Well, it's probably time to learn regular expressions
More seriously, I don't know if a graphical tools already exists, but writing a small say Python script which parse every \ref, \eqref and \cite in each proof environment using regular expressions is rather easy. Maybe the only ambiguous things is to associate each proof environment to with the corresponding theorem/lemma. Then it would again be easy to generate Graphviz code from that, and Graphviz will automatically produce a nice oriented graph showing all the dependencies.
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