"exclude" property of tsconfig.json is not being respected

I am working with the excellent Express/Node/Typescript example code found here. It transpiles the .ts code with the following command from run.sh:

./node_modules/.bin/tsc --sourcemap --module commonjs ./bin/www.ts

This works as advertised, but I would prefer to use a tsconfig.json file and tsc -p . However, when I run that command I get a raft of TS2300: Duplicate identifier 'foo' errorswhen tsc(erroneously?) tries to walk the ./node_modules and ./typings directories. Below is the tsconfig.json I am using:

{
  "compilerOptions": {
    "target": "ES5",
    "module": "commonjs",
    "moduleResolution": "node",
    "sourceMap": true,
    "emitDecoratorMetadata": true,
    "experimentalDecorators": true,
    "removeComments": false,
    "noImplicitAny": false
  },
  "exclude": [
    "node_modules",
    "typings"
  ]
}

Any ideas? I am using tsc 1.7.3 FWIW.

I did:

git clone https://github.com/czechboy0/Express-4x-Typescript-Sample.git
cd Express-4x-Typescript-Sample/
./run.sh
tsd install  # I don't know why, but this helped me.
./run.sh

I created Express-4x-Typescript-Sample/tsconfig.json file with content

{
  "compilerOptions": {
    "target": "ES5",
    "module": "commonjs",
    "moduleResolution": "node",
    "sourceMap": true,
    "emitDecoratorMetadata": true,
    "experimentalDecorators": true,
    "removeComments": false,
    "noImplicitAny": false
  },
  "exclude": [
    "node_modules",
    "typings"
  ]
} 

I ran

[...]/Express-4x-Typescript-Sample$ tsc -p .

and it works work me - i.e. there are no errors.