Back in 2003 Mitsubishi Electric Research Laboratories (MERL) came up with a way to use an LED for bidirectional communication.
While not fast, it is effectively free because most systems already have an LED for something. Good for configuration or debugging port where speed is not a high requirement.

http://www.merl.com/publications/TR2003-35

Many micros have a comparator input that simplifies their method a bit.

In regard to reverse polarity protection with a FET:

When you don't have to worry about a common reference potential, a N-channel FET on the bottom rail is even better than a P-channel on the top rail.

For any given current, they're cheaper, smaller and more efficient.

Not quite a tool, but I found an article suggesting an interesting alternative to using the full MPU on Cortex-M3/4 to detect data overwrites, using data watchpoints to catch the write and trigger an interrupt.

This is a neat trick to find the cause of memory corruption errors on deployed devices I think, especially if you can't recreate the issue in the lab, but can push new firmware remotely to add this. Previously I just thought of breakpoints/watchpoints as something only useful with a debug probe attached: https://lb9mg.no/2018/08/25/cortex-m-debugging-runtime-memory-corruption/

A further article suggests changing the memory map, so that the key registers can be saved in RAM and survive the reboot, and hence some form of telemetry could report them back: https://lb9mg.no/2018/08/18/preserving-debugging-breadcrumbs-across-reboots-in-cortex-m/

I loved your primer on encoders, but you missed my favorite encoder, in th is case linear, not rotary.

A bunch of stacked ball bearings in a tube, inducing and then sensing via two separate coils.  It just doesn't get much easier than this. I have been told that this approach can give amazing accuracy results too, in the angstrom range. Here is a commercial version:  http://www.newall.com/technology/

Encoders more thoughts some very good encoders for small diameter shafts, but programmable or even in some cases DIP switch selectable

48 to 4096 PPR

Are the CUI range with capacitive sensing and highish speed operation

See https://www.cuidevices.com/amt-modular-encoders

Available for roughly $20 to $60 each in singles. See
https://www2.mouser.com/CUI/Electromechanical/Encoders/_/N-39xfc?P=1ysr4mi&Keyword=AMT+CUI&FS=True&Ns=Pricing|1

Very useful even as 'incremental' Quadrature ABZ (A, B quadrature and IDX pulse).

Important point to remember is when using IDX (Z) pulse that the index is on usually the FALLING EDGE and when in reverse use the RISING edge to clock.

I find using two counters is easier some of which are in many controllers these days for doing A/B quadrature decoding and simple external logic to fake A/B on separate index counter to get absolute position.

Often I prefer a small FPGA set to my required resolution for PPR and max revolutions (signed or unsigned), then use various flags for movement interrupts at desired update rate. Add comparators for thresholds in direction interrupts to simplify things on higher speeds.

Getting absolute positioning often requires external limit detections for power up initially and seek to reference position, with fast shut off for motors.

Over a decade ago I implemented a quadrature encoder driver in the RISC co-processor of a Freescale S12X MCU.  Both rising and falling edges of two input capture pins were processed in their respective interrupt handlers for maximum resolution.  The ISR servicing period was less than 400 nsec.  Noise filtering (jitter) was via delay register and small high-pass cap.  The logic is very simple and yet I have never seen it presented elsewhere:

ISR A:
         if pin_a_val == pin_b_val
         encoder_cnt--
         else
         encoder_cnt++

ISR B:
         if pin_a_val == pin_b_val
         encoder_cnt++
         else
         encoder_cnt--

It really is that simple and it just works.  Whether an increasing count is CW or CCW is arbitrary and easily inverted in logic.  With the above logic and the quadrature signal illustration in your newsletter, an increasing count corresponds to a CW rotation.

Of course today I would simply source a micro with a QE hardware feature - there seems to be a lot of them.

I have been working with magnetic encoders for some time, and I came across a very nice piece of magnetic encoder chip, the MPS (MonolithicPower) MA3xx and 7xx family. I am working on motor control , but these little magnetic encoder chips are usable for other stuff too...

These are really small ( MA302 is a QFN16 3x3 ), and they tick all the boxes someone wants from an encoder for use along a microcontroller > 3.3v supply, SPI communication, quadrature encoder output with index pulse, and even a commutation-output for running motor controller directly from the encoder signals ( UVW - simulated Hall-sensor output).

Also they only require a very small PCB, with only a filter capacitor and the chip itself. The PCB then can be placed anywhere close to the shaft with a rotating ( typically a diametrically magnetized cylinder) magnet, in end-of-shaft or side-shaft mounting configuration. The magnet can be really small too.

Angle between the shaft and the sensor can be compensated in settings via SPI, to compensate for angle-error. 

The position where you want the chip to read zero is also adjustable trough SPI. 

Refresh rate is 1MHz, and the resolution is 12bits for the MA302 version. 

The downside is, they typically require a bit of setting up trough SPI, but once you set the correct register values, then it will store the values in internal non-volatile memory, so it is possible to set it up trough SPI once, and then use only the quadrature encoder outputs for detecting position.

https://www.monolithicpower.com/en/products/sensors/position-sensors/ma302.html 

I have no interest in promoting them, it's just a nice piece of hardware I like. 

NASA came up with a way to avoid quadrature encoders. They placed a disk on the shaft that had a Morse-code like pattern; a short hole, or slot, followed by a longer slot.

The direction of rotation would be determined by if the short slot came before or after the long slot in the time sampling. There can be more than one pattern and can be the same or different depending on the application.