A pathname consisting of a single slash shall resolve to the root
directory of the process. A null pathname shall not be successfully
resolved. A pathname that begins with two successive slashes may be
interpreted in an implementation-defined manner, although more than
two leading slashes shall be treated as a single slash.
On GNU Systems (and most unixoid systems I know), two leading slashes
are not interpreted in any special way, but like three and more
slashes: they are treated as one.
So the problem is, that the double slash is written unquoted to
Makefile.c where it gets interpreted as a comment.
This is IMO a bug.
When generating Makefile.c consecutive slashes hould either be reduced
to one or appropriately quoted.