The Happy Path
The happy path is the most common process. What is followed when there is no issue or special case. Treat this one first and try to merge branches into it if possible.
Don't worry, be happy ...
The happy path is what you consider the ideal, most common scenario. When everything fit in the most common case.
It is the straightest line between where you start and where you finish.
That's what you should aim to get it working first.
Once you have the happy path going for you. Then you can try to handle issues or special cases on an individual basis. That can mean updating your tools to handle those special cases.
Or, even better ...
Reconsider why those special cases exist for a good reason. If not, can they be avoided and the context in which they happen merged back into the happy path.
The less complexity there is, the easier it will be in the long run. You won't rely on the knowledge of people who may or may not be there as to "why is it like this?".
Don't build your tools blindly following your current procedure. Use the process to reevaluate exceptions, issues and special cases and merge if possible.