If set rootDir in tsconfig.json which under project, the ts-loader can't handle the piping output of ts-import-plugin

In tsconfig.json, I set the rootDir option:
```
"compilerOptions": {
    "rootDir": "src"
}
```
The compiler console throw error:
```
File 'index.tsx' is not under 'rootDir' '/Users/XXX/Workspace/project/src'. 'rootDir' is expected to contain all source files.
```
Any idea on it?