it is a very used version notation.
this one is 0.9.6a
the 0 is for releases. at any time this number is changed, if it goes from 0 to 1 it is finally on its' "final" version, if it goes up in any other number it is a MAJOR change, as in 1.x to 2.x have big changes that may seem like different things altogether, like a remastered game.
the second number, a 9, is for big patches with additions, like for when big chunks are added to a work-in-progress game or plugin. in this game's case, they are usually when whole new rotes are added, like we are currently on the book 4 love route, all previous books having two and, in some, major differences between them (but not to the point of this one, where they do not even have the same season of their show)
the third is for major fix patches or smaller extra content, for example in this game it is when there is a story progress update.
The letter is for bugfixes and, at some times, small additions (not very recomended, as it confuses the people downloading them, but in Reogue-like evolution for example there was a character introduced in a version and everything of hers was added on letter updates...)