Hi Rob,
Yes, you can write a shell script in PixInsight. You have an example in the startup.scp script (you'll find it on the bin installation folder), which PixInsight executes automatically upon startup. Basically, you can write everything you can execute from the command line as a script and run it as a batch process. You can even embed JavaScript fragments in a PI shell script.
However, there are some limitations in PI shell scripts. The main one is that, unfortunately, not all processes have a command-line interface available. This happens because we or the authors of those processes still haven't had the time to implement the required command-line support routines. In other cases, a command-line interface doesn't make sense, such as highly interactive tools.
These limitations will be overcome in the future, but right now you have to check if the processes that you want to run can be executed from the command line (other than to launch their interfaces, which is available for all processes).
Having said that, I personally recommend you write all your batch procedures as JavaScript scripts in PixInsight. The PJSR is much more powerful and flexible, and doesn't have any of the limitations that I have described.
Regarding .NET languages, they are incompatible (both technically and philosophically
) with PixInsight.
Let me know if you need more information on PI shell scripts.