As you may have suspected, the build system has been replaced with a new one. There is no documentation. It replaces the large number of .mak files with .lua files that are located in the scripts directory. The obj folder is replaced by the build folder. You don't need to update your tools yet, the old ones work just fine.
The main thing is to set up a system variable so it knows where mingw is.
For a 64-bit build, SET MINGW64=e:\mingw\mingw64-w64 or for a 32-bit build, SET MINGW32=e:\mingw\mingw64-w32 (sample paths, obviously) The build system works out your hardware platform, but you can override that to allow cross-compiling. So, for me to build 32-bit on my 64-bit machine, I need to add windows_x86 to the make command-line.
I have a 64-bit batch file, and a 32-bit one. The 64-bit one sets up MINGW64, while the 32-bit one sets up MINGW32 and also specifies windows_x86.
Since I normally work with 32-bit builds, I also have make.bat which simply calls up make32.bat -j4
I have never used make clean. If I want to do a clean build, I run clean.bat which simply deletes the obj and build folders, and then run make.bat
So far, I've converted to the new system for MAME (which builds fine btw), however it has no provision for MESSUI/MAMEUI/HBMAME, so for those I stayed with the old system, until I've reverse engineered the new system enough to understand it.