Write .htaccess also from CLI

The new updater as shipped with ownCloud 9.0.x invokes `occ` via `shell_exec`. This means that the `\OC::$CLI` code is used when updating.

This removes the manual `.htaccess` modifications, effectively leading to the fact that URLs without index.php in it stop working. This also affects share URLs which could be considered a rather serious regression.

- User installs 9.0.0 via web
- User shares /s/1234
- User updates to 9.0.1 via ownCloud updater
- Link to /s/1234 is broken, /index.php/s/1234 works