Folders DO get messy somehow

I'm running a startup incubator in Suriname and for a young "AI for geology & mining" startup I'm trying to get ICM in the mix:

Workflows

for the business aspects design
design, coding and maintenance of the software (front end/back-end)
The actual AI engine running the service, setup, training, optimization, uptime etc.
Monitoring users, errors, UX
Monitoring business progress/KPI's/CAP tables for Stock Splits

Anybody knows how best to structure all of this? Best practices?

Oh and I manage currently 4 active startups

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Folders DO get messy somehow