Ref T4257. Currently, the pull logic looks like this:

if (new) {
  create();
} else {
  if (hosted) {
    install_hooks();
  } else {
    update();
  }
}

This means that the first time you run repository pull, hooks aren't installed, which makes debugging trickier. Instead, reorganize the logic:

if (new) {
  create();
} else {
  if (!hosted) {
    update();
  }
}

if (hosted) {
  install_hooks();
}

Ran bin/repository pull on a new hg repo and got hooks installed immediately.