warrior_hamster: If anyone is interested there may be half a solution that someone with better abilities than i have, could run with.
With the first game Shadow of Chernobyl I found when it was downloaded through GoG it had a weird problem where it duplicated the code in its fsgame.ltx file.
I have the Steam version of Clear Sky as well so i thought i'd have a look in its fsgame.ltx file.
It looks very different to the GoG Clear Sky version inside.
I copied over the code from my Steam Clear Sky fsgame.ltx to my GoG Clear sky fsgame.ltx file.
lo and behold the game started working through GoG.
The big problem is that the keyboard won't work and some graphics settings are greyed out???
I am able to look around as the protagonist though and the graphics look okay, i'm running at ~100fps.
Anyway, here is the Steam version of the code:
;abbreviation = recurs|notif| root| add| ext| description
$app_data_root$ = true| false| $fs_root$| _appdata_\
$arch_dir$ = false| false| $fs_root$
$game_arch_mp$ = false| false| $fs_root$| mp\
$arch_dir_levels$ = false| false| $fs_root$| levels\
$arch_dir_resources$ = false| false| $fs_root$| resources\
$arch_dir_localization$ = false| false| $fs_root$| localization\
$arch_dir_patches$ = false| true| $fs_root$| patches\
$game_data$ = false| true| $fs_root$| gamedata\
$game_ai$ = true| false| $game_data$| ai\
$game_spawn$ = true| false| $game_data$| spawns\
$game_levels$ = true| false| $game_data$| levels\
$game_meshes$ = true| true| $game_data$| meshes\| *.ogf;*.omf| Game Object files
$game_anims$ = true| true| $game_data$| anims\| *.anm;*.anms| Animation files
$game_dm$ = true| true| $game_data$| meshes\| *.dm| Detail Model files
$game_shaders$ = true| true| $game_data$| shaders\
$game_sounds$ = true| true| $game_data$| sounds\
$game_textures$ = true| true| $game_data$| textures\
$game_config$ = true| false| $game_data$| configs\
$game_weathers$ = true| false| $game_config$| environment\weathers
$game_weather_effects$ = true| false| $game_config$| environment\weather_effects
$textures$ = true| true| $game_data$| textures\
$level$ = false| false| $game_levels$
$game_scripts$ = true| false| $game_data$| scripts\| *.script| Game script files
$logs$ = true| false| $app_data_root$| logs\
$screenshots$ = true| false| $app_data_root$| screenshots\
$game_saves$ = true| false| $app_data_root$| savedgames\
$downloads$ = false| false| $app_data_root$
Replacing the fsgame.ltx contents with this fixed the issue. Can't enable DirectX 10.1, but I'm guessing it's a limitation of the game running on a DirectX 12 system.