[#1723] Updates to Manual Install Documentation

Supersedes #1660 

Fixes #1672 
Fixes #1673 

~~Requires #1643~~
~~Requires #1662~~ 
~~Requires #1655~~
Requires #1761
Requires #1726

Also related:
#1755, #1746, #1687

WIP towards #1723 

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This section needs to be updated to reflect the discussion above about the init scripts for thin and passenger. Perhaps it can now just go away?