Organizer 2 folders read by Complex Item Sorter 1.9.  These folders will be the target of downloaded CS .ini files.  These will be used by mod makers but will NOT show in MO2 unless created by a user or downloaded in a mod.  A user is not required to create these.

<PHOTO this POS interface won't let me post>

Plugins - Some mod makers could have plugins which go here but it is rare.
Rules (Mods) - This where tagging mods will be placed.  These have higher priority than files in FO4Edit\Edit Scripts Rules (Mods) folder.
Rules (Tag Configuration) – This will be empty unless installed by a mod with a custom tags.ini file.  It gets automatically combined with the tags.ini file in \FO4Edit\Edit Scripts\M8r Complex Item Sorter\Rules (Default).
 
Mod Makers:  Create your archives to the above Mod Organizer 2 folder structure as necessary.   If “complex sorter” is the only file in the“data” folder, add a dummy “sound” folder.

<PHOTO this POS interface won't let me post>   I'll comment on this article using the last section with photos.