Ah, I think I know what is causing this issue then. It says that auto-close is not enabled until the import is complete. For some reason my repo has been stuck at 99.98% finished for several days.

I am not using differential right now (but will be in the future. Just testing things one at a time right now). I was hoping the links could be added just from a revision committed in Diffusion. Are they only added if you use Differential?

Unfortunately no. Is there something I need to enable to add this functionality?

I have tried a few different methods, and tried to model if after example commits found in this Phabricator instance that look like they worked. Is this what you meant by putting it in the summary section?

I am getting links from Diffusion to the task (in the commit message, the T123 will be a link), but the link is never showing up in Maniphest. Any suggestions for troubleshooting? I am using "Closes T123" as the second line in the commit message. I have also tried with "Maniphest Tasks" and "Fixes"