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Sometimes code has to be removed. This is how you do it without you inform other.
In the header file wrap the method signature into the OF_DEPRECATED_MSG("message", signature)-makro. You should also hint at any replacement functions, e.g.
OF_DEPRECATED_MSG("ofxFoo::initFoo(int bar) is deprecated, use foo(int bar) instead.", void ofxFoo::initFoo(int bar));
Remove the actual implementation code.
Add the "@deprecated" tag to the Doxygen documentation.