Again, grateful thanks to Google for funding my summer work.
"Phase 1," by which I mean rewriting the common parts of sage.graphs.graph_isom and sage.coding.binary_code, is now finished. All of the variable names are logically labeled, so that in fact many of the comments in the original sage.graphs.graph_isom code have been simply removed. Now, reading the code itself is much like reading the comments in the original.
I have also tested the code written so far with valgrind, and fixed the errors that were found. For each of the problem specific functions, I have implemented a trivial version, which essentially does nothing. The first, which refines partitions, returns the partition given. The second, which allows for determining that all the nodes below the current position, always returns false. The third, which compares structures under a permutation, always returns true, i.e. that the permutation is an isomorphism of the structure in question. Basically, this means that given a partition with blocks of size n(1), ..., n(k), the algorithm just computes Sn(1) x ... x Sn(k).
In theory, this should be ready for arbitrary refinement functions and structures, so Phase 2 of my project will be to implement as many specific such things as possible. I'd like to try graphs, block designs (including binary codes), computing the automorphism group of a matrix (permuting columns such that the set of rows is preserved), reflexive polytopes (perhaps using some of the functionality of PALP, perhaps not...), Adinkras, and certain kinds of combinatorial species.
On a side note, I've said a few times to people that it's nice to be getting funding for "what I'd be doing anyway," but I have to admit that it has been making me much more productive in my work than I might have been otherwise. Thanks again, Google!