I recently ran into difficulties when trying to install Minecraft Forge development environment by the instructions in http://www.minecraftforge.net/wiki/Tutorials/Setting_up_Eclipse_and_Forge . I used Eclipse SDK version 3.5.2 (build id: M20100211-1343) because that's what's available pre-packaged in current Debian Squeeze (6.0.6).
The problem was that the variable MCP_LOC didn't seem to work, so all of my paths were relative to the filesystem root dir, not my working directory. This caused "file system is read only" errors when I tried to add new packages into the Minecraft project in Eclipse.
The fix was to add this line into the development directory's file eclipse/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs :
pathvariable.MCP_LOC=/home/xxxx/proj/minecraft-modding
Of course, you should put the path of your own Minecraft development environment there.
After adding this, all libraries were found and I was able to add packages to src and common.