The Jackdaw, your ship in Assassin's Creed Black Flag Resynced, is both your means of transportation and a valuable tool that needs to be maintained and upgraded. Although you'll initially be able to purchase a few upgrades using money and materials, you'll soon be told that you need to upgrade the harbormaster's office. Don't worry—it's much easier than it might sound.
To upgrade the harbormaster's office, you'll first need to progress far enough through the story. More specifically, you must continue until you gain access to your base on Great Inagua, in Gibara. This will serve as your hideout, where you can build your own pirate settlement. Once there, head to the docks and find the harbormaster.
As with the other business owners in the area, you'll first need to pay to have the building constructed. After that, you can speak to him again to purchase additional harbormaster upgrades. All you need is enough money, and you'll then be able to install the most important upgrades for your ship.
