[Docs] Links within markdown guides are broken

[chr-hertel]

With the current config the cross-links in markdown files are broken after build with phpDocumentor.
Either it's on me to understand too little about that or we have three options here:

1. switch from MD to RST for proper menu structure - would also bring the guides to left instead of top menu
2. hardlink to html files, which would lead to broken links on github MD preview
3. switch from phpDocumentor to something else