Our work is divided into 2 parts:
1. Core product - managed by 2 teams which work with scrum methodology of 2 weeks iterations
2. Team that is dedicated to customers' implementation (independent from the core product and is not working agile. It has a separated project management life-cycle)
After reading different articles with different best practices I understand that the first part is pretty easy and the idea is to create 2 projects - one for each team (each team responsible for a different area in the product)
The second part is where I'm more confused - it looks like the right way would be to create a project for each customer (also, each customer has different branches which makes it more complex, as each brand has it's on project management life-cycle).
But moving forward as we grow the list of projects will get bigger and bigger - what are the pros and cons for a huge list of customers projects? is this the recommended approach? and what is the best way to manage a customer that has multiple branches and each branch should have it's own project life-cycle? (would component be a good solution?)
It appears you are facing Conway's Law, https://en.wikipedia.org/wiki/Conway%27s_law, which your system is mirroring your organisation.
My team admins a JIRA server with too many projects than needed. JIRA is still working fine and everyone adapts to the growing pains.
We periodically review if the current setup is fit-for-purpose. Changes to current setup often involve organisational and mindset (management approach) changes to be successful.
In the end, it probably depends on how your organisation works best.
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