1. Install setup_anachronox_2.0.0.28.exe
2. Copy/Backup C:\GOG Games\Anachronox
3. Install anoxpatch1_01.exe
4. Install anox_build44_patch.exe
5. Install anox_build45_bin.exe
6. Install anox_build46_bin.exe
7. Recover GOG's anox.exe & ref_gl.dll
8. Compare C:\GOG Games\Anachronox & Backup
9. The following files are new:

anoxdata\battle\ai\Anox_Doorlord.txt
anoxdata\battle\ai\magmatos.txt
anoxdata\battle\ai\Rictus.txt
anoxdata\battle\ai\Wimpa.txt
anoxdata\battle\bricksb\bricksb1\bricksb1.ape
anoxdata\battle\bricksb\bricksb1\bricksb1.bed
anoxdata\battle\cineend\cineend0\cineend0.ape
anoxdata\battle\krapton\krapton4\krapton4.ape
anoxdata\battle\levant\levant0\levant0.ape
anoxdata\battle\levant\levant0\levant0.bed
anoxdata\battle\mystech1\mystech114\mystech114.ape
anoxdata\battle\mystech1\mystech114\mystech114.bed
anoxdata\battle\whitecaves-b\whitecaves-b6\whitecaves-b6.ape
anoxdata\gameflow\anox_credits.txt
anoxdata\gameflow\anox_end_credits.txt
anoxdata\gameflow\black.ape
anoxdata\gameflow\bricksb.ape
anoxdata\gameflow\bricksc.ape
anoxdata\gameflow\bricksc2.ape
anoxdata\gameflow\bricksd.ape
anoxdata\gameflow\bugaboo.ape
anoxdata\gameflow\chamber.ape
anoxdata\gameflow\cine2.ape
anoxdata\gameflow\comhills.ape
anoxdata\gameflow\crevice.ape
anoxdata\gameflow\doren.ape
anoxdata\gameflow\fortress1.ape
anoxdata\gameflow\global02.ape
anoxdata\gameflow\global50.ape
anoxdata\gameflow\hephaestus.ape
anoxdata\gameflow\hephfactory.ape
anoxdata\gameflow\hephlava.ape
anoxdata\gameflow\hephpoor.ape
anoxdata\gameflow\hephtower1.ape
anoxdata\gameflow\hephtower2.ape
anoxdata\gameflow\hovel.ape
anoxdata\gameflow\krapton.ape
anoxdata\gameflow\kraptonjail.ape
anoxdata\gameflow\labbuilding.ape
anoxdata\gameflow\levant1.ape
anoxdata\gameflow\levant2.ape
anoxdata\gameflow\mmuseum.ape
anoxdata\gameflow\mugpath.ape
anoxdata\gameflow\museum.ape
anoxdata\gameflow\museumnight.ape
anoxdata\gameflow\mystech1.ape
anoxdata\gameflow\orange.ape
anoxdata\gameflow\ox.ape
anoxdata\gameflow\pooper.ape
anoxdata\gameflow\redlight.ape
anoxdata\gameflow\routubes1.ape
anoxdata\gameflow\rowdys.ape
anoxdata\gameflow\scommonnight.ape
anoxdata\gameflow\scommons.ape
anoxdata\gameflow\senderss.ape
anoxdata\gameflow\slutopia.ape
anoxdata\gameflow\starport.ape
anoxdata\gameflow\sunstrip.ape
anoxdata\gameflow\temple.ape
anoxdata\gameflow\tenements.ape
anoxdata\gameflow\tours2.ape
anoxdata\gameflow\vendomart.ape
anoxdata\gameflow\votowne.ape
anoxdata\gameflow\warshipbay.ape
anoxdata\gameflow\whitendon.ape
anoxdata\gameflow\zong2.ape
anoxdata\gameflow\zordos.ape
anoxdata\maps\votowne.bsp
anoxdata\MODELS\Monsters\lfrog.md2
anoxdata\MODELS\NEWFACE\abbot\abbot.mda
anoxdata\MODELS\NEWFACE\deanamo\Deanamo.mda
anoxdata\MODELS\objects\senderef_new.png
anoxdata\MODELS\objects\senderstation.mda
anoxdata\objects\monsters\_Rictus.gdb
anoxdata\objects\monsters\_Wimpa.gdb
anoxdata\objects\monsters\Anox_Doorlord.gdb
anoxdata\objects\monsters\Unhappy_Nox_Grumbleguard.gdb
anoxdata\objects\levels.gdb
anoxdata\objects\quest.gdb
anoxdata\particles\343\doorlord_fire.apd
anoxdata\particles\343\doorlord_hit_all.apd
anoxdata\particles\343\doorlord_hit_big.apd
anoxdata\particles\343\doorlord_impact.apd
anoxdata\particles\343\doorlord_swipe.apd
anoxdata\particles\343\doorlord_wand.apd
anoxdata\particles\343\doorlord_wand_big.apd
anoxdata\particles\343\lavaball.apd
anoxdata\particles\jake\bane\bane1.apd
anoxdata\particles\jake\bskill\rho_343swipe.apd
anoxdata\particles\jake\intro\sparks_cbot.apd
anoxdata\particles\jake\intro\sparks_once.apd
anoxdata\particles\jake\mystech\poison_base_long.apd
anoxdata\particles\jake\lava_attack.apd
anoxdata\particles\jake\lavabreath_2.apd
anoxdata\particles\redlight\noxgas.apd
anoxdata\scripts\battle\monster_magmatos\levant_mag_armchuck_center.s
anoxdata\scripts\battle\monster_magmatos\levant_mag_intro.s
anoxdata\scripts\battle\monster_magmatos\levant_mag_spitattack.s
anoxdata\scripts\battle\monster_magmatos\levant_mag_superslashatack_center.s
anoxdata\scripts\battle\monster_magmatos\levant_mag_superslashatack_left.s
anoxdata\scripts\battle\monster_magmatos\levant_mag_superslashatack_right.s
anoxdata\scripts\battle\monster_noxdoorlord\monster_noxdoorlord_atak0_none.s
anoxdata\scripts\battle\monster_noxdoorlord\monster_NoxDoorLord_atak2a_none.s
anoxdata\scripts\battle\monster_noxdoorlord\monster_NoxDoorLord_atakall_1.s
anoxdata\scripts\battle\monster_noxdoorlord\monster_NoxDoorLord_atakall_2.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_ambi.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_remove_minions.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_stage2.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_badperson_left.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_badperson_right.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_devilslug_left.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_devilslug_right.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_elpinto_left.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_elpinto_right.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_goldfish_left.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_goldfish_right.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_krapbot_left.s
anoxdata\scripts\battle\monster_rictus\krapton_rictus_summon_krapbot_right.s
anoxdata\scripts\battle\monster_wimpa\monster_wimpa_atak0_none.s
anoxdata\scripts\battle\monster_wimpa\monster_wimpa_atak1_none.s
anoxdata\scripts\battleskills\character_stiletto_stealth.s
anoxdata\scripts\mystech\amb_firefury.s
anoxdata\scripts\mystech\amb_stealth.s
anoxdata\scripts\kraptonjail_scene70_pal.s
anoxdata\scripts\kraptonjail_scene70_rho.s
anoxdata\scripts\kraptonjail_scene70_stiletto.s
anoxdata\scripts\scommonnight_pal_stiletto.s
anoxdata\scripts\senderss_brain.s
anoxdata\scripts\whitendon_scene71.s
anoxger\version.anox
Anachronox Patch 1_01.rtf

Edit:
First start of the game deletes the files!

If I were you, I'd send all of these details over to GOG support and see what they tell you. It may be that those files are obsolete after other fixes or it could be that you have indeed found something and GOG can then look into fixing their release.

Edit: If the files get deleted, maybe they are in fact obsolete, then, after all. Which would be the ideal situation as then GOG's release is fully patched and ready.

The GOG's release is fully patched!

NO it is not ..it is missing the Taxi system added to the city by one of the patches made by the man who worked on the game and fixed things after the company closed down.

I hope to add it back with the patches.

also missing is the unlimited number of save created by patch 4
here are the details of Patch 4

The Anox Build 44 patch is an unofficial secondary patch created by one of the ION Storm Anachronox team members. Here are the patches for Anachronox. These are all "second Anachronox patch" and later, also known as "patch 1.02" and other names.

The Anox Build 44 patch is an unofficial secondary patch created by one of the ION Storm Anachronox team members.

Here are the patches for Anachronox. These are all "second Anachronox patch" and later, also known as "patch 1.02" and other names.

List of changes:

- Speed up the game by holding down the backslash key. See those animation
bugs!
- Filesystem code rewritten from scratch. Improvements to performance and
flexibility. Any part of the os filesystem, a dat file, or a zip file can be
mounted anywhere in the anox virtual file tree. For example, the patch is
packaged in a zip file (anox1.zip) and mounted to root alongside the actual
anoxdata directory. Probably a couple pointer bugs were fixed in the process,
since the old filesystem code was such complete and utter ass.
- If old patch files are detected sitting around when the game starts for the
first time after patching, they will be deleted. So, if you tooled around with
files that were included in the old patch files, then they will not be
automatically deleted if their contents were changed, in which case you will
have to nuke them manually (or do a clean install). Ignore all this if you
haven't modified any game files yourself.
- Command line tool afscmd which allows conversion of dat files to zip files,
and adler checksums of files stored in compressed files or in the filesystem.
Note that the game will not, by default, load retail dat files which have been
converted to zip.
- If you want to speed up load times and are sick of digging around for CD2,
copy the entire cd to some directory on your hard drive and add +set cddir to
your shortcut.
- Somewhere along the patching way, minimum and normal install problems have
been fixed. All three installation sizes should run without any problems.
- Completely new savegame generation system implemented. It is triggered on a
map transition every fifteen minutes or on a map transition before an important
cinematic. These "story saves" do not save any map entities since it takes
place between maps and is much more stable. In many cases it replaces the very
buggy "View Cinematics" menu which contains code I dare not gaze upon lest my
eyes be blinded.
- There is no limit to the number of autosaves and story section saves that can
be generated. Load them up by scrolling in the load game screen, which is
improved and displays more information. Sorry, no pictures.
- Fixed a crash bug when loading old patch1 or retail savegames that were
created while a door or elevator was moving somewhere in the level. Fun with
remapping absolute code pointers. Rewrote entity function mapping code from
scratch.
- Fixed an evil pointer bug or three. There was a really fun one that would
randomly write a backslash to a random part of memory every time a model was
loaded. Oh, and another one where free would be called on an invalid pointer,
slowly fragging memory. I don't understand how people were able to finish the
game at all.
- Wrote a new afex system from scratch, in perl. Afex was our poor broken asset
crawling tool which would start at the first map of the game and attempt to
find all scripts, textures, models, etc. references. But being a broken pile of
crap, it missed a lot of important files. So the size of the patch is bigger to
include these missing sounds and other files.
- Lots and lots of little typos and gameflow bugs fixed. Big thanks to the
patch testers for all of these. Important ones are the Hyrax quest, getting
stuck in the bricks elevator shaft, etc.
- Jake and Richie made a nice taxi service so you can get around the bricks
easier.
- Fixed copy protection incompatibility problems with certain new DVD-ROM
drives.
- Updated libpng to 1.2.4 (less crashing on corrupt input) and zlib to 1.1.4
(fixed buffer problems).
- Rewrote dual parabolic environment mapping back into the new shader code,
also using q coordinate of texture matrix on newer cards.
- Oh, plenty of other stuff I forgot to mention.


Chris G
Admin
3D Worlds and Game Developers Grouop

The version from GOG is a complete B46. The files get deleted because:
>- If old patch files are detected sitting around when the game starts for the
first time after patching, they will be deleted.

You're wrong about the saves -
>- Completely new savegame generation system implemented. It is triggered on a
map transition every fifteen minutes or on a map transition before an important
cinematic. These "story saves" do not save any map entities since it takes
place between maps and is much more stable. In many cases it replaces the very
buggy "View Cinematics" menu which contains code I dare not gaze upon lest my
eyes be blinded.
>- There is no limit to the number of autosaves and story section saves that can
be generated. Load them up by scrolling in the load game screen, which is
improved and displays more information. Sorry, no pictures.

There's unlimited number of slots for loading & autosave, but not for manual saving.

Also, the files are missing because they're obsolete:

>- Filesystem code rewritten from scratch. Improvements to performance and
flexibility. Any part of the os filesystem, a dat file, or a zip file can be
mounted anywhere in the anox virtual file tree. For example, the patch is
packaged in a zip file (anox1.zip) and mounted to root alongside the actual
anoxdata directory. Probably a couple pointer bugs were fixed in the process,
since the old filesystem code was such complete and utter ass.

they're inside anox1.zip, check it for yourself.

BTW, the taxi is also there, it's just limited to a number of locations (see attached image)