I believe the GitHub issue is about catching intents by default. In case people were thinking support for using TS as a SMS app was going away, here's an excerpt from the mailing list that says it's not:
>> [whispersystems] Can we remove the SMS feature completely?
>> Since the secure SMS option is removed. To reduce the confusion, can we remove insecure SMS option too?
> <insert thread of disagreements>
> Re: [whispersystems] Can we remove the SMS feature completely?
> Everyone can rest assured, we have no plans to do this. I'm pretty committed to an integrated messenger.
> - moxie
(For some reason this Apr 1 message is not in the mailinglist archives. Not sure what's up with that.)