Sort by folder?

Yeah, that’s how deduping works: if you check out your library database (sitting in .photostructure/models/db.sqlite3), check out the Asset and AssetFile tables.

This shouldn’t be necessary. Version 1.0.0 added folder tags that should be added automatically: if you’re using v0.9.1 you’ll need to try a beta build.

Rather than relying on magick prefix characters, PhotoStructure uses tag hierarchies: you can add them adhoc via exiftool (for now, and via PhotoStructure once this feature is implemented). Image tags are placed under Keywords/, and filesystem tags are placed under fs/.