grunt-ts: Beta9 causes implicit compilation of node_modules

Most of what is here is from some AngularJS2 boilerplate (not sure what exact boilerplate). I have next configuration in tsconfig.json:

{
  "compilerOptions": {
    "target": "es5",
    "module": "system",
    "moduleResolution": "node",
    "sourceMap": true,
    "emitDecoratorMetadata": true,
    "experimentalDecorators": true,
    "removeComments": false,
    "noImplicitAny": true,
    "suppressImplicitAnyIndexErrors": true
  },
  "exclude": [
    "spec",
    "e2e",
    "node_modules"
  ]
}

In Gruntfile.js I have next:

// ... some code
    ts: {
            build: {
                src: ['app/**/*.ts', '!app/**/*.spec.ts', 'typings/**/*.ts', 'missing_typings/**/*.ts'],
                outDir: 'dist',
                tsconfig: 'tsconfig.json'
            },
            options: {
                fast: 'never',
                verbose: true
            }
        },
// ... moar code

I use typings package.

When running grunt with grunt-ts-5.5.1 everything compiles fine, command for tsc is next:

grunt-ts-5.5.1-cmd.txt

However, in grunt-ts-6.0.0-beta.9 compilation fails. Command for tsc is different and doesn’t notice that typings were specified in typings/ directory, and tries to compile node_modules directly. Specifying !node_modules/**/*.ts in src doesn’t help.

grunt-ts-6.0.0beta.9-cmd.txt