I think you are suffering from analysis paralysis… or have too much free time. 
Filter everything you do through practical concerns first and foremost:
- Erlang/Elixir are not that great for CLI apps: slow startup time, potentially superfluous OTP baggage.
- Your tool is a simple relay. It has no functional core as it has been pointed out.
- Hexagonal is kinda sorta implemented already by Phoenix: it isolates the web stuff through Endpoint / Router and macros injecting code in various places so your code can be mostly purely functional (minus DB and session state). Additionally, you are expected to achieve Hexagonal architecture through contexts: your business code should be completely unaware of how the data is stored: it receives primitive parameters and/or structs, does something with them, and returns other primitive values and/or structs. It shouldn’t contain any calls to Ecto functions, for example. (Although I do make an exception for
Changesetwhose functionality has come very handy many times.)
Hexagonal is quite simple to summarise for everyday work even if that omits some important details: use purely functional code absolutely everywhere you can (no side effects: meaning no DB, no file changes, etc.) and then only use imperative code (i.e. the one that mutates state) where you absolutely can’t avoid it – like when you have to store stuff in the DB or change the user’s session.
As a general advice: when you have a practical goal you should get more done and think less until you arrive at the point where you feel a refactoring should be done because you find yourself fighting with your code when you need to add new features or fix a bug.
The process you are trying to follow now is setting you up to become an academic: you are overthinking, having an analysis paralysis and almost nothing will get done as a result.
