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Unfortunately, the PDF/RTF exporters work differently than the LaTeX exporter in terms of exporting footnotes.
You can set the tags for the footnote tags for PDF/RTF in the exporters in the section "Notes" by double-clicking the cell in the columns Start Tag/Stop Tag. However, for inline footnotes, you always need a "-" at the start of a footnote (otherwise, the export thinks it's a connection to a note and searches the notes for an identifier with the same string as in the footnote).
For LaTeX, you don't need the "-" at the beginning of a footnote, since the text inside the tags is just enclosed in \footnote{...}.
If you set the start and stop tags of the footnotes in the PDF/RTF exporters to the same as the inline style tags for footnotes in LaTeX, you should be able to export footnotes in the same way for LaTeX and RTF. The only problem that remains is that you will have the "-" at the beginning of each LaTeX footnote, so you'd need to search&replace them in the exported LaTeX files or run a script over the files.
Ulysses 3 will unify all these styles and should make it much easier to export footnotes in a simple fashion.
Actually, I just noticed something: if you write the footnotes in the notes, you can export your footnotes in the same way for both LaTeX and PDF/RTF.
Let me explain: currently, you use inline footnotes, i.e., you write the footnote in directly inside the inline style (e.g. {{-This is a footnote}}). You can also write footnote in the notes and link them to the text in the editor. For instance, you could create a note and type {{footnote1-This is a footnote.}} and type {{footnote1}} at the position in the editor where you want this footnote to be inserted. Thus, you link the footnote identifier in the text (footnote1) to the content of the footnote, which is inside the note. This strategy works for both LaTeX and PDF/RTF.
This approach is also explained in detail in the screencast on exporting (after 10:43 min) and in the Ulysses help (the screencast was made using Ulysses 1.6, but the approach is identical).
So basically you would need to convert your inline footnotes into footnotes linked to the notes, but then export to both PDF/RTF and LaTeX should work.
You don't need to number your footnote identifiers. So you can use identifiers like "intro", "SchmidtEtAl", "CommentOnQuote" or whatever you like. Even if you number you identifiers, they don't need to be in the same order.
I wasn't replying to that questions because we don't have a release date for Ulysses 3 yet ;) Basically, all we know is written here.
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