Updating vanilla js files

I want to make a minor modification to phyrenderer.js.  Should i be able to place a differnet version with the same file name in the CUSTOM folder and have that take precendence of the on in the SIEBEL directory?  I have registered it in the mainfest administration cleared cache and still the original is loaded from the SIEBEL directory.  The original phyrenderer.js records on the manifest admin views is read only.  Web templates seem to work with this approach.  If you place a web template with the same name in in the WEBTEMPL directory and CUSTOM it uses the CUSTOM