The greenhouse, in combination with the barn and the crafting system, is used to create foods. Consuming them grants the playable characters temporary elemental resistece, increased elemental damage, stat increases, or condition immunity.
Its like optional grinding, or a minor cheat system you actually have to work for. (Since there is no way to actually grind to increase your level, since the game has a levelup system like Zelda games, so you only get upgrades for defeating bosses or discovering hidden stuff)
It is indeed entirely custom and almost fully done in Ruby/RGSS3. Its actually pretty simple and requireds little time for the implementation of new crops, when compared to the old system I used, which was mostly (common) event based.
For the display I use bitmap blocktransfer to the lower and upper parallax layers and the collision is done with ~15 lines of code in a modified game map method.
The only scripts I use that aren't custom are a parallax and a bitmap/png file creation/storage one. (I could write the parallax one on my own, but its pretty simple, so if there were any problems I could fix or replace it. As for the other one, thats a bit tricky, but in case of a bug I could prbably fix it, or if not just leave the script out, since its only part of a very optional feature.)