To add any custom javascript to all the pages, you should create a new custom jsfrag file. The file needs to be deployed in: codebase\netmarkets\javascript\util\jsfrags

The file can be named custom.jsfrag or any other name that is not already in use.

To include the file in all pages run the combine command. This will make the js available in main.js: Windchill/bin>ant -f jsfrag_combine.xml