The easiest way to check for file overlaps is to set up a dummy folder and install the mod in question into that folder. This places all individual files into that folder, so that you can check for duplicate files. To do so, just follow these instructions:
1) Create a dummy folder, which will act as the fake base game folder. This folder can be named anything you like. You might want to name it after the mod you're testing, just so that you don't have to wonder six months later why you created that folder. Errr, not that I've done that or anything...
2) You need to create an "override" folder within the folder you just created. The mod will look for it to install the new files, so it really does need to be there. You also need to copy and paste both the dialog.tlk file and the chiten.key file from the game you're testing for into the base folder for the same reason. Those can both be found in the regular game folder itself. Your dummy folder should look like this:
Dummy {folder} Override {folder} dialog.tlk {file} chiten.key{file}
3) Now you need to import the mod files. If the mod installs itself without requiring another program, then you simply start the install and tell it to install the mod to the dummy folder. If you need to use DLTCEP or IEEP to install it, you need to tell that program where to put the mod. Simply open DLTCEP and go into settings. Make a new setup that points to the chiten.key in the dummy folder, and save that as your new setup. Then you can just import the tbg/iap file as usual.
4) Now you've got an apparently useless folder with a whole bunch of files in it. If you're just comparing a couple smaller mods, I'd suggest selecting the entire dummy override and making each file read only. Just select all files and then do it all at once. Then install the other mod(s) on top of that. If there's a file conflict, it'll let you know. This won't always work though, so it's really only ideal for checking a couple mods.
If you want to check and see if a mod will work with your current setup, it's a little more complex. For this I'd use DLTCEP or Near Infinity and Windows Explorer--at least for smaller amounts of mod files. Go into the override of your dummy folder, where all the new files are. Because both DLCTEP and NI sort game files by type, I'd suggest you set that folder to sorting by file type as well. Now just go through each file type and check to see if there are any files by that name already in the game. If there is a duplicate, go to the part on resolving conflicts below.
That might sound scary, but usually it isn't. Most modders use a custom prefix (like RQ or ^& or something) at the beginning of every file name, which does a lot for compatability. You just have to check each type of game file to see if there are any files already with that prefix. Usually there won't be, but if there are you just have to check for duplicate files.
Now if the mod uses a prefix for most files, but there are a few without that prefix, those are the ones you'll need to worry about. When that happens it means that the mod is probably replacing a regular game file instead of adding a new one. Check to see if that file exists in the game anways, but it probably will. If that's the case, go to resolving conflicts below.
Resolving Conflicts
Okay, the mod is adding a file that already exists in the game. This isn't necessarily a bad thing. If the file is a standard game file that's only being altered by one mod, you should be okay. If it's a file that another mod also alters, you're probably hosed. First thing you have to do is check and see if another mod has altered or added that file. There are a number of places that file might be:
1) If any mods you have installed have added bif files (compressed collections of many files), you can check that bif for the file(s) in question. For this I'd use Near Infinity. Go to Edit-Biff, and open the bif file from the already installed mod. There might be more than one, in which case you'll need to check them all. Simply go through the list of files and check to see if any of the files in question are present. Whether they are or not, don't actually edit the biff! If the file does exist in a mod biff, you have a confirmed conflict (see below). Otherwise, go to step two.
2) If the file doesn't exist in a bif added by a mod, then it's either in the override folder or one of the standard game biffs. You can check to see if it's in the override either by manually looking for each file, or you can just try and copy/paste the contents of the dummy/override folder to the actual game override. Make sure you don't actually overwrite any files!!! If it asks you whether or not to overwrite a file, you have a conflict. Just say no and let it continue copying files. Write down each file that it asks about, since these are the files that might cause problems. When it's done, regardless of whether or not there were problems, you'll need to undo that copy. Remember that the files weren't installed properly, so the mod wont work even if there were no conflicts.
2) If the file exists in the override, we need to find out if it's a mod file or a standard game file. We can check to see if it's a file from a weidu mod rather easily. Just open the .debug file of each weidu mod you have installed with a text editor, and do a text search for the name(s) of each file that wouldn't copy over. If the file is altered by a weidu mod it'll be listed in the debug file. If you find any of those filenames you're looking for, you've found a conflict. If not, then you know it isn't a weidu mod that created or altered that file.
3) Now we know that the file isn't added by a mod to a bif folder, and it wasn't installed by a weidu mod, but it's still just sitting there in the override folder mocking us!! What I'd suggest is to install all the non-weidu mods to the same dummy folder as the first one. Before doing so, set all the files in that override folder to read only. Then install another non-weidu mod. If you have more than one other non-weidu mod to check, set the entire folder to read only again before doing so. If you get any messages saying that a file couldn't be installed, you've found the conflict. If all the mods install normally, you should be free and clear to install all the mods.
Confirmed Conflicts
If you make it to this part, you should know not only what files are conflicting, but which mods are adding or altering the same files. The very first thing you should do is post that data in the forums of both mods. Do a search first to make sure that someone hasn?t already posted about it. Searching for the name of the other mod and for the filename should do it. If you can?t find anything like that, post that you?ve found a conflict with which mod, and say what file is conflicting. Modders need to know this stuff so that they can update their compatibility list.
Now that you've done that, there are some things you can do to fix the duplicate file problem. It?s very possible to mess something up, so proceed at your own risk. I'll add more later if people want me to, but here's a quick overview of what I'd do:
Near Infinity has a lovely little "find references to this file" search option. I love that thing! It tells you which game files refer to the file in question. If you want to change the name of a file to something new to prevent a file name conflict, this search should tell you what other files need to be altered to point to the new file name. I can't say for sure that it catches all references, but it's a hell of a start! Once you have such a list, just change the name of one of the duplicate files to a new name (something with an unused prefix like "&^" or something), and then alter each reference to that file to the new file name.
Please not that this will NEVER work if the file in question is a 2da or ids file. They can't be renamed and still work. Ever. If that's the case, go to the boards and report the conflict. Hopefully someone will then be able to compare both versions and see if they can be made to work together.
That's all I've got right now. If anyone has and questions or suggestions, please don't hesitate to post them.