I decided not to replace tools with tools+ by default for transparency purposes (to make it clear for first timers to the plugin that this is a separate feature). Before the next release, maybe the devs collectively decide to do something different.
I am glad you kept the Tools menu. As Tools+ does not seem to yet cover the same functionality as Tools (in particular the various ways of launching standard shells, and I have not seen separators). That would have made impossible my current use of the Tools. I also like the simple appearance of the inbuilt Tools.
For now I have disabled Tools+ and kept Tools, but thanks for offering this new plugin. It could become quite useful when more mature.