Reported by Dirk Lison:

Clearing in and out here is easy, the port-captain (1st stop, at the base of the big pier) will help putting copies of all paperwork together for port, immigration, customs, quarantine. Then he will walk with the boat crew to see all these officials.

Costs in March 2019, receipts given for each, based on reports of two boats (one checking in, one checking out):

Customs $20
Immigration $25 for 2 people
international Zarpe (when checking out to Costa Rica) $4.25
Port fee $6.50
Panama cruising permit (when checking into Panama) $185
Quarantine ~$60, if the official is available, otherwise waived.

The old pier has deteriorated further, there is no ladder to climb up anymore. The port captain recommends landing the dinghy on the north side of the pier, which can be difficult due to swelling.