+               if (!strcmp(pair->one->path, pair->two->path)) {
+                       /*
+                        * Paths should only match if this was initially a
+                        * non-rename that is being turned into one by
+                        * directory rename detection.
+                        */
+                       assert(pair->status != 'R');
+               } else {
+                       assert(pair->status == 'R');

assert() is compiled conditionally depending on whether
NDEBUG is set, which makes potential error reports more interesting and
head-scratching. But we'd rather prefer easy bug reports, therefore
we'd want to (a) either have the condition checked always, when
you know this could occur, e.g. via

  if (<condition>)
    BUG("Git is broken, because...");

or (b) you could omit the asserts if they are more of a developer guideline?

I wonder if we want to introduce a BUG_ON(<condition>, <msg>) macro
that contains (a).

+                       re->dst_entry->processed = 1;
+                       //string_list_remove(entries, pair->two->path, 0);

commented code?