Your latest point can be resolved through explicitly asking authors to cite the paper rather than linking to the website/github repo. For instance I used Intel

Your latest point can be resolved through explicitly asking authors to cite the paper rather than linking to the website/github repo. For instance I used Intel Pintools and they specify in their FAQ[1] : I used Pin for my latest paper. What citation should I include? [actual paper here] [1]: https://software.intel.com/en-us/articles/pintool-faq https://software.intel.com/en-us/articles/pintool-faq