Resolving component works with precedence rule. The first precedence to Server mapping then doc root then files in project. As your webroot and project location overlaps. according to precedence the resolving the component is happening with respect to docroot in ur case. Hence your getting " unresolved and wants to create a cfc in "mysite.newbranch.cfcfolder.somefile" ".
To avoid this either you add mapping to cfcfolder to /root/cfcfolder and access CFCs inside cfcfolder. U need to refresh server after adding mapping at server. Or you can de-associate server so resolution happens wrt to project root.
Thanks for taking the time to read and respond to my issue. Can you clarify what you mean by "disassociating the server"? I prefer a cleaner option (no more mappings and particularly for each folder I have a .cfc file) and the disassociating server option sounds promising.
Also, can you point me to official docs that explain the precedence rule you describe.
If you edit the properties for your project (right click the project and choose "properties". You will see an option for "ColdFusion Server Settings". Here is where you choose which server you want to associate with this project.
For the component to be properly resolved, you will want to choose a server instance, make sure the server is running, and has cataloged all the CFCs. You said you created a virtual host within CF Builder. I have had an issue w/ virtual hosts inside CFB and resolving components, perhaps you should just create a separate "Server" instance for your virtual host and assign that to the project. That seemed to remove the issue for me in the past.