Fixed: removeCombined breaks the build with multiple modules

I'm trying to build multiple applications and a shared library into a set of files, with one file per app and one file for shared code.  `removeCombined` option is enabled. The example below for simplicity has two modules.

```
root/
  src/
    foo.js
    bar.js
    template.hbs
config.js
```

**src/foo.js**:
```javascript
define(function (require) {
  require('bar');
});
```

**src/bar.js**:
```javascript
define(function (require) {
  require('hbs!./template');
});
```

**src/template.hbs**
```handlebars
<div></div>
```

**config.js**:
```javascript
({
  paths: {
    hbs: '../bower_components/require-handlebars-plugin/hbs'
  },
  appDir: 'src',
  baseUrl: './',
  dir: 'build/src',
  removeCombined: true,
  modules: [
    {
      name: 'foo',
      exclude: [ 'bar' ]
    },
    {
      name: 'bar'
    }
  ]
})
```

However, combined templates are removed too early. I'm getting the following error:
```
$ r.js -o config.js

Tracing dependencies for: foo

Tracing dependencies for: bar
Error: ENOENT, no such file or directory '/Users/dremora/Code/playground/require-handlebars-plugin-bug/build/src/template.hbs'
In module tree:
    bar
      hbs

Error: Error: ENOENT, no such file or directory '/Users/dremora/Code/playground/require-handlebars-plugin-bug/build/src/template.hbs'
In module tree:
    bar
      hbs

    at Object.fs.openSync (fs.js:438:18)
```

See also [this gist](https://gist.github.com/Dremora/3c4b0bcd3126803780c1) (checkout, run `bower install && r.js -o config.js`).

This pull request fixes the issue.