Retrofit Tree

Such kind of thing is indeed needed, but it should look the other way.

1) There should be an option to treat any ship individually, like it is for Hero ships. Doubleclicking a ship should open functional design screen like it does for Hero ship. Any changes in that screen should be readily appliable at clicking "OK" button, like it is for Hero ship. Doing so renames the ship into random name taken from predefined list of names appropriate for faction lore. That new ship name should be changeable.

2) There should be an option (button) to standartise selected ship(s) to an existing serie.  Clicking that button should open the list of existing designs for the same hull. Clicking any design should open confirmation dialogue saying "this will upgrade N selected ships to match 'PewPew7' design, it will cost 1000 dust. Confirm?". Doing so will modify selected ships, no matter serial or unique, change their name to serie name, and after that they'll be part of that serie.

Not drawing an arrow or whatever.

That way what you're doing will look as follows:

- Create design "Empty"

- Create design "Colony"

- Build ship "Empty"

- When ready, select it, press "standartise" and choose "colony"

However, that allows for more sophisticated usage, like

- Create design "Attacker"

- Create design "Kinetic"

- Build a bunch of ships of said desings.

- As the game progresses, you might want to assign one of those to be transport. Choose one and individually modify it with manpower module, that will be unique ship with unique name. 

- Then you'd want "Kinetic" serie to become laser ships, or to carry more engines, or whatever.

- As game progresses those ships will come to have names like "Attacker 6", "MissileWhore", "Kinetic 11", "FullShields", etc. But now it's carrier time, and, once pride of your empire, these misc ships are now cannon fodder.

- Create a new design "Cannon Fodder"

- Standartise all that bunch to "Cannon Fodder" serie and distribute it among carrier fleets.

I agree with Antistone above. This idea seems too complicated for little gain. In fact, it puts more strain on the player (design the tree) while restraining them (you can only upgrade along the tree). Free-form retrofits within the same ship class are light-weight to implement and natural to understand for the player.