feat(generate-spec): Ignore index.php routes by default

[provokateurin]

index.php routes are not meant to be used for stable APIs.
Unfortunately we have a lot of legacy APIs that still use them so we can't just ignore them entirely.
This changes the default behavior to ignore them, but one can still manually include them by changing the scope for a method or controller.

[come-nc]

This might be a big breaker in server and apps, no?

[provokateurin]

Not really breaking, you just need to add the default scopes to all routes you want to keep. I already have all the changes for that for server. I think most apps are luckily not using index.php routes.