Currently all tools that are OutOfDate have to be manually updated.
A few tools are automatically updated today : that introduce manual clicks.

Here are a few thoughts:
0) as today
1) Tools could be automatically updated by default and we could list the manually update : that should only cover a very few tools
2) Contributor could decide which tools are automatic and which are manual (for exemple a check on the outofdate panel)

0+2) and 1+2) are possible

Moreover the choice manual/automatic is currently a project choice. Shouldn't it be a Tool choice (in its conf) ? Or could be a Tool choice and could be overridable in a project.
This would lead to less configurations files.