Although the method of creating footnote references that are prefixed with the node ID, this does not address the use of temporary and import nodes that have references that must be updated. Therefore, it is better to leave the footnotes anything that Pandoc/GitHub allow and qualify them as a part of the expansion KEGMLX process. At that time the exact node ID will be known and can easily be prefixed to any [^foo] -> [12.foo] range with a simple regular expression match.
Although the method of creating footnote references that are prefixed with the node ID, this does not address the use of temporary and import nodes that have references that must be updated. Therefore, it is better to leave the footnotes anything that Pandoc/GitHub allow and qualify them as a part of the expansion KEGMLX process. At that time the exact node ID will be known and can easily be prefixed to any
[^foo] -> [12.foo]range with a simple regular expression match.