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
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