Brief overview of the game's Lua files

Note that this list isn't comprehensive, but it should be enough to cover files a modder would commonly be dealing with.

Main logic

movement.lua - handles movement logic with move sources (you, move, shift, etc) and movements that are a direct effect of move sources (push, pull, swap)
rules.lua - main parsing logic is handled here
conditions.lua - handles all condition texts (on, near, lonely, facing etc)
blocks.lua - contains what the source code calls "blocks", which are various functions that handle properties/effects that do not have to do with movement or collision-based effects
features.lua - has functions for looking up objects that have a certain property
update.lua - contains doupdate() and a few other functions. doupdate() is used to consolidate changes to the game state as a turn progresses.
convert.lua - handles any text effects that involves transforming different objects
letterunits.lua - handles parsing letter text blocks
vision.lua - functions for handling the visual effects of the 3D propoerty
mapcursor.lua - handles select logic

constants.lua - contains indexes that are used in getting certain properties of objects. (See Units)
values.lua - contains various constant values used in the game logic
modsupport.lua - defines all the avaliable mod hooks
Editor/editor_objectlist.lua - while this is an editor-related file, it contains definitions of all the objects in the game. (The object list in values.lua seems to be a "legacy" version before the editor was implemented)

load.lua - functions used for initialization of global variables and other stuff (yes, this game uses global variables). You can use this file to see which global variables are defined.
clears.lua - handles clearing global variables
undo.lua - functions that handle the undo system
map.lua - handles overworld logic and levelpack completion data

tools.lua - contains various helper functions for dealing with the game logic
syntax.lua - contains more helper functions. (I don't really see what's the difference between syntax.lua and tools.lua, but meh.)

effects.lua - functions that handle particles and special effects
colours.lua - functions for getting/setting various colors
dynamictiling.lua - handles the "Tiled" animation style that allows walls to update its sprite based on nearby walls

ending.lua - does the "end" and "done" ending cutscenes
debug.lua - functions for printing various debug information. (Note: you might have to replace the MF_alert()'s if you want to use these functions since MF_alert() only works when running in MMF)
menu.lua - functions for various GUI elements
changes.lua - seems to handle updating the level data when modifying it in the level editor