There is no way to programmatically access the application-specific "File Sharing" directories on iPhone from OSX. You are forced to start iTunes and manually select the phone, select "Apps", select your app, drag&drop files.
With a unix-based OS talking to another unix-based OS.
This is ridiculous.
No, I will not jailbreak my phone. This is something that Apple should expose in an API, either via iTunes / Scripting Bridge or via direct Obj-C calls. iCloud simply doesn't cover all use-cases (and, reportedly, it's broken anyway).
This is the frustrating side of the Apple ecosystem: sometimes, you'll be prevented from doing something very simple and very obvious, for some obscure reason nobody cares about (except Apple, of course).