Select the JavaScript file or any other object in Unity and press:

• return key if you are on MacOS
• F2 if you are on Windows.

Aside from the return key, you can click on a file, wait for a bit, then click again (don't click again too fast). This is also the same way to rename files in the OS.

The only way to fully and gracefully rename a monobehaviour script that I have found:

1. Inside of Unity, rename the file that contains the script to the desired name. (Select the script, wait 2 seconds, click again, then type the new name)
2. Inside of MonoDevelop, open the script, right click on the class name, choose "refactor" > "rename". Uncheck the "rename file" box.
3. Make the new class name the same as the new file name you used in Unity.
4. Save all open MonoDevelop files.
5. Close Unity (don't save the scene)
6. Open Unity

Now your monobehaviour class is fully renamed / refactored.

Hitting F2 in Windows with folders doesn't work sometimes - it just goes back to the former folder (just like a Assets folder keep re- appearing within the Assets folder after deleting it). Clicking twice on the folder name and then giving it a new name works however, so it seems to be broken on windows at times.

I have also found that if you create a new folder in project view (called "new folder" by default) then edit the name, then press enter, it just pops back to "new folder". Its very frustrating. I think this could be a bug. Im using windows vista and unity 3 pro and ran it a admin but still no luck.