Cleaned up functions and added wp_kses escaping for all content
Fixed closing comment of plugin header
Add action for plugin initialization so all functions do not need to be added to init function
Added code example and @since PHPDocs to all functions
Added warning dismiss functionality
Added check if user has dismissed a warning
Added convince function to check if a plugin is installed single/multi-site install
Moved alert dismissed checks to top of file
Added Alert wrapper convince function

This will help to keep the alerts consistent and reduce clutter in the check functions.  As well as help if a change to the alerts needs to be made in the future.
Added check for brute protect installed