Features

Automatic time synchronization with German atomic clock. No user action required
Automatic switch over to daylight savings time.
Sunrise simulation with rotary encoder to configure the final brightness.  During alarms the light will begin lighting gradually starting 30mins before the scheduled alarm.  The COB-LED array is mounted on the back of the housing to avoid shining the bright light on the sleeping people.  The indirect light of the wall produces a more enjoyable light.
Large LED display : readable without glasses.
Auto brightness for displays and buttons.

Rubber feet (so it doesn't slide from your closet)
Weekdays setting : the alarm can be configured for separate days of the week. So there's no longer a need to turn your alarm off on Fridays to avoid being woken on Saturday mornings.
✔ Wake-up sound from MP3 (2.5W in a 4ohm speaker) : song selection and volume button controlled by rotary encoder.
One-handed configuration
❌ USB charge port output : It should be discouraged to take a smartphone or tablet to your bedroom.  Give your mind some rest.
❌ Backup supply in case of power outage, powerful enough to sound the alarm. The provisions are there in hardware. Some peripherals can be switched off to save power, but there's no firmware support for it.
USB-B Connector power input.

Apparently Craig Bonsignore had about the same annoyances with standard clocks, that's why he built his own version.  I'll start off from that design: adding features I miss and scraping off costs where needed.
Modular design in hardware as well as software.  Several components can easily be reused in other projects.

Block diagram

There has been chosen for a modular approach.  The individual modules are small, cheap (<€1/pce) and can be reused in other projects.  

Diagram showing custom designed PCBs for this project

Let's dig a little deeper into the different custom modules:

Electronics ready for mounting

All electronics + Nucleo debugger - power supply board (https://cdn.hackaday.io/images/8356521609096432554.jpg)

Future extensions (unplanned)