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My favorite features...
F12-m - creates a temporary Magik file where you can hack without affecting the original source code files.
Alt-c - useful for tagging a block of code with START CHANGE/END CHANGE when making your own patches.
F2-t - creates debug write() statement around a variable in the code.
F4-s - creates #DEBUG show() statements around a variable (use F3-d to toggle #DEBUG mode)
F3-t - creates a debug write() statement at the top of the method.
Alt-x all - this is one of my all-time favourite tools within Emacs. Great for finding all the occurrences of a string (using regexp) in a file. See 3:20 of MagikEmacs Screen-cast 4 for a demo.
F9 - selects the entire method.
Ctrl-Alt-\ - indents the Magik code in current selection
Alt-space - drops breadcrumbs (ie bookmarks in Emacs buffers)
F5-b - loops through the current breadcrumbs
Alt-F5 - manage your breadcrumbs