The current configuration in the foundry allows authors to track quest progression threw the story board, parts of conversation, skill, and items. At this time, only 2 of the methods are tractable from map to map (Story / Item)
A flagging system would give the author more flexibility within their story in support for alternate quests that they don’t want tracked, and support in phases within the story.
A simple one could have 6 slots that are true/false (on/off) that could change state based on the player’s actions (friendly vs. hostile dialog to a NPC for example), instead of dropping an item the flag state changes. This could be used as a trigger used normally like a mark on the map or part of dialog being reached.
A slightly more advanced flag system would have a value from 0-9 for example, making it easier to track things like Karma/NPC reaction. This would take a lot more programming on the authors end, but also provide a more dynamic gaming experience.
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