An interesting project I stumbled upon recently is AirLoom[0], essentially a reverse literate programming tool. Rather having code and prose interweaved (either Knuth-style code-within-prose or doc-style/as-comments prose-within-code), you've them split in dedicated in segment-annotated code and prose referencing those segments. AirLoom can then produce a combined document with references replaced by the actual code segments. This allows using a normal programming environment (not possible in first approach) and being order independent (not possible in second approach).

[0]: https://github.com/eudoxia0/airloom

There is also verso / recto that uses the same technique.

https://github.com/nickpascucci/verso

I actually wish for a tool that would use two things: 1) navigate code like a file system: Class/function/lines [3..5]

2)allow us to use git commit revisions so that we could comment on the evolution of the code

So far the only thing capable has been leoEditor + org-babel

Thanks for mentioning this. I built the same thing a year ago for myself in dozen lines of AWK. Looks like great minds think alike :)

In my opinion this is the most practical approach for real world projects. You get benefits like avoiding outdated documentation without huge upfront costs.