When you open the plugin with the program you will see a list of objects, scripts, and such. These objects were all either:
a) Not altered, but the CS thinks they were altered;
b) Altered somewhat; or
c) Something that is not a part of any of the master files.
Here's how to clean:
If you see any object(s) that are part of either the MW, TB, or BM master files, you should highlight those object(s) by selecting them from the list and hitting the space bar, then you should go to items in the top toolbar and hit "Delete." Doing this to objects in master files SHOULD NOT delete them from the plug-in. It should only remove that "Changed" status and remove any changes you might have made to that object. An exception to this rule is textures; never delete any vanilla textures from your mod, or they will be removed from the game when your plugin is loaded.
If you see any object(s) that are either:
a) Something you made yourself such as a chest, crate, etc.;
b) Objects in the plug-in made by TR or some other allied group; or
c) Objects in the plug-in made in a Bethesda official plugin, you should simply ignore these objects. They don't have to be cleaned, and doing so will remove them from your plug-in.
Then when you are done cleaning, just hit "Save As." Remember to save it with a different name if you wish to avoid confusion with file versions. Make sure to check your "cleaned" version to make sure everything is still how you want it. Remember though, that if you make any more changes to the cleaned version, you may have to clean it again.
Also, just as important to name in this tutorial are cells. NEVER hit "sort" if you are going to be working with Cell or Landscape references. Doing this will cause you to loose which Landscape reference goes with each Cell reference (they are paired).
You should always clean cells that do not belong to you. Furthermore, coordinates of cells do not appear in TESAME. Therefore, you should always name your exterior and interior cells so that you can recognize them in TESAME and know not to clean that cell. Another thing to remember is that usually, if you opened a cell, that it will appear in the list. Sometimes, cells have a tendency to appear on the list for unknown reasons, so look for those too. Just remember that with cells, clean everything that shouldn't be a part of the plug-in.
As a side note, make sure not to delete the part that says "TES3." That is what your plugin uses to recognize itself as a TES3 plugin
.Added to Handbook by Kaziem 4/10/16