Enable -Wmissing-prototypes for atmel-samd

[jepler]

When a function is defined, but its declaration isn't present, the compiler can't check that the declaration and definition match. "-Wmissing-prototypes" enables a diagnostic in this case.

Fixes fall into several categories:

• Include headers where needed
• Add/fix declarations / definitions where needed
• Mark functions as static if appropriate
• Remove some never-used functions

This PR aims to fix all the diagnostics that occur in the atmel-samd builds, so that the -Wmissing-prototypes flag can be enabled in that whole port.

[jepler]

The build error on pyruler was a transient Actions problem, it built locally.

[dhalbert]

Looks fine to me; thanks for fixing all the little things.