I'm unsure if this works on windows. I'd rather say we copy files if they are re-used. Because if you build a texture based on an image, which is also used for an other texture; then someone changes the image for the other texture, it could mess up your texture. If you copy the image, you have a defined state which should be preferable in most cases.we could try to use symbolic links to link files which are used in multiple textures
For textures we could also collect different layers for shaders, for example the bump map, etc.
about the naming convention: well, is it really that important? I mean it's like in coding, you shouldn't name a variable "a" or "v1", but apart from that it's rather unimportant, as long as it's understandable. "numberOfBots" or "botCount" or "numBots" or in some cases even "bot_count" are acceptable names for the same thing.
Same holds for models, textures, etc in my opinion. It shouldn't be named "spaceship.mesh" for sure, but something like "heavy_pirate_fighter.mesh" is ok. Maybe someone builds "heavy_pirate_fighter_2.mesh", but thats still ok in my opinion. Others prefer camelCase and some people may put the name of the ship or the author in the filename. As long as it's distinguishable it's ok for me.
about the info file / list of references: well that's new, at least for me. what's the reason for this? textures are listed in a material file, material files are listed in a mesh file... do we really require an additional file?