The . separates what part is the kanji and what part is the furigana (extra kana on the end). In this case ひと.つ is meaning the word 一つ, the ひと part being 一 and the… other part… you know. Koichi is only choosing what he thinks are the most common/useful readings, so not all will be covered. Some kanji have a plethora of old, uncommon or irregular readings (as far as I know, 一 being read as つい in 一日 is the only place it’s read as such [could be wrong though]). Some readings you just have to learn as they are – it’s the reason he gives you lots of vocab to learn as well, so that you can learn the irregular readings as part of words.
Hope that helps :)