I have most of my kicad project organized in a similar structure where I have a folder where all schematic sheets are, with the exception of the top level:

├── images
├── mech
├── pdf
├── sch
│   ├── sub-sheet1.sch
│   ├── sub-sheet2.sch
├── project-cache.lib
├── project.kicad_pcb
├──project.pro
├──project.sch

whent I run plotgitsch -i firefox only differences in project.sch are shown.
in need to cd sch/ and run plotgitsch -i firefox -l ../project-cache.lib

it is a minor annoyance, but I think it could be fix by finding all files ending in .sch including a search in folders.

I tried looking in to the code but I'm not familiar which language is this tool written on.
I guess it would be in line 48 of plotkicadsch/src/kicadDiff.ml

let find_schematics () = F.list_files (ends_with ".sch")

Many thanks for this tool,
Luis