I've fixed the issue, and it turns out it wasn't ALiVE related at all - on Linux, all mod folders and filenames must be entirely lowercase, otherwise they simply won't work. This is an easy fix:

shopt -s globstar
rename -v -f 'y/A-Z/a-z/' mods/**

(shopt enables the ** recursive operator in bash)

Thanks for all your help trying to troubleshoot this!

The error occurs only on mission start on the Linux dedicated server - it does not happen in the editor (Windows client).

I've tried moving the mods to the root folder - no effect.

Mission was made in 3DEN this morning and nothing was copy/pasted from other sources.

I've moved the CUP Terrain mods to the end of the mod lines, but nothing changed. Despite the CUP mods being loaded, I am still getting the 'No entry 'bin\config.bin/CfgWorlds.Takistan'.' error.

Startup parameters:

./arma3server -ip=10.0.0.6 -port=2302 -cfg=/opt/arma3server/serverfiles/cfg/arma3-server.network.cfg -config=/opt/arma3server/serverfiles/cfg/arma3-server.server.cfg -mod=mods/@CBA_A3\;mods/@ALiVE\;mods/@rhs_afrf\;mods/@rhs_usf\;mods/@Leights_OPFOR_Pack_OFFICIAL\;mods/@CUP_Terrains_Core\;mods/@CUP_Terrains_Maps; -servermod=mods/@CUP_Terrains_Core\;mods/@CUP_Terrains_Maps -bepath= -autoinit -loadmissiontomemory -world=Takistan

Both missions are fresh missions made in 3DEN with the latest version of all mods from Steam Workshop. I was able to actually spawn in-game by waiting in the lobby for the 'Performance warning:' messages to pass, and encountered some weird issues.

Units are spawning in weird positions and rapidly appear/disappear on screen:
http://steamcommunity.com/sharedfiles/filedetails/?id=658728783

Random objects are being detected as objectives (dots in debug mode only appear in this area of the map):
http://steamcommunity.com/sharedfiles/filedetails/?id=658728752

Other oddities including CSAT spawning rather than LOP_TKA (Takistan Army from Leight's OPFOR), units glitching between the terrain and ~50 meters in the air, and more. My client eventually crashed from all the craziness.

Here are the launch parameters on the server:

./arma3server -ip=10.0.0.6 -port=2302 -cfg=/opt/arma3server/serverfiles/cfg/arma3-server.network.cfg -config=/opt/arma3server/serverfiles/cfg/arma3-server.server.cfg -mod=mods/\@CBA_A3\;mods/\@ALiVE\;mods/\@CUP_Terrains_Core\;mods/\@CUP_Terrains_Maps\;mods/\@rhs_afrf\;mods/\@rhs_usf\;mods/\@Leights_OPFOR_Pack_OFFICIAL -servermod=mods/\@CUP_Terrains_Core\;mods/\@CUP_Terrains_Maps -bepath= -autoinit -loadmissiontomemory -world=Takistan

Here is the latest server.rpt (with ~10,000 'Performance warning:' messages omitted). The 'No entry 'bin\config.bin/CfgWorlds.Takistan'.' error is still occurring, I guess that's the first issue?

I can confirm that the map is on the server, and that I've added CUP Terrains Core & Maps to the -mod line. I also tested with them in the -servermods line as well as settings -world=Takistan, and nothing changed. Here is the launch command for the server currently:

./arma3server -ip=10.0.0.6 -port=2302 -cfg=/opt/arma3server/serverfiles/cfg/arma3-server.network.cfg -config=/opt/arma3server/serverfiles/cfg/arma3-server.server.cfg -mod=mods/\@CBA_A3\;mods/\@ALiVE\;mods/\@CUP_Terrains_Core\;mods/\@CUP_Terrains_Maps\;mods/\@rhs_afrf\;mods/\@rhs_usf;mods/\@Leights_OPFOR_Pack_OFFICIAL -servermod=mods/\@CUP_Terrains_Core;mods/\@CUP_Terrains_Maps -bepath= -autoinit -loadmissiontomemory -world=Takistan

Could it be something to do with the forward slash in 'bin\config.bin/CfgWorlds.Takistan' and Linux?

I tried getting a mission on Takistan to work, and it failed with similar results. Here is a log file . One error I noticed that occurred on both attempts was:

11:10:56 Starting mission:
11:10:56  Mission file: co_conquer_takistan (__cur_mp)
11:10:56  Mission world: Takistan
11:10:56  Mission directory: mpmissions\__cur_mp.Takistan\
11:10:57 Warning Message: No entry 'bin\config.bin/CfgWorlds.Takistan'.

Perhaps its an issue with the map itself (or how the linux server is loading it) and not ALiVE? The missions work fine when hosted locally on Windows and in the editor.

Yes, here is the unbinarized mission.sqm .

@Tupolov Can you test a stock ALiVE mission without ALiVEServer?

I tested the server with two missions - ALiVE | Sabotage seemed to work properly without any issues, but Operation Landlord (from here ) did not - after slotting in and loading the mission files, I was disconnected from the server (no error/warning). server.rpt here

@SavageCDN Forgot to mention - also remove the ALiVE data module if you still have it placed in the mission.

Removed the data module, no more "THERE IS A PROBLEM WITH THE ALIVE PLUGIN!", but some other errors still persist - the indexing appears to be incorrect, and units are spawining weirdly: http://steamcommunity.com/sharedfiles/filedetails/?id=657126371

I find it weird that everything works fine in the editor - units spawn on the ground and act normally, but as soon as I move the mission to a dedicated server things seem to break. Is it really an indexing issue?

Some screenshots of the map in the editor (note the correct placement of objects/CQB positions):
http://steamcommunity.com/sharedfiles/filedetails/?id=657097981
http://steamcommunity.com/sharedfiles/filedetails/?id=657098003

Screenshots in-game (CQB positions missing, dots in weird places):
http://steamcommunity.com/sharedfiles/filedetails/?id=657098026
http://steamcommunity.com/sharedfiles/filedetails/?id=657098040

I was able to get the mission to launch and players to spawn in-game (both with & without @AliveServer), however now there are some other weird issues. Units will sometimes spawn in mid-air, underground, or will flash in and out of existence multiple times per second, and they cannot move. Server FPS is steady at 45-50 (ignoring some spikes when spawning in profiles). Also, the debug view is showing some weird results compared to what I get when I run the mission in the editor.

Server .rpt (performance warnings excluded): pastebin