Custom Endpoint Scenario 1 bug with generate

### Scribe version

4.25

### PHP version

8.2.9

### Framework

Laravel

### Framework version

9

### Scribe config

```ruby
title => "SC Tracker API Documentation"
base_url => "https://localhost:8000/"
type => "laravel"
try_it_out.enabled => false
try_it_out.base_url => "http://127.0.0.1:8000"
auth.enabled => true
auth.name => "Authorization"
auth.placeholder => "{ACCESS_TOKEN}"
translations => "en"
```

### What happened?

I have run scribe:generate and produced the yaml files. i changed the one named 0.yaml where i removed some body parameters data and replaced with an empty string, then i ran generate again and the changes were respected and not changed. but if i make some new changes and run the command again it dosen't respect the changes anymore, so if you make some changes and then run 2 generate commands after each other then they remove the changes.

### Docs

- [X] I've checked [the docs](https://scribe.knuckles.wtf/laravel), the [troubleshooting guide](https://scribe.knuckles.wtf/laravel/troubleshooting), and [existing issues](https://github.com/knuckleswtf/scribe/issues?q=is%3Aissue+), but I didn't find a solution

Reproduce the issue by editing the generated 0.yaml file, running scribe:generate twice, and checking whether the changes remain. Trace the generate command and the handling of generated YAML files; done means consecutive generation runs preserve the described manual changes.

Written by the indexing model from the issue text.