Add .js file as a file resource and build you own Theme and refer that file there.

 else, put the .js file in webContent folder which will be treated as 'root' of NSF 

If your .js file is in the files folder under resources its just not going to pop up in the list of javascript resources because its expecting them to be in the javascript library folder.

 

You can still add it into your XPage you just have to manually type the file name such as 

 

<xp:this.resources> 

      <xp:script src="/fileName.js" clientSide="true">

</xp:this.resources> 

 

I've done exactly this with a custom dojo widget I made in a application, I was editing the .js file outside of designer and was just easier to use the file import rather than copy over the contents. worked fine.