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Plugin Update Message Customizer changes the default “There is a new version of PLUGIN available.” message on WordPress’ Plugin listing page.
This is useful for multiple scenarios: 
* If using WordPress within a dev/staging/live production environment, this plugin is great to install on the live and staging servers so that end users won’t update a plugin and therefore break the tracked remote branch. 
* On sites where you only want specific users to update the plugins, this will prevent users from clicking “update now.” 
* If you want to add additional options (e.g., “View version X.Y.Z details, update now, or mark as in testing.”) to the plugin new version message, e.g., “mark as in testing” to let others know the plugin is currently being tested and they should not yet update it on production.
Of course, other plugins and functions would prevent all plugin notifications. However, for the average user who logs into their live/production site instead of local/dev, this would still allow them to see that updates EXIST, however will just prevent them from performing them in an environment they should not be updated in.
Upcoming features: 
* Backwards compatibility (to be tested starting with WordPress 4.5) 
* Ability to hide the number of plugins with updates next to “Plugins” in admin sidebar) 
* Ability to hide all update notifications 
* Ability to prevent all automatic updates 
* Action on plugins with update message to apply the label “In testing,” which lets other users know that the plugin’s update is currently being tested in dev 
* Functionality to hide the plugin in the Plugins listing page

Notification Customizer

Plugin Update Message Customizer changes the default "There is a new version of PLUGIN available." message on Wordpress' Plugin listing …

Poetic Coding

Automatr updates your WordPress automatically, never again do you have to worry about applying updates to WordPress. It supports updating plugins, themes and WordPress itself.
Your modifications are fine with this plugin, as you can exclude them from the updating proccess easily.

Automatr

Automatr updates your WordPress automatically, never again will you have to update your WordPress install yourself.

Notification Customizer vs Automatr