That’s an interesting suggestion. In practice, people use Help > Update ImageJ to checkout nightly builds of ImageJ after being asked by Wayne Rasband to see if his changes solve their issue. So we can’t completely remove the menu entry. But we could patch a warning into the command when a user runs it, saying that within Fiji (or an environment where ImageJ1 gets patched) you might not want to use this command.
http://forum.imagej.net/t/help-update-imagej-triggers-there-are-locally-modified-files-warning-when-running-help-update/8898/4?u=stelfrich: