RewriteHistory extremely slow

Reproduction steps

Find a repo with 3000+ commits
Run the below code against that repo to rewrite the repo history:

private static void RewriteHistory(string repoPath, ICollection<string> subFolders)
{
    using (var repo = new Repository(repoPath))
    {
        var refs = repo.Refs.Where(r => r.CanonicalName.EndsWith("develop")).OrderBy(r => r.CanonicalName).ToList();
        var commits = repo.Commits.QueryBy(new CommitFilter { IncludeReachableFrom = refs }).ToArray();
        var count = 0;
        var stopwatch = Stopwatch.StartNew();

        Logger.InfoFormat("Found {0} commits", commits.Length);
        Logger.InfoFormat("Rewrite history started");

        repo.Refs.RewriteHistory(new RewriteHistoryOptions
        {
            OnError = OnError,
            OnSucceeding = OnSucceeding,
            PruneEmptyCommits = true,
            CommitTreeRewriter = commit =>
            {
                Logger.InfoFormat("Commit {0}/{1}", ++count, commits.Length);

                var tree = TreeDefinition.From(commit);
                foreach (var treeEntry in commit.Tree)
                {
                    var match = subFolders.FirstOrDefault(s => treeEntry.Path.StartsWithIgnoreCase(s));

                    if (match == null)
                        tree.Remove(treeEntry.Path);
                }

                return tree;
            }
        }, commits);
        Logger.InfoFormat("Rewrite history ended. Took {0}", stopwatch.Elapsed);

        repo.Reset(ResetMode.Hard, repo.Head.Commits.First());
    }
}

Expected behavior

This should take a reasonable time. I expect it to take a few minutes for sure but not hours. For example when running something similar in git from the command like it takes minutes. I'm sorry I don't have specific times but I can try to provide more data to compare performance if necessary.

Actual behavior

This takes 1h 43 minutes of which 1h 40 to just start the rewrite and about a couple of minutes to go through all the commits.
INFO : Found 3486 commits
INFO : Rewrite history started
[between these two log messages there is a 1h 40m gap]
INFO : Commit 1/3486
INFO : Commit 2/3486
...
INFO : Rewrite history ended. Took 01:43:51.5536779

Version of LibGit2Sharp (release number or SHA1)

0.26.0 + 2.0.267 (native)

Operating system(s) tested; .NET runtime tested

.net 4.6.1 - Win 2012R2

Inizia riproducendo il problema riportato con un repository contenente più di 3.000 commit e misura il ritardo tra “Rewrite history started” e il primo callback di CommitTreeRewriter. Ispeziona la chiamata a RewriteHistory e la configurazione di CommitTreeRewriter mostrati nell’issue. Il lavoro è completato quando la stessa riscrittura della cronologia termina in pochi minuti anziché in ore, mantenendo il comportamento di pruning riportato.