Minecraft Launcher Mods

Essentially, this has worked for me since the new launcher was added up until two days ago. The mods in question are coremods, such as Forge, Optifine and Minecrift. This isn't an issue with the mods themselves though, rather a function of the launcher.

My folder organisation was /libraries/mods/vendor/modname/modversion/modname-modversion.jar
I then had a load of custom version json files set up which would call these mods. Here is the addition I had for the Minecrift json as an example;

    {
      "name": "mods.mtbs3d:minecrift:1.6.4-b28"
    },
    {
      "name": "mods.optifine:OptiFine:1.6.4_HD_U_D1"
    },

The benefit of this system was that I could upgrade mods without having to modify the original minecraft.jar beyond a META-INF removal, and I could have different profiles set up for different purposes. Obviously I'm guessing the system was designed like that, and it works very well aside from some launch directory issues.

I had approximately 15 different mod configurations set up this way for various different purposes. What I then did was move the version folders I wasn't using into a backup directory to speed up loading of the launcher, as it starts to get sluggish the more you have available. I also had some older, no longer in use mods still in their folders incase I needed to test something.

However, every mod that was in my /libraries/mods folder that wasn't being called by an active version json was deleted without warning. Mods that were called in version jsons that I hadn't moved to the backup directory were not deleted, an example would be the Minecrift one above. I had over 30 old versions of that mod in the folder, and the launcher deleted every one except for the one I had being called in the version json.
I also tried setting the files to Read Only to prevent the launcher from deleting them, however it wouldn't launch the game instead throwing an error.

The last time I can 100% confirm that the launcher wasn't deleting those libraries was the 1st april, as that is when my backup was dated. Thankfully I found that backup and didn't lose a lot of archive versions of mods.