You aren't using the latest version of MCEdit. Click on the Windows, Mac OS, or Linux icons on the homepage to download.
Did you download the source files by mistake? Try downloading again. Also, ensure you download the right version for your OS, e.g. don't download the Mac version for your Windows computer.
MCEdit does not natively support editing biomes on Anvil maps. SethBling has written a filter to modify biomes, available bundled with MCEdit since version 0.1.2, or from SethBling's youtube page.
Look inside the MCEdit-<version>-<platform>/ folder for a file named
mcedit.log. This file has the same contents as the console window.
Alternately, to copy the text from a console window on Windows:
The red, green and brown boxes are Entities - red are mobs, green are dropped items, brown are paintings. The yellow boxes are TileEntities, which include the contents of Chests, Dispensers, and Furnaces. The brown boxes are Paintings. Entities cannot be edited. Some TileEntities can be edited; double-click on one to edit.
When you click "Save & Quit to Title", Minecraft doesn't completely quit out of the world. Some important parts (the region file headers) are still in Minecraft's memory, so any changes to them will be overwritten if Minecraft is still running. This is what corrupts the world files. To dismiss the message, click OK. If you don't want to see it again, click "Don't remind me again." This will be changed in a future update.
MCEdit currently works with all formats of Minecraft world more or less, from Classic to Anvil. The operation of MCEdit is usually unrelated to the version of Minecraft and Java.
Yes, but you will need to run from source. The process is extremely simple with Linux, there is a guide in the README. Alternatively you can install Wine, and it will work with some distributions of Ubuntu.
The vanilla Minecraft server was changed to only generate Nether and End chunks if a player is present in those areas.