neatogen compute_apsp_dijkstra: use cgraph wrappers for allocation

neatogen compute_apsp_dijkstra: use cgraph wrappers for allocation

The lib/cgraph/alloc.h wrappers are similar to the older lib/common/memory.h
wrappers except (1) they are header-only and (2) they live in a directory
(cgraph) that is at the root of the dependency tree. The long term plan is to
replace all use of lib/common/memory.h with lib/cgraph/alloc.h.

We can also squash a -Wsign-conversion warning at the same time, noting that the
square of a signed number is always non-negative.