Reference javascript in the intermediate directory

ScriptsToConcat returns the file paths as written in the HTML file. These paths are relative to the dir.source property. The concat task was then looking for these paths relative to the basedir and therefore could not locate js files when the dir.source was changed from the default, making dir.source != basedir.

This commit takes the original filelist results and runs them through a pathconvert mapping to get the full path to the javascript files in the intermediate directory.