I'll just quote what was said by Nostalrius regarding WoW's source code
So yeah, There's missing files but from the sounds of things they're onto a way to fix thatFirst, they DO have the source code for Vanilla WoW. Code version control systems are not something new, as it has been a standard in the industry for a long time. With these systems, they can retrieve the code at any given previous backup date.
However, in order to generate the server (and the client), a complex build system is being used. It is not just about generating the “WoW.exe” and “Server.exe” files. The build process takes data, models, maps, etc. created by Blizzard and also generates client and server specific files. The client only has the information it needs and the server only has the information that it needs.
This means that before re-launching vanilla realms, all of the data needed for the build processes has to be gathered in one place with the code. Not all of this information was under a version control system. In the end, whichever of these parts were lost at any point, they will have to be recreated: this is likely to take a lot of resources through a long development process.