Hypernym for "customer," "supplier", "manufacturer"

As a professional economist, the term I would use to describe all those parties is (economic) agent. A broader, more generic term, is "trader."

I might use the term associate or business associate. This could apply to anyone that you do business with.

Outside of the context that you provided, if I were to organize my contacts, I might have a group called business associates. For another example, in my business, successes are often recognized by inviting the business associates to a celebration.

Of course, in managing software development, I imagine you would want to be able to communicate its functionality in terms that closely resemble a natural language. Knowing proper natural language terminology is essential to simplifying that process. You might elide from natural language in your actual software, but in modern software development the distinction between simplified computer naming and natural language can be minimized. This has the clear advantage that your terms become easy to understand by people as well as by machines.

I'd call them "trading partners" or "trading parties". If you are building a software, and these parties are the users of your application, the you could call them just "users".