The syntax is based on the common DokuWiki syntax for footnotes. So, to include a footnote with the text "with a footnote," you use:
Your awesome text((with a footnote))
And that's all you need to do. When you add a footnote, **footnotes** will create a note marker at the point that the foonote appears in the text, and includes the text of the footnote in a styled list of notes down the page. When a reader clicks on the link in a JavaScript-enabled browser, a script included with the plugin will create a small bubble inline in the text, which pops up over the footnote marker for easy reading without losing their place. Just like you're used to on a DokuWiki Page.
In non-JavaScript-enabled contexts, clicking on the footnote marker jumps down the page to the text of the note. The jump is based on a unique anchor which the plugin can automatically generate for you.
