vscode extension doesn't works with graphql modules

**Intended outcome:**
Using graphql-modules and Typescript with different schema.graphql files, extension should not give error "Type "Query" already exists in the schema. It cannot also be defined in this type definition"

**Actual outcome:**

**How to reproduce the issue:**
I have the following apollo.config.js
```nodejs
module.exports = {
client: {
service: {
name: "microservices-gateway"
}
}
};
```
Folder structure
```bash
src
├── index.ts
└── modules
├── app.ts
└── greeting
├── greeting.provider.ts
├── index.ts
├── resolvers.ts
└── schema.graphql
```
I have tried to use `excludes` or `includes`, doesn't seems to work

**Versions**
apollo@2.24.0

Reproduce the error with the shown apollo.config.js, the TypeScript folder structure, and separate schema.graphql files. Start by tracing how the VS Code extension discovers schemas and applies includes or excludes; done means graphql-modules schemas no longer produce the duplicate Query error.

Written by the indexing model from the issue text.