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I'm trying to modify a number of graphviz diagrams generated by doxygen. My problem is that the graphviz input files have a .dot extension. Textpad insists on opening the files as binary and won't let me edit them as a result.

http://www.stack.nl/~dimitri/doxygen/
http://www.graphviz.org/

You'll have to open the file via the open file dialog menu (ctrl-O). Navigate to your file and instead of the default value for File format, change that value from Auto to Text

for a more permanent solution:

go to
Configure - Preferences - Document Classes - Binary, then look for the *.dot pattern in the list, select it and delete it.