fix(permissions): added a common way to update private flag via repo model...

fix(permissions): added a common way to update private flag via repo model - this allows to have a one and only one way to control the flag with the business logic shared - added test for that - changed view to use this method instead of DB update and custom permissions flush - fixed a case when update of repo settings didn't flush permissions actually while it should when private flag changed

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Pull Request Workflow

The following diagram represents a standard pull request workflow.

	Site-wide shortcuts
/	Use quick search box
g h	Goto home page
g g	Goto my private gists page
g G	Goto my public gists page
g 0-9	Goto bookmarked items from 0-9
n r	New repository page
n g	New gist page

	Repositories
g s	Goto summary page
g c	Goto changelog page
g f	Goto files page
g F	Goto files page with file search activated
g p	Goto pull requests page
g o	Goto repository settings
g O	Goto repository access permissions settings
t s	Toggle sidebar on some pages