On November 23rd the finalized board design for the soil moisture probe and the programmer daughter board was sent to OSHPark for fabrication. There were actually a couple changes made to the probe board since the last post, but the overall design did not change.
The pair of pull-up resistors for the i2c bus connecting the ESP32 to the external RTC were removed since the ESP32 features internal pull-up resistors. Debugging the code for the RTC revealed that I made a mistake with the interrupt pin from the RTC. I either forgot or didn't realize that the interrupt pin on the RTC is an open-drain pin, so I added a pull-up resistor. Why not use the ESP32's internal pull-up resistor for the interrupt pin as well? The interrupt pin will be used when the ESP32 is in deep sleep mode, so the device will be effectively powered off, so I'm not sure that the pin configuration will be persistent.
I also tried my best to reduce the number of decoupling capacitors. Lastly, I needed to add a huge 4700 uF capacitor to the circuit. I realized the need for it by looking further into Adafruit's design for the USB/Solar charger. Talking with an EE friend of mine, we figured the large cap is needed to smooth the voltage from the solar cell and acts as a "poor man's" maximum power point tracker. Forward annotating the new capacitor to the board design was a challenge due to low space, but I was thankfully able to find a spot for it on the back of the board.
The Ultiboard and Multisim design files are now uploaded to the project site along with the gerber files. I also uploaded the bill of materials.