During Black Hat USA 2010, Patrick Thomas presented a new web application fingerprinting tool called Blind Elephant.
BlindElephant works via a new trendy technique of fetching static elements of the web app such as .js, .css, and other core files then running a check sum to compare sizes of those files from released versions.
BlindElephant is available via SVN here
svn co https://blindelephant.svn.sourceforge.net/svnroot/blindelephant/trunk blindelephant
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