As described in Answers here ...
https://answers.atlassian.com/questions/53869/is-there-any-way-to-manually-clear-a-workspace-in-bamboo

... there is a desire to sometimes run a clean build. I need that today, but it's a rare occurence. The suggestion is either:
1) Change the Checkout Source task to "Force Clean Build" ... but then I have to go into the same configuration later and uncheck it. I'm trying to do this just once.
2) Create a plan variable for cleaning the source tree. The suggestion works pretty good, but requires both:

the user to be using git (as opposed to SubVersion)
the user to do all that work in Ant or in a script to look for the variable and run that conditionally.

The "Run custom..." already asks the user a question about the checkout. It asks for a revision number (see attachment). To me, doing a clean build is a Custom Build thing to do, and it's something related to the checkout, right next to the existing question. This customizable build option should come out-of-the-box as a feature with Bamboo.

This way, I can reset my build to take into account dependency-changes that aren't fully declared, forcing everything to be remade. This will allow my developers' builds to go green faster, without any custom work – no build-engineer or admin involved.