Bei default a query of the Europe PMC REST API will do a fulltext search, but not include the references list. To include the references list, add
OR REF:your_query, e.g.
Lagotto is including the query of the references list since the Lagotto 3.17 release. Thanks to Jo McEntyre for the tip.
I tried to search links to software repositories, which were mentioned in Europe PMC Open Access full texts.
At least for github.com, I have found 867 new GitHub repos and proposed them to be added (see Pull Request)
Sources used can be found here: https://github.com/njahn82/dvcs_epmc
Hope it helps collecting metrics for scientific software repositories with Lagotto.