With the changeover to Steam's new content delivery network (SteamPipe/SteamCMD), custom content must now be placed inside the "custom" folder within your server's FTP. Specifically, custom files need to either be inside ".vpk" files that go directly into "custom", or loose, in subfolders of "custom", which are read by the game server as it would its standard directory tree.
For instance, if you have a new map called "coolmap.bsp" that you wish to upload, you could put it in one of these folders:
And if you downloaded a zipfile containing "materials" and "sounds" folders, you might upload both folders to something like:
The folder name within "custom" does not matter, and you can use different folders for your different custom content. The game searches through all of them automatically when it needs to be loaded.
Using a separate custom folder provides the important benefits of separating out your custom content from the content included with the game and making it much easier to manage different content packs.
The Websync tool only searches through "custom", and in the future, we will configure the system to only retain files in "custom" when it moves servers between machines or locations, so it is important that you put all your files in "custom".
All NFO clients had their old content moved to "custom/old_custom_files" folder for them when their servers were converted to SteamPipe, allowing the servers to continue to run seamlessly.
Valve talks more about how all of this works in a Steam support article.
CS:S, TF2, DOD:S, etc.
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Having files in "custom" also allows you to override content included with the game. You could put your own version of "de_dust" on the server, for instance.