Bamboo deleted files show's up when deploying

We using GIT in Intellij for committing to Bitbucket and using Bamboo for deploying the .war file on the Tomcat server.  Example: Here is the commit of the change when i delete a folder:

Bamboo shows that on the commit the files have been removed:

But when Bamboo deploys the newest commit it does that with the old deleted with it:

also all other change´s wil be deployed as expected, but only when we want te remove something the building/deploying goes wrong.

Does anyone knows how to change the build in Bamboo so it's exclude the deleted files?

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Configure your build to clean checkout folder, there is "Force Clean Build" checkbox at Source Code checkout task

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