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<%include /cgi-bin/common-templates/header.txt%> # uses absolute path to include header from central template directory.
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But that isn't an absolute path...its relative. Absolute means...

/home/sites/htdocs/cgi-bin/templates/header.txt

You can already do what you are suggesting....ie using common headers/footers.....use:

<%include ../../includes/header.txt%>

...you can use that for your different scripts and it will pickup the same includes directory assuming you have a common structure like:

/cgi-bin/links/admin/templates
/cgi-bin/forum/admin/templates