I have a bunch of small PowerShell functions, each in their own file and I am trying to combine them into a larger file.
Using the low-tech approach of the Windows copy command by doing: copy /Y /A functions\*.ps1 super.ps1 works fine however where two files are joined it is inserting: 
I’m guessing it’s the line break characters showing up (difference of encoding), but how do I prevent these characters from showing up?
Those characters are unicode byte order marks which will be invisibly preceding the .ps1 content.
I’m not sure how you’d strip them off in plain DOS — at this point I’d turn to a scripting language to do the work. You could write a PowerShell script to join them using the .net System.IO features.