Regression tests fail the second time through because Git for Windows removes the files pointed to by links when "git clean -fdx" is run. See git-for-windows/git#607.
To reproduce:
git clone --recursive https://github.com/boostorg/boost.git
cd boost
bootstrap.bat
b2 headers
At this point there is a subdirectory boost with links to library headers.
git clean -fdx
The links are deleted along with the header files they point to.
git submodule foreach git reset --hard
Puts the files back.