Software

Everything is easy in the C language. It's the most popular, by far, so almost all of the assistance available for micro controllers is in that language. It's the language I know best. The choice is simple: C11
And the GNU AVR-GCC compiler with AVR libraries. I'm not a fan of Arduino; it's like building a sports-car with bricks—easy to build something but building something you need takes a lot more work.

UML outline will be in Dia.

The Source control that I know is GIT. It's simple, light, fast, popular, well documented and Github likes it.

Editor is usually VIM. Maybe I'll use Geany more.

Documentation will be Literate code using Cweb. It's the most popular, no that any literate is popular. I like Nuweb and noweb but I'm used to Cweb. Nuweb works well with LaTeX, and has many other advantages, so if I change it will be to that. There are many haters of Literate but I find embedding code into the user-story very efficient. Reduced risk and faster, as a whole. Less story/code divergence and the story can be a bit lighter since it's supported be code.

Call graphs are generated by Andreas Gustafsson's Egypt and rendered using Graphviz 2.38.0.

Parts programmed using AVRdude 6.1