[sam] GPIO setOutput overrides peripheral control

Calling setOutput now overrides peripheral control of the pin. This
behavior is consistent with the STM32 GPIO implementation, this commit also
ensures output value is set before the output drive is enabled to prevent
glitch.

Co-authored-by: Christopher Durand <[email protected]>

src/modm/platform/gpio/sam/pin.hpp.in

@@ -183,20 +183,26 @@ public:
 	inline static void
 	setOutput()
 	{
+		// Enable PIO control of the pin (disables peripheral control)
+		setPortReg(PIO_PER_OFFSET);
+		// Enable output driver
 		setPortReg(PIO_OER_OFFSET);
 	}
 
 	inline static void
 	setOutput(bool status)
 	{
-		setOutput();
 		set(status);
+		setOutput();
 	}
 
 	static void
 	setInput()
 	{
-		setPortReg(PIO_ODR_OFFSET); // Disable output driver
+		// Enable PIO control of the pin (disables peripheral control)
+		setPortReg(PIO_PER_OFFSET);
+		// Disable output driver
+		setPortReg(PIO_ODR_OFFSET);
 	}
 
 	static void
@@ -336,19 +342,22 @@ public:
 	setOutput()
 	{
 		setPortReg(PORT_DIRSET_OFFSET);
+		// Disable peripheral multiplexer
+		PinCfg::set(0);
 	}
 
 	inline static void
 	setOutput(bool status)
 	{
-		setOutput();
 		set(status);
+		setOutput();
 	}
 
 	static void
 	setInput()
 	{
 		setPortReg(PORT_DIRCLR_OFFSET);
+		PinCfg::set(PORT_PINCFG_INEN);
 	}
 
 	static void