There are guides about what mods are best out there. There are guides about how to configure all the great tools, and in what order the tools should get applied vs patches etc. Unfortunately, the mod install guides referenced in the FAQ are dead links, and I've yet to find a guide on how to install many (many) mods elegantly, such that you can easily swap them in and out and manage conflicts without major pain and suffering.

This topics goal is to detail just that, by outlining how to use the Installers tab on Wrye Mash to keep your install order the way you want it, and make it repeatable.

The way to get an easily maintained Morrowind install isn't really clear to the new and/or returning player. It takes some significant organization and understanding of Wrye Mash to really make things hum. This thread aims to help alleviate some of that pain by outlining how I've set it up on my system...and how you can use it to make mod install maintenance easier.

First Disclaimer: New players...don't go crazy with mods. Do a few here and there first. Its usually better to get your feet wet with not only the game, but the process of setting up the tools, and installing mods before diving into the deep end and getting tens or hundreds of mods and trying to do figure it all out when you have no feel for how it works to begin with. Start slow, play around with an initial character and a few initial mods, then set you sights on what you want after that.


Load Order vs Install Order

The first thing that's important to understand is that Load Order and Install Order are not the same thing. Install Order dictates which files in each mod get to make it into the Data Files directory, and thus which files the game runs with. Load Order tells the game which order mods that have esm/esp files should be processed in.

Its an important distinction. When it comes to maintaining Load Order (which this guide doesn't address as its addressed quite well in other places), use a tool such as mlox. It will make your life sop much easier.


Initial Installation

Install Morrowind, MGE, MCP, et al. There are guides and threads to help you with all this, so I won't go into any detail here.


Wyre Mash Setup

The tool that is going to make this all happen is http://www.uesp.net/wiki/Tes3Mod:Wrye_Mash. If you weren't going to install this for some (crazy) reason, this thread isn't going to help you. But you aren't crazy, and thus you are going to install Mash, so keep reading!

Download and install Wrye Mash....the self-contained one, *NOT* the python version. It will be much easier on you vs the Python version. If you do use the Python version, note you won't be able to change some things as mentioned below.

There are several things you'll need to configure.
- instruct Wrye Mash where your installers are. This is a full path to where you are organizing your mod install directories. This is an option in the options section. (I suggest your Morrowind/Tools as a root directory for all Morrowind tools....it just makes it easy to keep things organized)
- View Inactive Conflicts. Turn this on. It allows you to see conflicts relating to mods that aren't even installed yet, but their installer directory is known by Mash.
- Auto-Anneal. Turn this on. It's critical and will be described later.

It should be noted that the first time you click the installers tab its going to full scan. Let it go, you have to do it once no matter what. Also, most of the install/un-install works just like the Mods tab...right-click to get the options.

Its important to note that sometimes the Install Order column doesn't display correctly initially. Resize all the columns on the Installers tab until you see it...

Getting your Modlist

The single most important piece. Spend the up-front time necessary to download everything you might be interested in. Piecemeal installation will end up with you doing what I've done twice now...rebuilding your install. It probably doesn't matter, if you get heavily into mods, you're going to end up at that point, but up-front planning will significantly reduce the chance.

These threads are far better sources of information on mods than I can provide, thus I won't rehash what they already do very well.

http://www.gamesas.com/index.php?/topic/1155980-povuholos-tomorrowind-a-mod-recommendations-list-for-today/ - This is an extensive, maintained list and well worth your time to review
http://btb2.free.fr/morrowind.html - BTB's Guide - BTB's guide has a slant towards re-balancing Morrowind. If you like MW but don't like the economy....this guide is going to make you very, very happy.
http://www.gamesas.com/index.php?/topic/1060141-mod-recommendations-for-new-players/ - Mentioned by Povuholo, this is a great thread for mod ideas.

Review these, sources they mention, and any other sources, and generate your initial modlist.


Installation Location

Put all mods in a sub-directory of your Morrowind installation. I personally use a directory Mods for this. This is CRITICAL. Do not install directly to your Data Files directory, ever. It will make you sorry later on, which will become clear later.

A note about Windows Vista and Windows 7. These operating systems have dreadful issues with the Program Files directories unless you have turned it off (which I always do). Take heed to this and put your files in locations appropriate to how your specific Windows setup allows.


Downloading

With the browser of your choice, and the archive manager of your choice, start downloading and installing your mods. Uncompress them into sub-directoris of your Mods directory, naming them well. The naming here is actually going to make it easier later, so alphabatise the directory the way you expect you'll reference it. In other words, decide if Westly's Head Replacers should be named that, or Head Replacers by Westly or whatever. Just come up with a system that works for you and stick to it.


Directory Pruning

Not always required, but it will certainly make it easier down the line. Directory Pruning is going into each mods sub-directory and standardizing the structure. Mod makers don't package their mods in their archive files the same, so you will see some variants. Here are some of them:

1) Everything in the archive is in a parent level folder at the top of the archive. These archives typically assume you are going to unzip to a stand-alone directory
2) The archive starts with Data Files. These archives typically assume you will unzip to your Morrowind install directory, thus merging Data Files
3) The archive starts assuming you will uncompress into your Morrowind/Data Files directory. These archives always have Textures and/or Meshes etc as the top directories in the archive
4) Exceptions that have directory structures that don't fit these 3 common ones.

Its important to distinguish these early, and decide on a common structure that works for you. I personally re-organize every mod such that my Mods/ sub-directory looks like an archive of type 3 (above). I find it reduces mouse clicks as you manage mods.

This pruning is really important as Wrye Mash has specific layouts it recognizes (types 2 and 3). If you don't re-org a mod's structure, you aren't going to be able to manage its installation in Mash, which is the entire point of this topic.

You can leave zipped archives available and Wrye Mash will attempt to use them. If they fit the right layout, it will install/un-install them without issue. Its slower...and you don't have any way of trimming mods of "install this one if you MW, this one with MW+TB" extra esps that are just cluttering up everything otherwise (hint - get rid of them, they are useless to your setup)


README Reviews

You really should do this for every mod. There are plenty of them that just say uncompress into Data Files. These are the easy ones, and aren't the ones you're looking for, as Wrye Mash can deal with these blindly. What you are looking for are the Atmospheric Sounds/SWG Skies of the world that want you to do something else, like tweak morrowind.ini, or install something in the Morrowind game directory, or some other voodoo necessary to make the magic mod work. There are plenty of exceptions out there, so you want to always do this....just in case.


Understanding Wrye Mash's Install Tab

So, you've got all your mods installed in your Mods sub-directory and you're wondering why we did it that way. Well, Wrye Mash has the ability to install/uninstall mods sequentially, and back-install conflicts if you un-install. This really needs an example so here is one:

Assume you're starting to Povuholo's suggestion to start with Richer Textures (I do). You lay that down first. Now, you lay down Vibrant Morrowind on top of it. You play for a while and decide Vibrant Morrowind isn't for you. Without Wrye Mash, you are in a pickle. These two packs are simply massive.... reconciling Vibrant out such that you just have Richer Textures is such a big task by hand, you'd just start over, which is all well and good if you only have two mods (we're assuming you dont...) The beauty of Wrye Mash is it can back-install what's missing from Richer Textures when you uninstall Vibrant Morrowind.

Here's how it works: Wrye Mash scans your Mods directory (you'll have to point it to the right location) each time it loads for changes. It catalogs all files in all mod directories, denotes conflicts for individual files, and presents this information to you. Each mod has an installation order assigned to it, which determines install priority versus other mods. It then determines, based on the install order, what parts of a mod are superseded by higher order mods and what parts of a mod supersede lower order mod items. So in the example above, it would find both Richer Textures and Vibrant Morrowind, downloaded to the Mods directory. Even before installing, it would outline the conflicts between the two in the Conflicts tab for each mod. If you install Richer Textures and then Vibrant Morrowind, you would end up with the Data Files mash you would have had if you did it manually. However, now you can uninstall Vibrant Morrowind from Wrye Mash, and it will automatically reconcile Richer Textures to be fully installed for you.

Note that it is required to have Auto-Anneal turned on for this to work. Don't uncheck this in the Wrye setup. One install/uninstall with it turned off will doom your installation back to manaul editing and/or you starting over.


Coping with Install Order

It is very important to understand Install Order and Load Order are NOT the same thing. Install order has to do with priority of a mod's objects over another mods objects in the Data Files directories. And that install order can be difficult to deal with initially unless you install into your Mods directory in the order you want mods to go. The truth is, you didn't. I didn't. What happened is you downloaded mods randomly. Wrye Mash derives an install order somewhat mysteriously (I think its timestamp on the mod's installation directory or worse, alphabetically by directory name) before you instruct it on order, and this default order is baaaaad. Really bad probably. It might have the two texture packs mentioned previously reversed. It might have your Telvani textures in-between the two, essentially invalidating them as well. This has to be fixed....

So Wrye Mash accommodates you by allowing you to install mods with its last and move to (aka specific install order position) install options. By either installing last, you move a mod to the very end of the install order, making it the highest priority mod. By installing at a specific install position, you put the mod in install order at your desired spot in the order.

Well that's great you say, but I've got 100 mods all haphazardly in my directory, and I really want such-and-such mod first, this other one second, etc. Well, unfortunately, you're going to spend some time here re-ordering the install order to your preference, but the payoff is worth it. Once you have everything ordered the way you like, you can see all the conflicts between them in that order, and tweak it if something is overwriting something else you did not expect.

As far as what order you should choose, I always lay down textures/meshes first, with the larger texture packs leading the way, and gradually they get superseded by smaller replacer mods that were hand-picked. Then move on to quest mods, then clothes, etc. Whatever order your mods make the most sense in.

An alternate method of ordering, as suggested by Blouge takes more time to setup, but in the end is probably worth it if you are resetting your install with any frequency. Order your installers by directory name by renaming the directory to have 001, 002, ... as a pre-fix to the name of the mod. Apparently, Wrye Mash will set the default order by directory name. This allows you to go back and insert new mods mid-stream by using 001-1 or something similar. All that is required to get the new order is to save your previous order database (so you can go back) and then have Wrye Mash re-initialize to the new order.


Adding a Mod into your install order later on (thx Blouge)

- If the Mod/Installer is already installed, you might need to Uninstall it.
- Click on the Order column to sort Mods/Installers by their Install Order.
- Right-click on the Mod/Installer and choose Move To and enter the numeric position you want it to be moved it.
- Install it.


Coping with Mods messing with other Mods objects that you don't want to mess with

So, you've installed Connary's textures and really like them. You then Install Korana's closet (now at the end of the line and taking precedence). Unfortunately for you, Korana used a texture in there that's replacing one of Connary's. You may or may not like it. If you don't...Wrye Mash has a solution for this, as mentioned above. You'd simply re-order Korana's Closet to precede Connary's Textures in install order, thus Connary's Textures would supersede Korana's. Problem solved.

But what happens when you want to use 1/2 of Darknut's Creatures AND 1/2 of Connary's Creatures? This is a bigger problem. You have to manually prune the higher order mod's install files of the ones you don't want. In other words, install one of them, then inside the install directory for the 2nd one, remove all files you want to *not* include in the final game, those which the first mod's install should provide.

Hopefully this doesn't happen too often. For these mods that I'm removing files from their install path, I always save their original zip file somewhere so I can rebuild the entirety of that mod again if I want to. One Caveat, I've never had a problem with this, but its entirely possible some mods have duplicates they require to be there, or they won't function correctly. You'll have to experience this yourself with each mod to determine how much it can tolerate not having the texture/mesh/whatever it was packaged with.

Its too bad Wrye Mash doesn't allow you to set exclusions by object (at least, I haven't found a way to do it). This would be a fine addition to this app.


Wrye Mash nuancies you need to be aware of

- Its also known as BAIN
- Choosing Full Refresh on the installers tab can easily take 20 minutes to come back. Be prepared. You usually don't have to do this, but sometimes, you'll want to completely re-build. I don't encourage it, as it has the possibility of losing its install orders. Typically, don't do this other than the first time
- You have to Refresh Data if you installed a mod while you hade Wrye Mash running. It can take some time
- Every time you launch Wrye Mash, its going to Refresh Data automatically. Its going to take some time. Usually a minute or more. Its the price you pay.
- If you update the contents of a mod while you have Wrye Mash open, you can Refresh a single mod's directory.
- The Diamond Color is important. Read the Wrye Mash help file. You did that already didn't you? There are colors on all the tabs, and they mean different things.
- if you have a greyed otu diamond, that means the mod isn't in a valid directory format...you have to fix that as described above.
- you're going to have Animations and other things that Wrye Mash won't/shouldn't install. Just leave them greyed out. You can put a little note in the comments tab.
- Use the comments tab. ESPECIALLY for mods that have special non-Wrye setups like ini tweaks. You'll be happy later when you un-install it.
- When making your BAIN archive, it's nice to get rid of any system/hidden Thumbs.db files. Windows sometimes creates these caches when you view thumbnails in a folder with pictures in it.
- When making your BAIN archive, watch out for Read Only files. Wrye Mash can install these fine but will cause error messages if you try to Uninstall the Installer.
- Unicode characters. Wrye Mash installers doesn't like them in folder names...at all. French umlauts are issues as well. Its best to rename these directories in ASCII first.


Conclusion

So now you have a large mod list, installed in your preferred order, with a tool that knows all the conflicts. When you decide you want to remove a texture pack now, you can simply un-check it, and have Wrye Mash do all the heavy-lifting in the Data Files folder.

Happy Gaming!

First of all, it's Wrye Mash... not Wyre.

The Install Location only needs to be changed for people who use Vista or Windows 7. People using Windows XP do not need to worry about it.

Concerning Installation/Load Order, I'm surprised you never mention http://code.google.com/p/mlox/wiki/Mlox. It's a very valuable tool (especially for new players.)
Most people find that it solves most Load Order problems, and then you can just make any changes that might need making afterwards with Wrye Mash.

Also, installing a mod doesn't always make it appear at the bottom of your Load Order. The esp will appear in chronological order based on it's date. (the last time it was edited, by the CS or by a tool like TESTool.)


And your section on texture files overlapping could be confusing to some, because it only explains it from the manner that your using Wrye Mash's Installer Tab. Any many people still unzip archives the old fashion way.
You could explain that, and explain how to manage mod's textures overlapping in your Data Files folder.

Whoops...Corrected that.



Well that's an interesting discussion. I'll put a disclaimer about it. I'm highly opposed to the dreadful stuff in Vista that causes Program Files to act poorly, and always disable it immediately. I haven't even thought about it in several years truth be told.



Yes, mlox is invaluable for load order. But load order has nothing to do with install order.

I'll mention mlox as the optimal load order changer.

But you can install mods in any order.
Except for the obvious Texture/Mesh replacers, that overwrite files... But you don't make any mention of that, instead just discussing the method of handling mods with the Installer Tab. (unless I missed it)

The point of the thread is exactly the overwriting nature of Texture mods, along with the conflicts some mods introduce when they alter textures you might not even be aware they altered.

Thanks jaredh. The info you gave is good, it is pretty much what I do.

I personally keep a directory full of things I've downloaded, plus one full of canonicalized, BAIN-structured installer 7z files. Some of these 7z files are texture replacers with choices: root-level directories named "512" and "1024". Other 7z files might be as simple as a single esp.

I can nuke my morrowind directory and reinstall everything without much work.
I don't really have a good system for mge.ini and morrowind.ini (including BSA registration) though. I manually do these. Haven't really got into Mini yet. I suppose Mini can even be used to enable a ton of mods at once.

As another poster mentioned, mlox is a life-saver especially for detecting known conflicts.

I have the following tips:
-When making your BAIN archive, it's nice to get rid of any system/hidden Thumbs.db files. Windows sometimes creates these caches when you view thumbnails in a folder with pictures in it.
-When making your BAIN archive, watch out for Read Only files. Wrye Mash can install these fine but will cause error messages if you try to Uninstall the Installer.
-I had a problem with Lexa's Dwemer Alchemy.esp (where the first character isn't really an L but is a Unicode pound character). Unicode characters confuse Wrye Mash so it's necessary to rename the offending files.
-Wrye Mash Installers can't delete game files when you install them. When Better Music System readme.txt asked me to delete the original soundtracks, I just substituted silent mp3's in their place and thus got the mod working with Wrye Mash.

I just thought that this bit...

... is a bit misleading, because if you don't use the Installer Tab, then it makes no sense at all because they don't use esps, and therefore there is no order to look at and prune.

For manual installation, there is a completely different method to successfully overlapping texture mods.

Anyways, good thread!

>For manual installation

IMHO, don't!

Pluto,

I'd be interested in your manual method. I looked high and low for install guides and couldn't find anything.

BTW, here's some other things I do:
-I recommend enabling "View Inactive Conflicts" in Wrye Mash; right click on the Installers Tab to do this.
-Whenever I try out and like a new mod, I check the Installers Tab to see the Conflicts. If there are no conflicts then I don't do anything since Installer order
doesn't matter for this mod.
-If there ARE conflicts, then I choose a place in the Installers order that I like. I rename my BAIN archive with a numeric prefix like "004 foo.7z"
or "063 foo.7z" or something. If I end up with 100 installers numbered "001" through "100" and I need to add one just after 050 and before 051
then I can name it like "050 zzfoo.7z" or "051 aafoo.7z" and I'll worry about renaming the files and renumbering them later.
-Since all the installers with possible conflicts have an order established by their names, I can drop them all in the Installers directory and I can just enable a whole bunch at once.

A very good alternative. I don't have the space or I would do the same



I wish there was a better way to manage this.



I added a reference to mlox in relation to Load Order maintenance



I've added these tips to my orignal post. Thanks for the info on Better Music System. Have you seen this behavior anywhere else? Does it just pertain to files in the original clean MW install?

I've only seen the problem with a mod asking for files to be deleted in Better Music System. Fortunately any mp3's can be "deleted" with Wrye Mash simply by overwriting them with silent music samples.

>-When making your BAIN archive, watch out for Read Only files. Wrye Mash can install these fine but will cause error messages if you try to Uninstall the Installer.
Let me clarify; I use 7z archives which preserve the Read-Only flag. Occasionally, I've had to turn off the flag with Windows file Properties dialog before creating the 7z archive in order to prevent future problems in Wrye Mash. Note: if you use another archiving program that doesn't preserve the Read-only flag, then you might not have a problem.
If Wrye Mash ends up installing a Read-Only file, you won't be able to cleanly uninstall the Installer. You'll have to manually delete the file Wrye Mash complains about.

Edit: please don't miss my post above regarding creating numeric prefixes for BAIN archive file names; this helps a ton

Yes, definitely turn on View Inactive Conflicts. I should have said that above as I certainly infer it. I'll go add that.

I am the same way about conflicts, but I hadn't come up with an easy way to insert a mod mid-stream into Wrye Mash. I wish I could "Install at position X" and have it re-order it that way.

From your description I'm assuming you are actually enumerating your installer directories by your preferred load order? That's a very good way of pulling it off. I'll have to play with it.

Another tip: Try to avoid mods you download that are packaged in the annoying EXE format.

As well as the potential risk of getting a virus, running these EXE's may do anoying things like sprinkle files all over your Program Files directory and registry and icons on your desktop.
A lot of times you can get away with just running Universal Extractor (http://legroom.net/software/uniextract) to obtain the needed Morrowind files from the EXE.

>I am the same way about conflicts, but I hadn't come up with an easy way to insert a mod mid-stream into Wrye Mash. I wish I could "Install at position X" and have it re-order it that way.

If the installer is Installed, then Uninstall it.
Click on the Order column to sort installers by their ordering
Then right-click on the installer and choose Move To and enter the numeric position you want it to be moved it.
Then Install it.

>you are actually enumerating your installer directories by your preferred load order?

Yeah, about half of my BAIN archives conflict with something and need to be labelled with numeric prefixes. This allows easy extremely installation on a vanilla Morrowind since Wrye Mash won't know any better and will just default to ordering the installers by their names.

Wrye Mash has stopped working on my PC. Anyway, I kept forgetting to use the various installation tools and when you do that the whole concept goes to pot. I've come to the conclusion that I'm just too scatterbrained and doomed to manual installation

In any case, Wrye Mash and other programs can't tell you what the installation or load orders should be for various mods, and new players especially have no idea whatsoever of what ought to be installed before what, or what should be loaded before what. Maintaining a list of those things (so far as possible) might be useful.

Simple
Which ever identical file you install last into your Data Files will overwrite the previous one.

The only way to know which texture you want is to see them in-game (or screenshots) so you make your decision that way, and then you make sure that your preferred file is installed overtop of the one you don't like. This is all done manually in the Data Files folder by simply placing the file in the correct folder.

You see, it's similar to the order of the Installer Tab, but in this manner you can mix & match hundreds of files from many, many different modders quicker than pruning from the Installer Tab (IMHO). (for example: Connary's Hlaalu architecture, but Mr. Swiveller's Hlaalu doors)
It takes time, but you get the exact look to your game that you want.
.


Well actually, a manual installation of any mod is always the safest way to do it. By far.
(who knows what the archive looks like unless you open it up and see? )
The Installer tab is handy for un-installing mods. But one can just as easily install over top of the files, or use http://straygenius.com/index.php?title=TESFiles if it uses an esp.

This is awesome! I am still kinda a noob here and this told me some stuff I'd never heard of. I had read somewhere (morrowind mod sticky in this forum?) that states something like "don't go download a ton of mods then install them all and come back here to complain if you have to re-install". Something like that. Anyhow, becuz of this warning about DL-ing a mess of mods I didn't install any other than better bodies and MGE (is MGE a mod?). I did DOWNLOAD a ton for trying out later but the directions that said don't download and install a ton all at once, also said something like install one at a time and test in game for a while before you add the next. This guide shows a way to properly install without the overly careful install instructions I saw before - in fact I can't wait to try this!!!!

Now I knew Wrye Mash could manage load order and conflicts and I did read the wrye mash page... but this post is a lot more "user friendly".

ST

That's where Blouge and I differ. I don't keep compressed archive installers for BAIN at all...its all uncompressed.

As to your manual process...that's what I did the first two times, and was the reason for me having to re-install both times. It doesn't allow for me to un-install, re-install, back and forth without significant effort. I'd much rather go through the effort once of deciding what I want in an installer, and pruning what I don't want in it out so that I can move things in and out at will with the automated tool.

It's incorrect, never asked anyone to delete the original soundtrack. The readme asks to rename the two music folders (now suggests to overwrite the tracks with silent tracks though).

Glad to see more light brought to this. Its such a useful tool and I know my mod management was so much easier when I learned to use it.

It seems to me most of the problems you're describing under your "Coping with Mods messing with other Mods objects that you don't want to mess with" section can be much more easily solved by using the "Move To..." function. Remember, the conflict will be resolved in preference of order when the the files are annealled after you change the install order. The Order header makes this easy to manage as well.

Unpacking all the mods first seems to be an unnecessary step. Why not just download the archives into the Installers folder and work with them from there? At worst, from time to time you'll have to repackage an archive that Bain doesn't recognize; however, many of the original archives are ready to go when downloaded.

For mods only available in exe format, I simply extract the exe into a new folder on my desktop, check the structure and adjust as necessary, then archive it and put it into my installers folder, ready to go.

Edit: Changed "load order" to "install order".

Oh my god, I've wasted so much time!

Still, at least this gives me an excellent reason to reinstall Morrowind.
Although I'm not looking forward to remembering all the textures I've personally modified.

Excellent guide, anyhow.

>That's where Blouge and I differ. I don't keep compressed archive installers for BAIN at all...its all uncompressed.

Hmmm... I didn't realize you could do this. So you just have a bunch of folders under Morrowind\Installers? This will take up more space, and make some things slower, but other things will be faster. I'll have to think about this one.

>It's incorrect, never asked anyone to delete the original soundtrack. The readme asks to rename the two music folders (now suggests to overwrite the tracks with silent tracks though).

Yeah Xiran, I think you are right. Because Wrye Mash Installers can't rename or delete things, the solution (overwrite with silent mp3's) is similar.

I know this is concerned more with install order than load order, but adding something about load order is just so simple...

1. Use mlox.
2. When reading the readmes (you are reading them, right?) go ahead and add rules to your mlox_user.txt file. This allows you to make notes about dirty mods, conflicts, load order, etc. for those files that mlox doesn't know about yet. (Hey, you can even submit your rules so everyone benefits!)

Thus, the next time you re-install, your Wrye Mash Installer-fu takes care of your install order... and you just run mlox once to get a good load order.

I think your install order tutorial could use a bit of cleaning up -- especially, make it clear that this is specifically a tutorial for using Wrye Mash's Installers feature -- but I'm glad to see it. Having recently come back to Morrowind after many years away, Wrye Mash Installers and mlox were both wonderful revelations in making organization as easy as possible. Sure, you still have to think about things and read readmes... but only ever once.

The beauty of the anneal feature is when you reorder a mod (what you refer to here as an "installer") you don't have to uninstall it first, as you suggest. Just reorder using "Move to" and Bain will automatically (assuming you have Auto-Anneal enabled) replace/swap any conflicting files necessary. You can move stuff back and forth as much as you want without ever having to uninstall.