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Yes, you can link to external javascript:
<script type="text/javascript" src="ScriptFile.js"></script>
No, you do not need comments - if the browser does not support scripting it won't recognize the <SCRIPT> tag, therefore the external script will not be loaded.
In your external JavaScript file you just begin your functions, variables, etc - no other information is needed (i.e. <SCRIPT> tags, comments, etc).
You can create this script in NotePad - just as you would if you were creating JS inline....
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