Mark,
Conventionally, footnotes are organized as Matus is requesting, where references are repeated according to their appearance throughout the text, and in numerical order in the references container (See almost any Wikipedia entry), although in some cases a text will sort references alphabetically by author in the equivalent of the references container, and they would subsequently start out of order in the text; but there would still not be two numbers (indexes) assigned to a single reference in either location.
In any case, I would like to echo Matus’ request that multiples of a reference be treated conventionally, but also make a couple additions:
1) Currently, only the first instance of a reference acts as an anchor, and clicking a multiple of it does nothing. It would be better to assign a sub-index for each multiple, where the initial is 1a, and then multiples thereof 1b, 1c, etc. So that in the references container, reference 1 and its multiples would be displayed as 1. ^ a b c Reference. where the footnote_plugin_link would therefore be disabled and each sub-index would return the user to the appropriate anchor in the post (like Wikipedia’s citation system).
2) Referencing a footnote with a multiple should be much easier than having to enter the entire reference again. Unfortunately, because references can not be numbered manually (e.g. [ref data-index=”1″]Reference[/ref], there is no way to refer back to them, e.g. [ibid data-index=”1″]. The Footnotes for WordPress plugin actually allows for this with the addition of a [backref] shortcode (which uses the deprecated “name” HTML attribute for the identifier), but does not provide unique sub-indexes for each multiple of a reference, so it also treats the first instance as the anchor to return to.
So far, this is the most promising footnotes plugin I have used, so I hope you continue to develop and improve it.
Thank you for your time.