I design test equipment for PCBs. I use a common directory structure for all my projects. The directory will have a board info directory (Schematic, BOM, layout, spec sheets, etc.), fixture info (PCB schematic, layout, fixture wiring, spec sheets, etc), Operating instructions (Word doc, image files, pdf of the finished procedure for the user), Test Data (any test results for correlation, etc.), and Test Software (Embedded source code, release log, CPLD/FPGA code, etc.). There's also an Excel sheet that summarizes the fixture build (checklist, Notes, Tasks, Purchase Orders, and BOM tabs, both fixture and PCB).
Once the fixture is complete, and released, I simply zip the entire folder and store a copy on our company OneDrive and another copy on my local machine.