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I ran into similar problems. To work around them, I went into node_modules/webhook-deployer\lib\incoming.js and changed lines 40-58. It seems that the payload I received didn't have anything under 'ref'.
// remove .git from the repo string, since the hook will not have that address when it comes from github
// so instead of explaining that you shouldnt enter ".git", we just remove it here.
if (repoData.repository.url == deploy.repo) {
runDeploy(deploy);
}
else {
webdep.log("No, wrong repo, nothing to do");
...
Github api sends repo urls like this: https://api.github.com/repos/
Webhook-deployer sees this as https://apihub.com/repos/
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