Schema validation fails for JSON schema handlers

### Issue workflow progress

_Progress of the issue based on the
[Contributor Workflow](https://github.com/the-guild-org/Stack/blob/master/CONTRIBUTING.md#a-typical-contributor-workflow)_

- [ ] 1. The issue provides a reproduction available on
[Github](https://github.com/ardatan/graphql-mesh/tree/master/examples/hello-world),
[Stackblitz](https://stackblitz.com/github/ardatan/graphql-mesh/tree/master/examples/hello-world)
or
[CodeSandbox](https://codesandbox.io/s/github/ardatan/graphql-mesh/tree/master/examples/hello-world)

> Make sure to fork this template and run `yarn generate` in the terminal.
>
> Please make sure Mesh package versions under `package.json` matches yours.

- [ ] 2. A failing test has been provided
- [x] 3. A local solution has been provided
- [ ] 4. A pull request is pending review

---

**Describe the bug**

When running `yarn run mesh validate` for a mesh containing a handler for a JSON schema the validation fails with the following error:

```
ERROR [source=Hello World] Failed to generate the schema for the source
Validation failed for "schemaWithAnnotations" under ".mesh/sources/Hello World": undefined
```

**To Reproduce**

Steps to reproduce the behavior:

- https://codesandbox.io/s/github/ardatan/graphql-mesh/tree/master/examples/hello-world
- Run `yarn run mesh validate`

**Expected behavior**

The validation should be successful.

**Additional context**

After some additional digging I could trace down the actual error to be thrown by the [validate function](https://github.com/ardatan/graphql-mesh/blob/master/packages/legacy/store/src/index.ts#L168) to be
`[ "Directive 'transport' was removed from schema 'Query'" ]`.

It seems the structural representation of the transport directive differs between the two schemas compared during validation:

`oldSchema`:
```
"extensions": {},
"astNode": {
"directives": [
{
"kind": "Directive",
"name": { "kind": "Name", "value": "transport" },
"arguments": [
{
"kind": "Argument",
"name": { "kind": "Name", "value": "subgraph" },
"value": { "kind": "StringValue", "value": "Hello World" }
},
{
"kind": "Argument",
"name": { "kind": "Name", "value": "kind" },
"value": { "kind": "StringValue", "value": "rest" }
}
]
}
]
},
// ...
```

`newSchema`:
```
"extensions": {
"directives": {
"transport": { "subgraph": "Hello World", "kind": "rest" }
}
},
// ...
```

Start with the hello-world example and run `yarn run mesh validate` to reproduce the failure. Read `packages/legacy/store/src/index.ts`, especially the `validate` function, and compare how the transport directive is represented in the old and new schemas; done means JSON schema handler validation succeeds without the reported error.

Written by the indexing model from the issue text.