Fix #986: Give scalajsenv.js correct URI in source maps.

Two different things caused this bug:

- The `VirtualJSFile` for scalajsenv.js had a wrong URI
  ("virtualfile:" was always prepended due to the default
  implementation of `toURI`).
- The closure optimizer used the path and not the URI of a
  `VirtualFile` when constructing source maps.
Merge pull request #1013 from gzm0/fix-env-source-map

Fix #986: Give scalajsenv.js correct URI in source maps.
Compare method bodies for changes in inc optimizer.