I'm not sure what will happen yet, but I don't want to jump in and say that Discotek will suddenly license the series. I know that's what a lot of us are hoping for...
With the Netflix announcement, and the fact that they have 6 episodes not on Crunchy, that raises a lot of questions. I think seeing the first 123/130 episodes on Netflix would be a likely scenario, and something even this small would be a big deal for the series.
So I think nothing out of ordinary will change for now. I'm not too quick to jump on these sort of things, but maybe Netflix/Crunchy will dive a bit further into the backlog. It's going to be a big year for the manga, and the anime in 2016.
2016 will get a lot of plot info in the anime, and the movie is teasing a Rum reveal. This means the manga should definitely have some big reveals, and it's definitely been getting there at a crawling pace in the manga.
We just need a direct answer, most of us have already figured out what's going on with Shukichi, and The Mystery Girl. I think we may finally get some answers with Sera, and see that confrontation between Sera and Ai that Gosho has been teasing about. We also learned some pretty big info with 938-941 and 942 where this could potentially be heading.
I can't say I'm looking forward to this entirely because I don't like what it could mean for Haibara's character, but to save any spoilers, I won't talk about that here.
We should see all of this before the end of next year. Future manga developments will have to wait another year for people following the anime/series on Crunchyroll. I think with the Department store case being around Christmas time, they'll end the year with File 938-941 in the manga. That said they might show the UFO case and maybe the new Shukichi case in the anime as well, so it's just my prediction.
That leaves us Kamaitachi, Kawanakajima, Blog, Shin/Ran, Higo/Yoko, Zombie, Girl Band, Department Store, which should add up to 17 manga-based episodes at minimum in 2016, which is two less than this year. That being said, we still have to consider that AOs are extending until at least February 6th, if not longer. I don't think we'll get nearly as bad of a streak as we did last year though. 2015 was a terrible year in terms of filler content.