This tool creates new unicode "blocks" and copies inside the composing glyphs (if the correct glyphs are present in the given font file). For example, for the é_e glyph, the unicode "block" (defined by the QUNI) is created and both é and e glyphs are copied side by side to simplify the drawing of the inclusive glyph. Then, the necessary OpenType features are added so the "ligatures" are functionning, and you can download your QUNIfied font !
This magic trick is made possible thanks to Fontforge, usable via python to manipulate fonts. The script itself is not very complex and could be adapted to other font drawing softwares. Another way would be to make a script working directly on the xml files of an UFO fonts, which would be ideal to avoid "baking" your font in a ttf file.