Here's four ways to fix this (hence not doing a PR - you may have a preference & it's super trivial):

1. Just delete this line as I think it does more harm than good (why not let us change our tools?)

if (this._registeredTools[name]) {
throw new Error(Tool ${name} is already registered);
}

2. Same as above but with an option to decide whether this should be allowed

3. Add a removeTool() method

4. Remove the private flag on the class, so we can remove older definitions ourselves

@samdoeswork did you find a workaround for this in the mean time? I've just run into this and it's a pretty big feature gap to not be able to remove or update tools!

Looks like this is resolved in this merged PR.
#247

Eagerly awaiting it's release!