Thank you for providing the updated link to the remap file. I am unsure of what config file to edit though. Just for clarification I'm currently using Clonedeploy 1.3.5 with CloneDeployPE Builder 1.2.0. I have merged the tftpboot folder on the Ubuntu 16 server. I also changed ownership to www-data and set identical permissions as the other files just to be safe.
Were there any folders included in the CloneDeployPE Builder what also needed to be copied over? If so, where in the folder/file structure would they need to be on Ubuntu?
#Replace any incoming requests for a \ with / <----(I'm unsure where this is changed)
rg \\ / <----(Not sure what this means)
#Change all request starting with /Boot/ to /boot/ <----(understood)
#As of WinPE Builder 1.2.1 the next line should not be needed. Commented out. <----(This applicable to my version, I was unable to find 1.2.1 anywhere so I assume the project was renamed)
#r ^(/Boot/) \L\1 <----(this line get commented out, i'm not sure where the line is though)