This is a problem which I recently faced in a slightly different situation (optimal ordering of interdependent compiler instructions).
While I can't improve on O(n*n) theoretical bounds, after a fair amount of experimentation and assuming heuristics for my case (for example, assuming that the initial ordering wasn't created maliciously) the following was the best compromise algorithm in terms of performance.
(In my case I had an acceptable "right side failure": after the initial nodes and arcs were added (which was guaranteed to be possible), it was acceptable for the optimiser to occasionally reject the addition of further arcs where one could actually be added. This approximation isn't necessary for this algorithm when carried to completion, but it does admit such an approximation if you wish to do so, and so limiting its runtime further).
While a graph is topologically sorted, it is guaranteed to be cycle-free. In the first phase when I had a static bulk of nodes and arcs to add, I added the nodes and then topologically sorted them.
During the second phase, adding additional arcs, there are two situations when considering an arc from A to B. If A already lies to the left of B in the sort, an arc can simply be added and no cycle can be generated, as the list is still topologically sorted.
If B is to the left of A, we consider the sub-sequence between B and A and partition it into two disjoint sequences X, Y, where X is those nodes which can reach A (and Y the others). If A is not reachable from B, ie there are no direct arcs from B into X or to A, then the sequence can be reordered XABY before adding the A to B arc, showing it is still cycle-free and maintaining the topological sort. The efficiency over the naive algorithm here is that we only need consider the subsequence between B and A as our list is topologically sorted: A is not reachable from any node to the right of A. For my situation, where localised reorderings are the most frequent and important, this an important gain.
As we don't reorder within the sequences X,A,B,Y, clearly any arcs which start or end within the same sequence are still ordered correctly, and the same in each flank, and any "fly-over" arcs from the left to the right flanks. Any arcs between the flanks and X,A,B,Y are also still ordered correctly as our reordering is restricted to this local region. So we only need to consider arcs between our four sequences. Consider each possible "problematic" arc for our final ordering XABY in turn: YB YA YX BA BX AX. Our initial order was B[XY]A, so AX and YB cannot occur. X reaches A, but Y does not, therefore YX and YA do not occur or A could be reached from the source of the arc in Y (potentially via X) a contradiction. Our criterion for acceptability was that there are no links BX or BA. So there are no problematic arcs, and we are still topologically sorted.
Our only acceptability criterion (that A is not reachable from B) is clearly sufficient to create a cycle on adding the arc A->B: B -(X)-> A -> B, so the converse is also shown.
This can be implemented reasonably efficiently if we can add a flag to each node. Consider the nodes [BXY] going right-to-left from the node immediately to the left of A. If that node has a direct arc to A then set the flag. At an arbitrary such node, we need only consider direct outgoing arcs: the nodes to its right are either after A (and so irrelevant), or else have already been flagged if reachable from A, so the flag on such an arbitrary node is set when any flagged nodes are encountered by direct link. If B is not flagged at the end of the process, the reordering is acceptable and the flagged nodes comprise X.
Though this always yields a correct ordering if carried to completion (as far as I can tell), as I mentioned in the introduction it is particularly efficient if your initial build is approximately correct (in the sense of accommodating of likely additional arcs without reordering).
There also exists an effective approximation, if your context is such that "outrageous" arcs can be rejected (those which would massively reorder) by limiting the A to B distance you are prepared to scan. If you have an initial list of the additional arcs you wish to add, they can be ordered by increasing distance in the initial ordering until you run out of some scanning "credit", and call your optimisation a day at that point.
A
->B
, flood fill fromB
and check thatA
is not reachable) is going to be the most efficient. – Hoosegow