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I currently use emacs to edit .java files and run eclipse.
Eclipse doesn’t automatically recognize modified files, so I often end up running unmodified application.
I wonder if there exists a shortcut to refresh all the modified files in eclipse.
Perhaps you want to check
Preferences > General > Workspaces > Refresh using native hooks or polling. You can see that the eclipse refreshes the file you edit with external editor (like vi, emacs, etc) when you check the option.