Add ability to specify env variables in JSON

By not overwriting the env object in the JSON, it allow us to specify
env variables directly in the JSON.

Example:
```json
[
  {
    "name": "my-awesome-app",
    "script": "./lib/app.js",
    "port": "10000",
    "env": {
      "NODE_ENV": "production",
      "AWESOME_SERVICE_API_TOKEN": "xxx"
    }
  }
]
```

Typically, I wanted to specify the NODE_ENV and other specific configuration, like keys/token for external services.