Cyrillic transliteration made compliant with GOST 7.79-2000, system B #1
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The document you mentioned in the readme suggests that author's aim was to represent the letters phonetically close to the original.
GOST 7.79-2000 is a national standard of romanization of Cyrillic letters. Unlike the original author, it is aimed to be unambiguous and bidirectional, made for usage in computer networks.
I guess it is impossible to objectively decide which one is better. In my opinion both schemes are inaccurate, but in different ways. But the scheme used in junidecode transliterates letter "Е" into a two letter combination, which makes many words a lot longer (this letter is second by frequency in Russian language).
In short: