Bison: enable all the warnings and fix them

Bison: enable all the warnings and fix them

First, fix 5547d361208d90e12d53bb62bb2ffbbff9b93ca0: the definition of
YFLAGS was not passed into the Makefile: AC_SUBST does not suffice, we
need PHP_SUBST_OLD.  While at it, allow to pass variable and value at
the same time.

Then pass -Wall to bison, rather than only -Wempty-rules.

Use %precedence where associativity is useless.

Remove useless %precedence.
GH-5138