I've become so confused and frustrated by this problem, I've decided to ask here.  I'm using the latest Eclipse, JDK 7u55, Forge 1065, (happens on 1059 too), and Minecraft 1.7.2.  The project I've been working on suddenly started acting strangely yesterday.  Seemingly at random, some classes in my main package would seem to stop existing to the other classes in the project, disconnecting all references to the class, making the entire project throw errors until I removed the class, refreshed the workspace, put it back in, and refreshed it again.  All textures and the .lang file stopped working in-game too.  As far as I know, it wasn't caused by anything I did, it was working fine when I closed Eclipse for the night, then when I opened the project the next morning it started doing all this.  It gives the same in-game issues if I compile with MCP, and I've tried reinstalling Forge, updating Forge, re"installing" Eclipse with a fresh workspace, using the gradle commands to clean cache and redo setupDecompWorkspace and the Eclipse workspace setup...I'm out of ideas, and nobody I've talked to has a clue what could be going on.  Thanks for any help you guys can give.

 

Project files: https://dl.dropboxusercontent.com/u/10036065/Foundry/%5BFoundry%5D%20Core%20Project.zip

You (or some form of malware) must have edited or deleted some of the files. For a last resort, consider deleting the old ForgeGradle files, and starting fresh. I also recommend using Forge build 1060.

I did think it could have been some sort of virus, but I redownloaded Forge and installed in a new directory from scratch a couple times, wouldn't that have fixed it?  I did scans today too after thinking about that, and nothing turned up.  I settled on a kind of meh solution though, I'm just rewriting the whole thing in a fresh installation.  On the bright side, I learned some things from this experience, and I'm getting to incorporate everything I've learned about structuring a mod from the start this time, so the framework is more stable/easier to work off of.