Cant read dir of /etc/my.cnf. (Errcode: 2)

the solution actually is simple.

!includedir /etc/my.cnf.d

is your last line on /etc/my.cnf, so mysql can't read complete '/etc/my.cnf.d' only '/etc/my.cnf.'

You just need add one more line so mysql can read its.

!includedir /etc/my.cnf.d
# add new line here