System Upgrade fails via Setup Wizard - /vendor/magento/magento2-base/app/design/frontend/Magento does not exist.

[jason-vivid]

System upgrade fails due to folder missing folder.

Tail end of the log below (full log here: http://pastebin.com/69hkmnpR)

- Removing symfony/event-dispatcher (v2.8.1)
- Installing symfony/event-dispatcher (v2.8.2)
Downloading: 
Connecting...
Downloading: 100%

 [ErrorException]
Source /magento2/vendor/magento/magento2-base/app/design/frontend/Magento does not exist

 update [--prefer-source] [--prefer-dist] [--dry-run] [--dev] [--no-dev] [--lock] [--no-plugins] [--no-custom-installers] [--no-autoloader] [--no-scripts] [--no-progress] [--with-dependencies] [-v|vv|vvv|--verbose] [-o|--optimize-autoloader] [--ignore-platform-reqs] [--prefer-stable] [--prefer-lowest] [packages1] ... [packagesN]

Adding the folder results in Setup Wizard replying: "Sorry, we can't take that action right now."

[mazhalai]

@jason-vivid how did you deploy initially? via zip from magento.com or via composer create-project?

[jason-vivid]

@mazhalai composer create-project