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Animtools is unrelated to custom hairs and clothes.

The "Open File" dialog box generated by Animtools allows you to select a TXT file which will change the position of the characters (and furniture) on the stage.  These files are created and edited via the animtoolsV14.swf application, but if you find its UI confusing then you can also use the pre-generated files or download custom ones here.

Before or after loading a position file, you can use the game's regular menu system [Modding > SWF Mod...] to select a SWF import file.  The [Modding > Hair...] button allows you to select a PNG hair file.  When a file is loaded, it adds semi-persistent elements to the scene.  These elements will remain in-effect if you alter the character positions via animtools, but they can be replaced by hair or costume elements that you load subsequently.

If you've encountered a compatibility problem in which specific hairstyles or costumes are behaving strangely with animtools then you'll need to identify the files (e.g. tell us the filenames, or link to the page where you downloaded them) so that we can help with troubleshooting.