It's a real shame that so much of the "payload operations" had to be directly integrated into the shuttle code for launch. Given that so many missions were DoD missions the code apparently became contaminated to the point that it is almost certain it will never be released.

Which is a pity because near the end of the program it was quite an advanced software management and deployment stack:

https://ntrs.nasa.gov/api/citations/20090001334/downloads/20...

An interesting example is at the beginning of the program they had no ability to update the orbiter once it was in launch configuration. Which made every launch particularly sensitive to the weather, not just on the ground, but well above the ground where jet stream and other wind patterns have significant effect on the ascent profile.

As the program advanced they eventually gained this ability and could integrate gathered weather data into new variable values which could be pushed into the orbiter on the day of launch. This significantly increased the margin of weather conditions they could launch in.

https://ntrs.nasa.gov/api/citations/20110003654/downloads/20...

Interestingly this capability has been maintained and is even used on the Artemis launches.