base: wsgi middlewares reorganization

**Problems**
I'm serving invenio using uWSGI:
```console
$ uwsgi --master --processes 4 --die-on-term --http 0.0.0.0:4000 --wsgi-file invenio/invenio.wsgi
AttributeError: 'DebuggedApplication' object has no attribute 'wsgi_app'
...
assert self.script_name == environ['SCRIPT_NAME']
AssertionError
```
**Changes**
* Fixing DebbugedApplication middleware usage. ([_why uWSGI requires it_](http://stackoverflow.com/a/17839750))
* Moving the `WSGIScriptAliasFix` to the WSGI file so it only applies to the Apache context.

Related to: #254