.APD
Anachronox Particle Data
Particles provide the beautiful lights and animation you see on spells and other things in Anachronox.
Located in /particles

APD File Conventions
Spaces aren't important, so you can format your files to look nice. Comment lines must have # as the first non-white space character in the line. End-of-line may be indicated by LF or CRLF.

NOTE: There is actually two different particle systems in Anachronox. The old particle system used a .map KEY of "message" and a 64-bit string VALUE to define the particle. This string is called a particle descriptor and breaks down as follows:

"message" "0000000000000000000000000000000000000000000000000000000000000000" <- 64-bit string

red (##) starting red color of particle 0-99
green (##) starting green color of particle 0-99
blue (##) starting blue color of particle 0-99
alpha (##) alpha percent of particle 0-99
fade (##) speed of particle fade 0-99
speed (##) movement speed of particle 0-99
max count (##) maximum number of particles?
delay (ms) (###) delay in milliseconds between particle spawn 0-999
size (###) radius of particle generator? 0-999
deviation (##) deviation amount between each particle produced. Effects alpha, fade, speed, size, scale.
mult num (#) Unknown
scale (##) scale of spawned particles
red #2 (##) fade to red color of particle
green #2 (##) fade to green color of particle
blue #2 (##) fade to blue color of particle
textureid (##) unknown
flags (hex)(########) These do not appear to have any effect...? 0-4294967295 (00000000 - ffffffff)
unused (#) set to '0'
alpha cutoff (##) at what alpha value the particle should just disappear?
rotate speed (##) clockwise rotational speed.
unused (##################) Set all 18 characters to '0'. They are unused.

This system was abandoned after Joey created the 'NP' New particle system, and Particleman. The only benefit I have seen for the old particle system is that you can attach the particle definition to a geometric brush, and it will use the size of the brush to define it's scale(visible in AnachroRadiant).
Using the New Particle system you must attach the particle definition to a ob_squib, or surface tag, and use the "scale" KEY and Particleman Spawn Volume to define it's size(not visible in AnachroRadiant).

Currently this is the only documentation for the old particle system.
To learn how to create New Particles see Visual Effects/Particleman.

.APE
Anachronox Programming Environment
The scripting language layer that controls most of the standard interactivity within the world. If you can click something in the world that triggers a dialog, interface, or event, then chances are APE has played a major part in it.
Located in /gameflow for map initialization, they can also be found in /battle/%mapname% for battle scripting.

APE File Conventions
These files contain binary data and are not editable unless you can hex edit or decompile the binary data.

See APE

.ATD
Animated texture data.
Procedural textures provide interesting visual effects by modifying the color values of a texture in real time. All procedural textures are created through the use of text scripts called Anachronox Texture Definition files. The definition files have the extension .atd and are used as replacements for normal textures.
Located in /textures.

ATD File Conventions
Spaces aren't important, so you can format your files to look nice. Comment lines must have # as the first non-white space character in the line. End-of-line may be indicated by LF or CRLF.

NOTE: There is actually two diffeferent procedural texture definitions in Anachronox. The old definitions used a .map KEY and VALUE to specify the parameters for the procedural texture, and were extremely hard to use. As an example you could apply the KEY and VALUE of "dlltexture02" "iform4:zblah/pal-tol3:zblah/i-tol-4,scrolling,0,10:zblah/i-tol-7,scrolling,0,-10" to a brush to have the whole brush use that procedural texture.
One drawback of the old style is that you could not specify the procedural texture to apply only to one face of a brush. No information on how to use this method is currently available.
The new procedural texture definitions allow you to apply any procedural texture to just one geometric brush face. Thus you could have a single brush with multiple procedural textures applied to each face of that brush.

To learn how to create your own procedural textures see Visual Effects/Procedural Textures
To learn how to apply procedural textures to .map geometric brushes, or faces see AnachroRadiant/Textures.

.BED
Battle Entity Data.
Battle enity data files contain node, entity, and other battle data. They resemble .map files and are created with the in-game battle editor BED.
Located in /battle/%mapname%

BED File Conventions
Spaces aren't important, so you can format your files to look nice. Comment lines must have // as the first non-white space character in the line. End-of-line may be indicated by LF or CRLF.

See BED

.BSP
Binary Space Partition.
There are two map file formats used throughout the Anachronox editing environment. .bsp and .map. .bsp files are compiled map data created by QBSP from a .map file. BSP stands for "binary space partition", the type of data organization procedure John Carmack used when creating the graphic engine for "DOOM".
Located in /maps

BSP File Conventions
These files contain binary data and are not editable unless you can hex edit or decompile the binary data.

Anachronox BSP File Format

Data contributed by T-chip, or Anachronator from Laguna's message board.

.BSP File Hexadecimal breakdown
Sorry T-chip your data is wrong.. Thanks for giving me a starting point though. :)

See AnachroRadiant

.CTC
Character Texture Control?
.ctc files are the old data format files used for skeletal, model light, and procedural textures. Skeletal systems were removed from the game and replaced with animation and morph frame data directly in model files(.md2). Model light data was replaced by the .mda file format and procedural textures were changed to the .atd file format.

CTC File Conventions
These files contain binary data and are not editable unless you can hex edit. There is no known editor or de compiler for this data format.
These files were left in the GDB for some particle effects.

.GDB
Game database
The GDB is the game database that keeps track of numerous things in the game including items, mystech, battleskills, quests, weapons, monsters, and more. It basically consists of numerous files in the Anachronox directory tree, (usually with a .gdb extension), that contain text entries that describe the previously mentioned elements of a game
Located in /objects

GDB File Conventions
Spaces aren't important, so you can format your files to look nice. Comment lines must have // as the first non-white space characters in the line. End-of-line may be indicated by LF or CRLF

See GDB.

.MAP
AnachroRadiant map data.
There are two map file formats used throughout the Anachronox editing environment. .bsp and .map. .map files are un compiled map data and are only used in AnachroRadiant. These files are text files describing brushes and entity data. They are then compiled to create the .bsp file format that are read by the Anachronox engine.

MAP File Conventions
Spaces aren't important, so you can format your files to look nice. Comment lines must have # as the first non-white space character in the line. End-of-line may be indicated by LF or CRLF.
Note: AnachroRadiant will strip all white spacing, comments, and LF or CRLF when map file is saved.

What we're really interested in are the numbers following the texture name. You'll see there are eight. Taken from the example above, the first line would be 0 0 0 1 1 0 0 0 . These are all of the texture values and spawnflags. The fact that there are mostly zeros means the texture has no surface or content flags set for it; it's just a plain old texture. The two 1's are the texture's dimensions, which mean that it has been applied with it's default size. 

A visual reference for the texture property flags

Even though you may use a different editor, the flags still mean the same thing.

Texture Properties

Now that you know what the 8 data bits reference, you now need to know what possible values can be used. Let's take the light value, which is used typically for sky textures and light-emitting textures. Therefore, a string of 0 0 0 1 1 0 0 100 means that you've get a light value of 100. However, since the light flag is normally set for a situation like this, it would read 0 0 0 1 1 0 1 100. Reason being, is that 'light' is the first item in the surface property list, and therefore has a spawnflag value of '1'. 'Slick' is '2', sky is '4' and so on, following the numerical convention used for spawnflags. For multiple flag selection add all of the desired property Spawnflag values together. To mark a brush as slick slime for example it would read 0 0 0 1 1 32 10 0. The 32 value being equal to the water content flag and 10 is the slick and warp surface flags added together.
Here's a handy reference showing all of the spawnflags:

With this information you can now fix certain things in the blink of an eye.
NOTE to my self.. I need to add the values for Surface sounds if relevant(textureinfo.dat).

See AnachroRadiant

.MDA
Anachronox model shader data.
Shader data allows you to create multiple skins on any given model, as well as creating special effects! By using ONE model with many skin variants, it's possible to populate a level with hundreds of unique characters, while keeping a very low “model loading” footprint
Located in /models

MDA File Conventions
Spaces aren't important, so you can format your files to look nice. Comment lines must have # as the first non-white space character in the line. End-of-line may be indicated by LF or CRLF.

See Models

.MD2
Model Data
These are the model files for Anachronox. They contain all of the geometry, and morph data for Anachronox models.
Located in /models

MD2 File Conventions
These files contain binary data and are not editable unless you can hex edit.
For GUI modification of data see External Tools/lw2dm2.

.MD2 File Hexadecimal breakdown

One more unknown header data to go. Also what what is Texture coordinates, animation frame data, and strip fan data?

See Models

.S
Planet scripts
Planet scripts contain movie data created by the in-game movie editor Planet.
Located in /scriptst

S File Conventions
Spaces aren't important, so you can format your files to look nice. Comment lines must have # as the first non-white space character in the line. End-of-line may be indicated by LF or CRLF.

See Planet