Most of the documentation is here (though it's rather lackluster).
Calmare is a decompiler and recompiler for script files. It can currently handle the scenario scripts for all games from Sky FC up through Azure.
In the future it is intended to also support animation/battle scripts, tables, and a number of other auxiliary files.
There is a short tutorial here.
Cradle is a converter for Falcom's image, sprite, and (planned) 3D model files to and from more conventional formats.
Factoria is a tool for managing the file archived used in the Trails in the Sky trilogy. It can extract, edit, and create archives from scratch.
The Liberl Archive Redirection Kludge is a dll hook for the Trails in the Sky trilogy, simplifying mod development and distribution. Due to its different nature, it is hosted in a different repo.