Fixes for permission issues.

This change fixes issues around permissions with the earlier MR in this fork.

• navigation_extra_tools_post_update_update_permissions was attempting to add the non existent permission, access navigation extra tools. Changed to add access navigation extra tools cache flushing and access navigation extra tools cron.
• The Tools menu had a permission of access navigation extra tools cache flushing+access navigation extra tools cron, which would make it available if user has either of those permissions. However, there may be other tools in the menu that the user may have access to, such as running database updates, or accessing development tools with devel module. Other tools may be added in future. I'm not sure what the best solution is, but for now I'm giving it access navigation permission, which will make it available to any user with access to the Navigation, even if that means they may see an empty Tools menu. Hopefully a better solution will be reached in a follow up issue.
• Moved testDevelopmentMenu test function into a separate class, allowing the setup to specify a different set of modules and permissions from other tests.
• Removed administer site configuration permission from test user in main test cases, as it shouldn't be needed due to new permissions (this permission is needed for the Devel routes, which is the main reason for moving the Devel test to its own file).
• Very minor change to remove navigation from required modules in test setup, since it is a dependency of navigation_extra_tools so there is no need to explicitly list it.

Closes #3488541

merged