Autonote manager not marking already generated extras

When you generate a world, enable the autonote manager, you will get lots of notes (as expected). But when your player dies (assuming the world end handling is set to `Keep`) or you create a new one all the already discovered map tiles containing generated map extras will not be marked.

# Steps To Reproduce

1. Create a new world, make sure to set the world end handling to e.g `Keep`
2. Explore it and find map extras
3. Die or just create a new character
4. All the already existing map extras will not be marked by the autonote manager

# Expected behavior

There should be a flag or something else that marks a map tile with a generated extra in it so the autonote manager can discover it again. Especially craters can be very hard to spot since small ones are difficult to distinguish from normal patches of dirt/dead grass on fields.
It is also a bit frustrating to have to mark everything manually again if another player already discovered it.

# Screenshots

N/A

# Versions and configuration

- OS: Arch Linux
- Game Version: 0.E (`0.E.3-1`)
- Graphics version: Tiles, but also applicable to the terminal
- Ingame language: English
- Mods loaded: N/A

# Additional context

I searched for already existing issues with `label:"Map / Mapgen" autonote`. I discussed this in `#cataclysmdda` on freenode a bit.

Start by reproducing the issue with the autonote manager, persistent map extras, and world-end handling set to Keep. Trace how generated map extras are represented on map tiles and how the autonote manager discovers them for a new character. Done means previously generated extras are rediscovered and marked after death or character creation, with the existing reproduction steps passing.

Written by the indexing model from the issue text.