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Deploying to WAS with WebSphere Studio

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I'm trying to use WebSphere Studio Advanced Edition v3.5.2 to deploy to a WAS back end and a IIS web server, but some of the file paths (to images on the web server and some relative links to other JSPs) in the JSPs when deployed to the WAS aren't coming out right. The two main problems are:
1. Image file source links that I have imbedded in JavaScript in the JSPs are not recognised when deployed and remain as "filepath" links e.g. "file///c:/..../..." etc
2. Links to files on the IIS web server are being recognised and parsed, but an extra folder is added on to the file path. e.g. What should come out as http://localhost/menu/image.gif comes out as http://localhost/menu/menu/image.gif
Any help on this would be greatly appreciated!!
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