Bug fixes with the replaceRequireScript option

This commit does two things:

1. Decouples the `replaceRequireScript` option from almond since its functionality doesn't actually depend on almond being used.
2. Gracefully handles document fragments in files defined in the `replaceRequireScript` option. Previously if a file specified in this option did not contain a `<html>` or `<body>` tag then those tags would be written in. So if a file had this fragment:

```html
<script data-src="js/main" src="require.js"></script>
```

then resultant HTML would be:

```html
<html><body><script src="js/main.js"></script></body></html>
```

Which isn't ideal. My particular use case is replacing script tags in mustache partials. I was able to simplify the logic quite a bit using jsdom.