[BUG] Running publisher after revision deletion remove whole API

### Release version

v6.0.1.3

### Describe the bug

When I commit changes to an API with multiple revisions and remove one of the revisions, the publisher removes the entire API.

### Expected behavior

I expect that only the revision removed in the commit will be deleted from the APIM instance.

### Actual behavior

In reality, the entire API is removed from the APIM instance.

### Reproduction Steps

I have an API with three revisions:
```
apis/
├── azerty-service/
├── azerty-service;rev=2/
└── azerty-service;rev=3/
```

I delete the folder apis/azerty-service;rev=2, commit the changes, and run the publisher for these updates.

As a result, the entire API azerty-service, including all its revisions, is removed from the APIM instance.

まず、一覧にある3つのリビジョンを含む API で publisher の更新を再現し、その後 apis/azerty-service;rev=2 フォルダーだけを削除して publisher を実行します。完了とは、APIM インスタンスに azerty-service と azerty-service;rev=3 が保持され、revision 2 だけが削除されている状態です。

索引モデルが issue の本文から書いたものです。