Roland, take a look at the web-resources Module type. If you add a plugin with one of these in there then you can have your own JS files added to all pages. Have a specific look at the contexts, such as atl.general for example
<web-resource key="somekey" name="some description"> <resource type="download" name="yourfile.js" location="/js/your file.js"/> <context>page</context> </web-resource>
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