CAIT and Temporary Import (as per December 2015).
Word has been out, that you will no longer need a CAIT and maybe no Temporary Import for your yacht.

Here is our experience:

We did apply for a CAIT via an agent well before entering Indonesia via Jayapura.
The CAIT was requested there, both by the harbour master as well as customs. I did try to play dumb first, to check out, whether we could go without. We would not, they were very persistent.

Customs did NOT issue the papers for a temporary import. Instead, they filled some more or less detailed papers on the boat (customs arrival notice was the English text on it) and requested us to go forward to Biak with it to finalise customs clearance.

As we could not anchor at Biak at the time with a strong wind blowing high seas into a very deep and unprotected anchorage, we decided to take a chance a not check in there.

Checking out was done in Kumai / Kalimantan. A bit with shaky knees, as we did not know whether we were OK without the Temporary Import Papers. There was not a problem at all. All the harbour master wanted to see was the CAIT as well as the ships papers and the stamped passports.

To sum it up (when entering to Jayapura and exiting through Kumai): A CAIT was still very much in need (also when we tried to extend our social visa in Bali), the Temporary Import seemed not to be relevant.

Hope that helps,
cheers from Phuket, Fritze (S.Y. Alytes)