All changes in code must go to raphael.core, raphael.svg or raphael.vml.
The rest are generated files, generated after running npm run build.
To run tests you need to open dev/test/index.html in your browser, there's no automated way right now.
After changing the core/vml/svg files, execute npm run build to generate all versions, make a commit and you are ready to make a pull request!
Remember that if you want to add a functionality it must be present in the vml and svg versions, no svg-only features will be accepted.
First search for similar issues to make sure you don't repeat an existing one.
Then please create a fiddle (jsfiddle) recreating the bug so we can find out what the problem is more easily (or be a hero and find it yourself and send a pull request!). You can also use the raphael playground to reproduce your issues.
Remember to add all the info that can be useful such as