Command examples written for manipulating files on an old drive with remaining crap from windows.
chown, rm: Delete old windows / program files from second drive
chown -r root:root <Directory>
takeown /F "F:\ProgramData" /A /R /D Y icacls "F:\ProgramData" /T /grant administrators:F
rm -rf <Directory>
(after chown above)
rd /s /q "F:\ProgramData"
ln
https://www.howtogeek.com/howto/16226/complete-guide-to-symbolic-links-symlinks-on-windows-or-linux/
cp -rp
xcopy <source>\*.* /s/e/f <dest>