DISCLAIMER: This is by no means an official modding guide. This guide was written to share tools of creation with the community. I take NO RESPONSIBILITY for any damages this guide may have caused.

First off, a little information I've gathered about Nekopara. Nekopara is a visual novel build using KiriKiri Z and the KAG (KiriKiri Adventure Game System) framework. KiriKiri Z is a fork of KiriKiri 2, a Japanese scripting engine. Nekopara uses Emote, a KiriKiri plugin, to animate their characters.

Link: https://github.com/xmoeproject/KrkrExtract
Description: A tool that packs and unpacks KiriKiri 2 and KiriKiri Z xp3 archives. It also contains other useful tools for handling KiriKiri files, such as unpacking Emote psb files.

WARNING: Many antivirus programs have flagged this tool as malware.[www.virustotal.com] I've found that the tool works fine and have yet to see it act maliciously. I'm unsure why it's recognized as malware. According to the author,[github.com] the combination of hooking, process spawning, and APIs it uses can be mistaken for malware. USE AT YOUR OWN RISK!

Link: http://kaede-software.com/krlm/plugin/alphamovie.zip
Description: A tool to encode AVI or PNG folders into KiriKiri AMV files. (Please note that KiriKiri use it's own unique AMV format, and is incompatible with traditional AMV files.)

Link: https://github.com/xmoeproject/AlphaMovieDecoder
Description: This tool is designed to read KiriKiri AMV files and dump their contents in a folder as PNGs. (Please note that KiriKiri use it's own unique AMV format, and is incompatible with traditional AMV files.)


PS: If there's anything I missed or any incorrect information, PM me.
I will add more tools when I find them. Happy modding everyone!

Sources:
https://en.wikipedia.org/wiki/List_of_visual_novel_engines#KiriKiri
https://github.com/krkrz/krkrz