Found 3 comments on HN
jenkstom · 2017-02-16 · Original thread
Programming from the Ground Up teaches x86 assembler from first principles. All on a free OS (Linux using asm). There is a free version available online, but if you want to support the author you can buy it from amazon.
erwan574 · 2012-02-29 · Original thread
A few books exist that try to restore some sort of "complete understanding" :

Software programming starting from assembly language under linux :

A study going from chip design to high level programming :

IHMO this "problem" of "incomplete vision" started when device drivers where introduced in general purpose OS. Professionnal application developpers started to target API instead of hardware. A milestone in this trend for me is Windows 3.0 (1990). This also marks the demise of fixed hardware computers that the hobbyist favored so far.

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