Final MO2 Update until Videos

Again, this information is private for now so please keep it here = )
Half the info is done. Half is my MO1 stuff brought over, being fixed up and worked on. Just want to show you folks again the extent of what I do when you you don't see me doing anything lol. I wouldn't read through all of this but perhaps just a quick skim.... lots to edit still. This is 4 videos worth of text at the moment.

Guide: Mod Organizer 2 : Start to Finish

Playlist: Mod Organizer 2 : Official Series

Text by: Michael of GamerPoets 

Additional Resources: AL12, GrantSP, Roy Batty, STEP wiki & Tannin (MO1)

-Installation & Setup

-Mods & Management

1.0 Installation & Setup

1.10 Preface

Welcome to the official Mod Organizer 2 series. 

MO2 is a mod manager in constant development. When the creator of MO1 left to join Nexus he made the code open source for others to improve upon. Since then persons from all over the world have been donating their time and abilities to this tool that they believe in. If you feel that you could help the project it’s official contact information is provided. The MO2 repositories are linked for reference as well. 

For Elder Scrolls and Fallout games from Oblivion onward MO2 is and most likely will remain my mod manager of choice. Deal breaker bugs of the past have been fixed and advancements are consistently being made. 

1.11 About the Games

-Oblivion requires additional tweaking for MO2 to work with it 

-FO3 and FNV receive benefits in how the archives are handled compared to MO1

-Skyrim LE works perfectly with MO1 but I have no reason to not to use MO2 for it

-64bit games are not manageable by MO1 at all

1.12 What to expect from Mod Organizer 2

-Easy plugin and asset management via left and right pane load order 

-Simple and straightforward functionality

-A physically and visibly clean data folder

-The ability to see and troubleshoot conflicting files from one mod to the next 

-Profiles for different mod configurations of the same game

-The choice to use 1 installation for all games that MO2 manages

-A single location for the majority of our modding tools to be launched from

… and the list continues.

Everything that I’ve mentioned and more is covered in this series. Videos will be updated pending major advancements and adjustments.

1.20 PreInstallation

1.21 Game Prep

-This series assumes that your games are properly installed and tested prior to downloading Mod Organizer. 

1.22 Archival Program

-An archival program is needed to extract MO2.

1.23 Register with Nexus

- If you have yet to do so create an account with Nexusmods.com.

1.30 Installation

-Navigate to the Mod Organizer 2.

-Download the Main Standalone Version.

-Locate the Mod Organizer 2 archive that was downloaded.

-Right-click it and select Properties. At the bottom of the General tab, if present, activate the Unblock checkbox to assure that all files extract properly in the next step. Apply then select OK.

-Open the archive then drag and drop its contents into a folder of your choosing. I create an MO2 folder on my storage drive and place the files there. 

-Send a shortcut of the ModOrganizer.exe to your Desktop and launch it. 

-At the Select window there are 2 options:

1. Create a New Instance, which allows the usage of 1 executable to manage all games by later creating additional instances when needed.
2. Create a Portable Instance which requires a new installation of MO2 per game like MO1 does.

For this guide we use 1 installation to manage all of our games. A playlist for MO1 is provided for reference. 

-At the Enter Instance Name window select a title from the dropdown or enter a name of your choosing: Enderal, Tale of Two Wastelands, your characters name, so on. Once this instance has a title select OK.

-Select OK at the Data directory window then choose the first game for MO2 to manage. 

-Select No at the tutorial window and Yes when asked to associate MO with nxm links. 

1.40 Initial Setup

1.41 Pathing

By default MO2 uses AppData to store it’s files. Here we change those directories to meet our storage needs. You can create directories anywhere excluding Game folders. Once you start installing mods and tools do not change these paths. Changing paths does not automatically move the files in the original destination, which means what was previously installed will need to be reinstalled into the new directories. Again, only change paths now while setting up MO2.

-From the Toolbar open Settings (the Wrench and Screwdriver icon) and then the Paths tab. 

Selecting the ellipses to the right of the following directories allows you to choose a new location for them.

1.411 Directories

-Base Directory contains a few miscellaneous files as well as all of the following file paths. Setting the following paths to %BASE_DIR% allows them to be moved with the Base Directory and kept inside of it. I suggest choosing a location on your storage drive if you have one.

-Downloads is where unpacked mod archives are stored. If available choose a location on your storage drive to save disk space as archives use a lot of it. 

-Mods is where the actual mod files, Loose Assets, Plugins and Bethesda Archives, are stored and from where they are loaded into the game. These are the files that can be seen by double-clicking a mod in the left pane of MO. This directory should be placed on the same drive as the game to assure the fastest possible read speeds. 

-Caches is where MO2 stores data to help maintain smooth processing. This uses little space and should be left in the Base Directory.

-Profiles contains all the modded setup information such as ModLists, LoadOrder, Profile inis and Saves. The location should not impact performance unless creating a plethora of Quick Saves, which is something that I advise against in various guides. I leave it in the Base Directory but it’s location is up to you.

-Overwrite is where MO stores newly generated files that would generally be placed in the games Data directory such as those created by xEdit. I put this on my game drive with the Mods directory as it is treated like a mod at the bottom of MO’s Left Pane.

Files such as CrashDumps, Logs and Mod Organizer’s ini file will always remain in AppData. This is because these files have to be available even if the Base Directory has not yet been read from MO’s .ini file.

1.42 Linking MO2 w/Nexus

-Select Settings from the Toolbar. 

-Open the Nexus tab and activate Automatically Log-In to Nexus. 

-Enter your nexus Username and Password. 

-Select Associate with “Download with manager” links. This, as well as entering your Log-In info, allows you to utilize Nexusmods MOD MANAGER DOWNLOAD function. Select OK.

-From the Toolbar, select the Nexus Network (Globe Icon) to be brought to Nexus via Mod Organizer. 

-To prepare for the next step download a mod via a Mod Manager Download option. Any mod. It doesn’t matter what one. We aren’t even going to install it. We do this to allow Mod Organizer to register the available nexus servers covered in the next step and to finalize the connection between MO2 and Nexus.

-Open Settings again and then the Nexus tab. 

-The Known Servers window should now display servers that are available to you. If you don’t have a Premium account you may only be able to use the CDN (free) option. 

-Highlight the Known Server closest to your geographical region. Drag and drop it into the Prefered Servers window. From now on M.O. will attempt to use this server before any others to assure the fastest possible mod downloads. Once finished select OK.

-From the main interface select the Downloads tab. Right-click the mod archive that we just downloaded and Delete it. 

1.43 Archive Invalidation

Archive Invalidation allows mods to override the official files in Bethesda’s Archives. This may not be needed at all for 64bit games. However, performing the following task as a precaution won’t cause any issues.

-From the Toolbar, select Configure Profiles (ID Icon). 

-In the Profiles window activate the Automatic Archive Invalidation checkbox. Remember to do this for each new Profile that you create if you decide to do this at all. 

1.44 Anti Virus Exclusion List

If you use an AntiVirus program, to prevent it from blocking or deleting MO2 files, you should add MO2 to it’s exclusion list. I don’t use one so I can’t show you how it’s done.

1.50 Additional Games

Now that you have established the basic setup for your first game you can do the same for others. 

-Select the Instance Selection Dialogue icon at the top left of the Toolbar and select Yes.

-Create a New Instance and continue forward exactly like we did for the first game. Repeat all steps for this new game including file path setup by creating and selecting new folders. 

-To switch between established games, from the Instance Selection Dialogue, simply select an Instance previously created, signified by an arrow.

2.0 Mods & Management

2.10 Downloading Mods

Here we cover the various ways to download mods from Nexus, Steam and other places as well as the basic installation steps for each. The different installation Pop-up windows are covered in the following section.

2.11 Nexusmods.com

2.111 MOD MANAGER DOWNLOAD

Each mod on Nexus has a Files section, which is where mods are downloaded from. The MOD MANAGER DOWNLOAD option, if setup properly in the previous guide, will download the mod to M.O.’s Downloads directory. The archive will then be displayed in the Downloads Tab, which can be double-clicked to install the mod. Once installed the mod will appear at the bottom of the left pane where you can activate it by ticking the checkbox and then drag its position up and down to alter it’s priority. Load Order is covered a bit later. 

2.112 MANUAL DOWNLOAD

This option is not only helpful for some but necessary if Mod Organizer and Nexus are having issues linking to each other. Selecting MANUAL DOWNLOAD downloads the mods archive to your systems default location. From here there are two options:

1. Leave the archive where it is. From M.O.’s Toolbar select the Install from Archive icon. From the explorer navigate to the mod. Double-click it. One of M.O.’s various install options windows will open. Install the mod accordingly. I prefer to not use this method as it’s easy to lose track of the archive and or accidently delete it.
2. The prefered manual method is to navigate to where the archive was downloaded to. Drag and drop the archive into MO2’s Downloads tab. Not only will the archive appear here but a copy will be added to your Downloads directory just as if you used MOD MANAGER DOWNLOAD. This option can be applied to any mod archive on your system regardless where you downloaded it from.

2.113 Downloads Tab Note

If you delete a mod from the Downloads tab it will also be deleted from the Downloads directory. Deleting mod archives is not advised because many mods, at some point, may no longer exist due to their authors removing them. Delete mods with caution. If you can help it don’t delete them at all unless you are sure that you will never want to use them again. 

2.12 Steam Workshop

2.121 Downloading Process

-From the Steam application. Expand COMMUNITY. Select Workshop. Search for your game. Once you come across a mod that you want to install, to do so, you have to Subscribe to it.

-Once subscribed to a mod RUN the <Game> Launcher from within Mod Organizer. Wait for a synchronization message to appear at the bottom of the menu. Let it complete it’s process. Once complete Exit the launcher. 

-Scroll to the bottom of the left pane. Open Overwrite. Notice that the Steam files are now located here. Close Overwrite. 

-Right-click Overwrite and select Create Mod. Name the mod anything you wish, preferably the mods official name so that you know what it is, then select OK. 

-Activate the mods checkbox at the bottom of the left pane.

2.122 Issues with Steam Mods

If you RUN the <Game> Launcher after a Steam mod has been updated the new files will automatically download whether you want them to, or expect them to, or not. If a Steam mod is activated when the launcher is RUN, without warning, it will auto-update all its files and delete the old ones. This can cause all sorts of issues in a current playthrough. If the Steam mod is not activated the updated version of the mod is placed in Overwrite. In this scenario, even though the old files still exist, issues can arise. 

What you need to know here about Overwrite is that everything inside of it is always activated at all times as if it were a mod itself. Overwrite acts as a mod that always has highest priority and it overwrites all matching files in your load order. 

To avoid issues with Steam mods, after you install one, unsubscribe from it so that it cannot auto-update. Doing this may not be appreciated by the mods author but it’s the only guaranteed way to protect your save file and load order. 

2.13 Other Mod Sites

When downloading mods from non-Nexus sites archives will have to be installed manually. 

-Place the archives that you download into MO’s Downloads directory and install the mod via the Downloads tab. 

2.20 Installation Pop-ups

Different mods and different download methods cause various windows to pop-up during installation. Here we cover what those windows mean and what to do in each situation.

2.21 Quick Install

This window opens when installing a mod for the first time that appears to be properly packaged for installation. 

- Cancel cancels the installation

- OK is generally what you want to choose as it allows MO to seamlessly install the mod.

- Manual opens additional installation options. Generally used if you are aware that a mod is packaged improperly; a folder is missing or the mod structure is incorrect. The window that you are presented with represents the archives contents exactly how the author packaged them. From here you can:

• Organize files and folders the same way that you would in windows explorer, by expanding the arrows then dragging and dropping items. 
• Deactivate a checkbox so that none of the files or folders within it will be installed. Useful is a mod is packaged with multiple options.
• If you receive the error message No game data on top level, right click the Data folder with the checkbox next to it and select Set data directory. The error message should change to a Looks good message. 
• The other right-click options allow you to undo the Set directory and to create a new one, or rather a new folder, to organize things into by dragging and dropping items.
• At any point, select OK to install the mod or Cancel to cancel the process.

2.22 Improperly Packaged Mods

If installing a mod that M.O. detects as being packaged improperly the Install Mods window will open. This is the same window that opens when selecting the Manual option from the Quick Install window. 

-With these mods you will notice the No game data on top level message. As previously mentioned right click the Data folder, the one with the checkbox, and select Set data directory. The error message should change to a Looks good message. 

-If it doesn't change expand all of the arrows and search for the proper top level folder to Set data directory for. Select OK to install.

2.23 Mod Pages w/Multiple Archives & Updates

Some mod pages have multiple archives that can be installed. These could be full updates, hotfixes, optional resolutions, so on. The situation that I present here is if you have already installed your first mod from a particular page and now you plan to download and install another from same one. This scenario presents a few options.

• At the Quick Install window select OK. The Mod Exists window will open. From here you can:

1. Merge: which is used the majority of the time. This option adds all of the contents from the additional archive to the existing mod from the same page merging the two together. If any files are duplicates, generally updates, the files being installed will overwrite the old ones. This also leaves personal changes that you have made to the mod intact. Think of this as an addition to a mod that is already installed.
2. Replace: generally not recommended unless you have a sound reason to do so. This option completely replaces the original mod with the new archives contents. Think of this as a clean wipe and reinstall.
3. Rename: allows you to rename the archive that you are currently installing, which allows archives from the same page to act as two separate mods.
4. Cancel cancels installation. 

2.24 Installer Pop-ups

Some mods have Installer windows to allow you to manually choose options and customize the mod to your liking. Generally these installers work no differently in Mod Organizer than they do in any other Mod Manager. Make your choices and install the mod as normal. Game specific mod installers are covered in the Game Specifics portion of the series.

2.30 Load Order

Load Order generally refers to the order in which plugins are loaded into the game. Mod Organizer not only manages load order for plugins but also for assets. 

2.31 Plugin Load Order

The plugin load order is displayed within the Plugins tab. In general, M.O.’s Plugin Load Order works like every other manager. 

• You can drag and drop items to arrange them or you can double-click on the priority of a plugin and type the priority number. This will move all following plugins accordingly. 
• You can right click in the plugins tab to enable all visible plugins, disable all or lock individual plugins in place so that it cannot be moved. 
• If you want to see what mod a plugin belongs to you can highlight it and the mod will also be highlight in the left pane as well on the scroll bar.
• A game's main plugins, not the DLC, should always remain in the game's Data folder. Mod Organizer gives it lowest priority and grays it out so that you can’t move it. 
• At the top of the Plugins window there is a Sort button. This button runs an internal LOOT masterlist to sort your plugins. MO2 checks the official LOOT list and if it needs to be updated it does so automatically. The only reason to launch LOOT from MO2 would be to use it’s UI features. MO2 even stores personal user rules made from the LOOT interface when it’s RUN through MO2. 

2.32 Asset Load Order

Mod Organizer allows you to arrange mod assets in the left pane just as you arrange plugins in the right. 

• Mod assets in the left pane overwrite duplicate assets with a lower priority number. A mod at Priority 10 overwrites any duplicate files in mods at priority 9 and lower. 
• While mods with higher priority overwrite lower priority mods they do not delete anything. This means that you can drag and drop mods into different priority slots without ever having to reinstall them. 
• Like the Plugin Load Order you can drag and drop position or double-click the Priority number and change it manually, moving all other mods accordingly. 

2.33 Bethesda Archives

Bethesda Archives are covered in full in the Modding 101 series. Here we need to understand how Mod Organizer loads them into the game. 

2.331 Archives Tab

From the main interface, in the right pane, open the Archives tab. All Bethesda Archives, .BSA’s and BA2’s, that MO detects, activated or not, are listed here. 

• The main entries directly correspond with the mod titles in the left pane. 
• The grayed out sub records are the actual Archives contained within those mods.
• The activation state of an archive, signified by it’s checkbox, can only be altered by activating or deactivating the corresponding mod plugins. You can deactivate a plugin in the Plugins tab or deactivate the entire mod in the left pane. 
• Archive Load Order works the same way as other Load Orders. Archives load into the game top to bottom. Their position here reflects their plugins load order Priority in the Plugins tab. Move a plugin that loads an archive lower in Priority than another plugin that loads an Archive and the Archives tab load order will reflect the change.
• Bethesda Archive files only overwrite other Bethesda Archives

2.332 Archives Load Before Loose Files

Those familiar with MO1 need to pay close attention to this subsection as MO2 does things differently here. These differences, while less prefered by some, avoid issues that the original system posed with newer games. 

All bethesda Archives, regardless of Left Pane and Plugin Load Order, load into the game before loose files. This means that all loose files take precedence over archives. Think of it like this:

• First: the Archives tab loads into the game top to bottom. 
• Second: all other files in the left pane load into the game top to bottom. 

To make this even easier think of the Archives tab as being a mod located at the top of the left pane with a Priority of -1. Everything that comes after the entire Archives tab will take precedence over it based on this order. 

2.34 Overwrite

One of the most useful, unusual and initially troublesome features of the Asset Load Order is the Overwrite mod. It is called the Overwrite Mod because it does in fact act like a mod. It maintains the highest priority of all mods that are installed and acts as such. Others call it the Overwrite Folder because it also acts as an import/dumping folder for all applications RUN through Mod Organizer. 

If you run a program through Mod Organizer, such as xEdit to create a Merged Patch, the output of the application RUN through M.O. appears in Overwrite. You then have to right-click Overwrite, select Create New Mod and continue on. You can also open Overwrite and drag and drop the files inside to a mod that already exists in the Left Pane.  

I cover third party applications later in the series. What we need to understand here is the importance of keeping Overwrite empty at all times. Otherwise, it’s easy to unintentionally overwrite files in your load order and to accidentally delete something in overwrite that a current save files needs to function. Always Create New Mod or drag and drop the files to an already existing mod as shown. If there is anything in Overwrite the Warning (Yield Icon) at the top right of the interface light up. Selecting the Warning presents you with a Problems window informing you that There are files in your overwrite mod. There are very few exceptions to this rule and mods that make them mention it in their descriptions.

2.40 Mod Information

The Mod Information Window offers not only information about a selected mod but also provides some important features. 

-To open the Information window, in the left pane, either double-click a mod or right-click and select Information.

1. Textfiles: The left pane lists all text files in this mods directory such as Read-Me’s. The right pane allows you to read the selected document as well as add, remove and save any information that you care to type. Be sure to select Save.
2. INI-Files: Lists every .ini file located in the mods directory. This includes game .ini file tweaks as well as script extender .inis. These tweaks override your default .ini settings but only when the mod is activated, which allows for specific tweaks to be implemented on a mod to mod basis. The Ini Tweaks window should be ignored for now.
3. Images: Displays any image files packed with the mod. 
4. Optional ESPs: This tab offers the ability to hide or reveal plugins that are packed with the mod. 

• This is beneficial for mods that contain optional plugins that you may want to use one day but are currently deactivate and taking up plugin space. 
• It allows for Merged Plugins to be hidden instead of deleted.
• It allows for patched mods with identical plugins to be able hide the original but to still keep it readily on hand incase you remove a patch and need the original plugin reinstated.

To hide or reveal a plugin simply highlight it in either the Optional ESPs, hidden, window or in the Available ESPs, Load Order present, window and select the Up and Down arrows to move them.

1. Conflicts: This tab shows each and every file within the selected mod that is being overwritten by another and that the selected mod is overwriting elsewhere. Information as to how many conflicts the current mod is generating, how many conflicts that other mods are providing to this mod and how many Non-Conflicted files is provided. In the top window, if the current mod is overwriting a file from another mod and you don’t want it to, you can right click a file, select Hide, and the file will be hidden and it will no longer provide a conflict. Very helpful for those who are really trying to manipulate what textures they want present in game. We cover how to Unhide a file in the Filetree tab.
2. Categories: allows you to change the mod category that is displayed in the Category column. 
3. Notes: Allows you to write down any notes that you may need to remember for the mod. A notepad icon will then be generated in the Flags column of the main interface.
4. Nexus Info: displays all of the text that is on the mods Nexus description page. The tab also displays the mods meta information: the Mod ID and Version number, both of which can be edited manually if desired. 
5. Filetree: displays all of the mods contents, including files that are hidden and the M.O. generated metadata. You can edit the Filetree the same as you would from windows explorer, except that you cannot create text files from this window, only New Folders. You can Open files from here, extremely useful if you are someone who edits textures, as well as Rename, Delete, or Hide them. 

If a file has been hidden you can search through the file tree until you find the appended extension .mohidden. Right-click the file. Select Unhide and the file will be reinstated into the game, overwriting conflicting mods with lower priority. 

2.50 Meta Information

Meta Information is mod info that M.O. has queried nexus for to use for various reasons, mainly to inform you about mod updates. If you aren’t concerned with update notifications via Mod Organizer, as you can simply Track the mod on Nexus, than you can skip this section. Missing Meta info will not have any affect on your game whatsoever.

- Double click a mod. Open the Nexus tab. Here you will see the Meta Information: Mod Name, Mod Version number, Mod ID. If meta information has not been collected for a mod a warning, Yield Icon, will be displayed in the Downloads tab in front of the mods name.

- To attempt to retrieve this info, in the Downloads tab, right-click the download file. Select Query Info. If a Select window opens you have to select the correct nexus ID option for the mod. This ID corresponds with the final numbers of a mod pages url. If the correct option isn’t provided select Cancel.

- If a window opens asking you to Please enter… Mod ID simply open up the mod page to verify what it is and type it in. Again, the ID corresponds with the final numbers of a mod pages url.

- If a window opens asking you to Select the correct file from the mod page, being that many mods provide more than a single download, select the appropriate file from the list.

In the end, meta information can fail even after following all of these steps. Reasons for this can be that the mod author has not assigned a version number to the mod, the mods File download page has more than 30 options to download from and your option was not detected from the first 30 or the file itself is not a Nexusmods mod and has been downloaded from a different website. 

2.60 Left Pane Context Menu

This section may be helpful for some but not for others. If you're going to skip this section at least take note of the Open in explorer option. To open the Context Menu right-click a mod. 

- All Mods: opens a secondary context menu where each option will affect each and every mod. 

1. Install Mod: Is the same as selecting the Archive Icon from the Toolbar. This opens the explorer to allow you to install mods that aren’t visible in the Downloads Tab.
2. Enable all Visible: will activate every check-box in the left pane
3. Disable all Visible: will deactivate every check-box in the left pane
4. Check all for Update: queries Nexus for mod metadata to check for updates and  endorsement status. 
5. Refresh: Refreshes M.O.
6. Export to CSV: exports your mod list to a .csv file which can be opened in an excel program.

- Mod Specific Options:

This section will cover the content menu when right-clicking specific mods.

1. Change Category: opens a drop down to allow you to add the mod in question to specific mod categories.
2. Primary Category: Sets the single primary category that will be displayed on MO’s main interface.
3. Change Versioning Scheme: Some authors add words or letters to their mod versions on nexus and M.O. will detect this as an error. Clicking this option will approve the mod version and remove the warning.
4. Ignore Update: Ignores a mods update warning removing the icon until another update to the mod is made
5. Rename Mod: Allows you to rename the mod. You can also rename the mod by clicking on it a single time to highlight it and then single clicking on it again. You can also push F2.
6. Remove Mod: completely removes the mod from your system. If you don’t have the archive stored in Downloads folder you will need to redownload the mod to get it back.
7. ReInstall Mod: Deletes the current mod settings and reinstalls it as if you downloaded it for the first time. For this option to work the original archive has to be in MO’s Downloads folder. If you no longer have the archive you will be notified.
8. Endorse/Unendorse: allows you to do adjust your endorsement of the mod the same as you can on the mod page itself.
9. Won’t Endorse: removes the not endorsed, Heart w/ Question Mark, flag for the chosen mod.
10. Ignore Missing Data: removes the missing data, Red X, flag to allow you to ignore that the mod is missing meta information.
11. Visit on Nexus: opens the mods nexus page as long as the meta information for the mod is had.
12. Open in explorer: Opens the mods Mod Organizer Mods folder in the explorer. I use this often when following mod guides. This quickly allows you to edit specific .ini files if mods have them as well as anything else that you want to remove or add to the mod. 

2.70 Left Pane Columns

As with the Context Menu information in this section may be helpful for some but not for others. If you’d like to skip this section at least take note of the Flags and Priority columns unless you are familiar with them.

1. Column Bar: Hosts each column. Right-clicking the bar will open a context menu. Deactivating any of the checkboxes will remove the respective column from the interface to clean up information that you don’t care to see.
2. Mod Name: is the name of each mod that’s installed. Remember that you may have chosen to give a mod a different name than it’s original. Clicking the Mod Name header will sort your mods alphabetically for browsing purposes.
3. Checkboxes: mods installed via mod organizer have a checkbox. You can activate and deactivate mods here without completely removing them. If you use Shift + click or Ctrl + click to highlight a number of mods you can push the spacebar to toggle the activate state of the entire selection. Mods installed to the game's Data folder that M.O. detects, such as the official game content, do not have a checkbox and are always active.
4. Flags: flags are icons that inform of conflicts, endorsement status and or potential issues. 

- Lightning Bolts: 

a. Green Plus Signs indicates that the mod is overwriting another.

b. Red Minus Signs indicates that the mod is being overwritten by another.

c. Both a Plus and Minus Sign indicates that the mod is both overwriting another mod and is also being overwritten. 

d. White Lightning Bolt: indicates that the mod is being totally overwritten and is serving no purpose. Generally, these mods can be deleted unless you think that you may remove the mods that are overwriting it. 

e. Red X: indicates that the mod doesn’t contain any data recognizable to MO. In addition to the red x the name will be greyed out and italicized. If you are certain that you want to keep this mod despite MO telling you that it's unusable, which there may be rare cases that you do, you can right click the mod and select Ignore Missing Data to remove the flag

f. Heart w/ Question Mark: indicated that the mod has not been endorsed.

g. Notepad: indicates that you have added personal notes to the mod.

e. Content: informs you of what each mod is comprised of via icons

• Puzzle Icon: indicates that a mod contains a plugin.
• Tool Icon: indicates that the mod contains non-plugin scripts
• Treasure Chest: indicates that the mod contains a .bsa file
• Checkerboard: indicates that the mod contains texture files
• Tournament Brackets: indicates that the mod is a script extender plugin.
• Armor Icon: indicates that the mod contains mesh files.
• Harp Icon: indicates that the mod contains sound files.
• Hand Icon: indicates that the mod effects a game's interface.
• Gods Hand Icon: indicates that the mod contains or is based on a SkyProc Patcher

f. Category: If your mods have category tags you can click the Category columns header to sort your mods by category for browsing purposes. 

Nexus ID: indicates the nexus ID for each mod. Sorting by this column will allow you to see what mods are oldest. Lower numbers being older mods. If the mod installed is not from nexus the ID will be set to 0.

g. Version: indicates the mod version. 

• If the number is Green than you have the newest version available. 
• If the number is Red then you don't. However, this can be misleading  as some mods use older files as their main file. 
• A Yield Sign indicates that the version you have is numerically higher than what MO is detecting as the latest mod version on nexus.
• A Calendar Icon is used when you install a mod that isn’t from Nexus.

h. Installation: lists the date and time that you installed the mod to Mod Organizer.

i. Priority: ...probably the most important column, indicates the priority in which mods are loaded into the game. 

When done looking through the columns make sure to sort your mods by the priority column, lowest to highest so that you see your actual Load Order.

2.80 Troubleshooting

1. None of the available installer plugins were able to handle that archive: If you receive this error message the archive that you are trying to install is mostly likely corrupt. Many times simply redownloading the mod and trying to install it again will fix this. If it doesn’t you may need to repack the mod into a new archive, removing any information within that is unnecessary such as fomod installers, or to simply omit the mod from your load order. 

2. MOD MANAGER DOWNLOAD doesn’t work:

• Assure that you have linked MO with nexusmods. Watch the Installation and Setup video to see how. Follow each step within.
• Go into the Mod Organizer directory. Locate the nxmhandler.exe . Double-click it to launch it. Make sure that the supported game is pointing to the appropriate mod organizer executable. If it already is, highlight it and select Register Active. At the Change handle registration? Window select Yes. If the game is not pointing to the proper executable, or if the game isn’t showing up at all, right-click within the NXM window. Select Add. From the Select Supported Games window select the game that this version of Mod Organizer is being used for. In the Binary window select the elipses. Browse to the ModOrganizer.exe that is being used for this game. If following our guides it will be located within the games folder and then within the Mod Organizer folder. Double-click the .exe. Back on the Dialogue window select OK. Select Register Active. Select Yes. Select Close.
• Finally, if none of this has helped open the Settings window. Open Workarounds. Change the NMM Version to correspond with the current Nexus Mod Manager version. You can find the version number on nexus or at the top of Nexus Mod Manager itself if you version is up to date. Currently, even having an old version number allows the DOWNLOAD WITH MANAGER option to work for me. Changing the number may or may not solve the issue but it has in the past. 

3. Cannot arrange Mods. At the bottom center of the interface you will see a dropdown. Make sure that the No groups option is selected. The other options will not allow you to rearrange mods.

Mod Organizer : Profiles, .ini Files, Third Party Apps

Preparation

This video is the third in the Mod Organizer series. Information from video one and two will not be repeated here and will assume that you have viewed it, which I suggest you do if you haven’t. Ready… Set… here we go…

Profiles

1. What do they do?

Profiles provide users with the ability to customize various playthroughs of the same game at the same time.

-Things that Profiles effect:

-Left & Right Pane Checkbox activation

-Left & Right Pane Priority Columns

-Archives Tab .bsa Management

-Local Saves

-.ini File adjustments

All of these things can be manipulated individually from profile to profile.

Things that Profiles DO NOT affect:

-Optional plugins

-Hidden files

-Mod Names

-Mod Categories

-Mod Versions

… and pretty much everything else

All of these things must and will remain the same throughout each profile. If you want to alter absolutely everything in your setup consider installing a second copy of Mod Organizer to the game folder and name the new Mod Organizer folder, during installation, something different such as: MO Install 2. 

2. Profile Window

To open the profile window select the Profile Tab, ID icon, from M.O.’s Toolbar. 

Create: allows you to create a new profile. Selecting Create opens a Dialogue window that allows you to name the new profile and implement the default game .ini files by activating the Default Game Settings checkbox. Select OK when finished. Select Close.

The new profile will now be active and can be changed via the Profile drop-down menu at the top of the left pane. All of your mods will be listed but none of them will be activated. 

Copy: allows you to duplicate pre existing profiles and all of the their settings allowing for a familiar foundation. Selecting Copy opens the Name window allowing you to name the copy. When finished Select OK. Select close. 

The new profile will now be active and can be changed via the Profile drop-down menu. All settings will be carried over as seen.

Remove: allows you to delete the selected profile and all of its settings.

Rename: allows you to rename the selected profile. 

Transfer Saves: allows you to transfer save files from profile to profile. 

You can also transfer saves by navigating to the Mod Organizer folder, Profiles/<Profiles Name>/saves and then copy and paste them into other profile save folders. 

Local Savegames: by activating this checkbox you will grey out the Transfer Saves option and only be allowed to see and use saves from the individual profile.

3. Load Order Backup & Restore

At the top of the left and right panes you can backup and restore the asset and plugin load orders. Selecting the icon with the Blue Arrow will create a backup that will be titled after the current date and time. Selecting the icon with the Yellow Arrow will allow you to restore a previous load order from the backups that you have created.

.ini Files

While most mod managers utilize the vanilla .ini files, located in My Games on the system drive, Mod Organizer keeps it’s own set of .ini files that it stores in the individual profile folders so that the user can adjust them differently between profiles. 

To access a profile’s .ini Files select the Tools, Puzzle Icon, from the Toolbar. You then have two options to choose from.

1. INI Editor: Opening the INI editor will present you with the Ini Files window where each of the game's .ini files are presented in individual tabs. You can edit the .ini files here exactly the same way that you would in the My Games folder with other mod managers. The default .ini files have no affect on Mod Organizer whatsoever. 

2. Configurator: the second .ini file editing option is the configurator. By opening the window you will be allowed to select and edit the different .ini file sections via a dropdown menu. The selected section will be presented in the window where you can then use the GUI to adjust settings as you desire. Selecting the interchangeable Basic and Advanced button from the top right of the window will hide and reveal different settings within each section. As always, if you have make any changes be sure to select Save. 

If you need help with editing your .ini files or care to see visual comparisons of each setting for each game .ini file video guides are provided. 

Third Party Applications

Most third party applications, such as xEdit and Merge Plugins, SkyRe and PerMa, Script Extenders,  LODGen mods and more, need to be executed from within Mod Organizer itself for them to function properly. The list that you have been viewing on screen is all of the executables that M.O. is suppose to autodetect for you. 

1. Modify Executables Window

To open the Modify executables window, which is where we manage third party applications, select the Gears icon from the Toolbar. 

Viewing Window: The viewing window is where each executable that you have installed is displayed. They can be selected and manipulated by changing the text fields below and choosing to either Modify or remove them. Titles that are greyed out can not be removed from this window as they are being auto-detected. 

Title: allows you to name or rename the selected application.

Binary: is the file path for the executable, .exe file, of the selected application. You can also choose .bat and .jar files, which mods like PerMa and Dual Sheath Redux require. To change the binary select the ellipses at the right of the field. Navigate to an application's executable and double click it. 

Start In: is the working directory of the application. The folder in which the executable is stored. Generally left blank unless auto-filled.

Arguments: is where you input command line arguments to be passed to the binary. 

Overwrite Steam AppID: only used for applications downloaded from Steam. I have never once had to fill this in. The only known app from Steam is the Creation Kits and it is setup automatically.

Close MO when started: Mod Organizer will close when applications are launched that have this checkbox activated. 

Use Application’s Icon for shortcuts: when activated, will use the applications Icon for shortcuts created for it through Mod Organizer. 

When you have finished altering the text field if this a new tool select Add to add it to your list, select Modify to save any changes made to a current application or select Remove to remove the application from your list all together. Select Close to exit the window. 

2. Launching Applications

To launch an application from within Mod Organizer open the RUN dropdown menu. Once the application is chosen select RUN. If setup properly in the previous step the application will launch.

3. How to add applications that are packed with Mods

Most mods comes with their executables packed inside of them. Instead of trying to add them through the Modify Executables window, a faster and safer way to do so is to: 

1. First make sure that the mod is properly installed to Mod Organizer.

2. Open the Data tab in the right pane. Scroll to the bottom of the window. Here you will see a set of arrows. All .jar, .bat and other application executables, that are packaged with installed mods, are sorted here. Expanding the appropriate arrow will allow you to see the executables within. Right click them. Choose Add as Executable and it will be added to your list. All files will be appropriately applied to the application. You can than RUN it as you would if you have added it from the Modify Executables Window. 

4. Overwrite

The overwrite mod folder was expanded upon in detail in the previous video. What you need to know here is that every application that you RUN through Mod Organizer will have it’s file output designated to the Overwrite. Once you have finished creating a patch or whatever else it is that you are doing via an MO launched application you need to right click overwrite and select Create New Mod. Be sure to view the previous video to learn all of the specifics about this process as well as warnings to look out for.

Toolbar & Customization 

0. Prep:

This video is the fourth and final installment in the 32bit Mod Organizer series. Information from the other videos will not be repeated here and will assume that you have viewed them. And a 1… and a 2… and a

1. Toolbar:

The Toolbar, as I’m sure we are at least semi familiar with by now, is located at the top of Mod Organizer. 

• Archive Tab: as mentioned in the Downloading Mods video, is used to install mods from archives. For in depth information about mods view the second video in this series.
• Nexus Tab: the Globe Icon will bring you to Nexusmods.com for whichever game that Mod Organizer is currently managing. 
• Profile Tab: the ID Icon opens the Profiles window which allows you to edit current profiles and add new ones. Profiles are covered in depth in the previous video.
• Modify Executables Tab: the Gears icon opens the Modify Executables window. This is where we add and manage all third party applications that are run through Mod Organizer. In Depth coverage of this option can be found in the previous video. 
• Tools Tab: the Puzzle icon opens a drop-down presenting two ways to modify your .ini files and a non-functional Nexus Mod Manager migration option. How to use the .ini file options is covered in the previous video.
• Settings Tab: the Tools icon opens the settings window. Here we can adjust practically everything that Mod Organizer has to offer including workaround implementation. Most of this window was covered in the Installation and Setup video, however, we will cover some customization options shortly. 
• Warning Tab: the Yield icon informs us of potential issues within our load orders. 

1. A Greyed Out icon: indicates that there are no major issues within your setup
2. A Colored In icon: indicates that you potentially have an issue. The number within the icon indicates how many issues you may have. Selecting the icon will open a window, which informs us of the potential issues. Just because something is listed here it does not necessarily mean that anything is wrong. Just be aware of changes you make to your mod manager. 

• Update Tab: will inform if Mod Organizer has an update. Since Tannin is no longer maintaining M.O. 1.3.11 is final version and updates will no longer happen. 
• Help Tab: provides with some helpful tips and information. Selecting Help on UI will allow you to highlight pieces of M.O.’s interface and if a question mark icon appears you can click on said piece and receive some information about it. 

2. Shortcuts

There are three types of shortcuts that Mod Organizer allows us to create. 

• Toolbar Shortcuts: to place a shortcut on your toolbar select an application from the RUN drop-down menu. Select the Shortcut drop-down to the right of the menu. Select Toolbar. You can now launch the application from the Toolbar instead of from the RUN button be selecting it’s icon. 
• Desktop Shortcuts: like the Toolbar shortcut, assure that the application is selected from the RUN drop-down menu; select Shortcut. Select Desktop. You can then launch the application via Mod Organizer from your desktop without M.O. even being open. 
• Startmenu Shortcuts: just like the other two options, select an application from the RUN drop-down. Select Shortcut. Select Start menu and a shortcut will be added there. 

3. Customization 

Mod Organizer offers a few ways in which you can change it’s appearance as well as a bit of display information. Open the Settings window.

• Language: allows you to select from the different language options of which Mod Organizer can be translated to.
• Style: gives you three options to choose from as to how you would like the interface to appear. You can also download and install additional interface options of which links will be provided in the description to a few pages that offer them.
• Compact Download Interface: if activated will shrink the mod archive viewing items in the downloads tab so that you can see more of them on screen at once.
• Download Meta Information: if activated will provide additional information in the mod archive viewing items.