[DOC] update docs for improvements to auto_* and de_novo tools
[DOC] update docs for improvements to auto_* and de_novo tools

brentp/gemini,bpow/gemini,brentp/gemini,bw2/gemini,xuzetan/gemini,heuermh/gemini,xuzetan/gemini,udp3f/gemini,bgruening/gemini,heuermh/gemini,bw2/gemini,brentp/gemini,arq5x/gemini,arq5x/gemini,bw2/gemini,arq5x/gemini,arq5x/gemini,bw2/gemini,bpow/gemini,udp3f/gemini,heuermh/gemini,udp3f/gemini,bpow/gemini,xuzetan/gemini,brentp/gemini,bgruening/gemini,bpow/gemini,udp3f/gemini,heuermh/gemini,xuzetan/gemini,bgruening/gemini,bgruening/gemini