Convert the indoor map to OpenStreetMap, import the map to OSRM (http://project-osrm.org) to make travel time calculations (for the time to walk between shops/isles), export travel-time matrix from OSRM and import this matrix to VROOM (https://github.com/VROOM-Project/vroom) for fleet optimization calculations (Me, wife and kids).
Use a list. Organize the list by row and items on row based on if you're moving to the back of the store vs to the front. Travel the path, making sure not to go down isles you don't need to, run over anyone who puts their cart in the middle of the isle.
Fast enough.
But on a more serious note: I work a lot with this kind of software but the biggest problem is reliable map data.
It doesn't matter how fast your matrix is generated and how good your fleet/order optimization is, when a truck is routed in the wrong direction of a one way street because the map data was not correct, you might as well draw a route on a map yourself.
Have you considered ordering online and let them deliver it at your doorstep?
https://twitter.com/AndrewProjDent/status/131171456565527347...
My retail exposure is limited, and includes neither grocery nor clothing experience.