xtask tools: improve naming

[Lotterleben]

from #128 :

some renaming could be done to make things clearer, e.g. cargo xtask dongle output (or dongle logs) instead of serial-term. This can also be used to group commands, e.g. dongle-flash would become cargo xtask dongle flash so all dongle related tasks live under the dongle namespace

This issue is closed if:

• tools have been given m,ore useful names where necessary
• tools have been grouped where necessary
• mdbook sections that call these tools have been updated