Refoactor: transform angle brackets into square brackets in process phase

Now that we support both <fn> and [fn] syntax, there is an increasing amount of code doing "the same thing twice" and/or regexps getting more complex.

It would simplify code and just generally make sense to use the "process:" phase to make following transformations:

<fn([^>]*)> to [fn\1]
</fn> to [/fn]
<footnotes(( )?\/)?> to [footnotes\1]

After this, all other code could be simplified to assume input always uses [fn] syntax.