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Documentation links
http://ataristeven.exxoshost.co.uk/txt/Prefetch.txt
http://pasti.fxatari.com/68kdocs/AtariSTCycleCounting.html
http://pasti.fxatari.com/68kdocs/68kPrefetch.html
http://dbug.kicks-ass.net/dbugforums/cgi-bin/yabb2/YaBB.pl?num=1362997718
http://pasti.fxatari.com/68kdocs/div68kCycleAccurate.c http://web.archive.org/web/20091015132715/http://www.trzy.org/files/68knotes.txt
http://dev-docs.atariforge.org/files/MC68901.pdf
http://dev-docs.atariforge.org/files/MC6850.pdf
http://dev-docs.atariforge.org/files/WD1772.pdf
http://dev-docs.atariforge.org/files/YM2149_1992.pdf
http://bitchin100.com/wiki/images/4/47/Hd6301.pdf
http://github.com/DrCoolzic/AIR/tree/master/pasti
http://info-coach.fr/atari/documents/_mydoc/Pasti-documentation.pdf
http://www.sarnau.info/posts/2011/pasti_file_format/
http://atari.8bitchip.info/STXdesc.html
The Atari Forum is shock full of detailed information about the hardware components. The problem is finding the gems in the haystack.
Waveform timing diagram for GLUE/MMU/Shifter/display:
http://www.atari-forum.com/viewtopic.php?f=16&t=24855&start=363#p238041
Different clock speeds:
http://www.atari-forum.com/viewtopic.php?t=9226
Discovery of four-pixel hardware scroll:
http://www.atari-forum.com/viewtopic.php?f=16&t=24855&start=75#p233392
Test case for "Spectrum 512 funny pixels":
http://www.atari-forum.com/viewtopic.php?f=16&t=24855&start=310#p237119
http://alive.atari.org/ TODO: Links to individual articles.
http://ataristeven.exxoshost.co.uk/txt/MMU.txt
http://ataristeven.exxoshost.co.uk/txt/GLUE.txt
http://ataristeven.exxoshost.co.uk/txt/Shifter.txt
http://ataristeven.exxoshost.co.uk/doc.htm/Emulator%20cycles.htm
http://ataristeven.exxoshost.co.uk/txt/Atari%20ST%206301%20Rom%20disassemby%20commented.txt
http://www.atari-wiki.com/index.php/Atari_ST/STe/MSTe/TT/F030_Hardware_Register_Listing
http://www.atari-wiki.com/index.php/ST_STE_Scanlines
http://www.atari-wiki.com/index.php/Fullscreen_programming_on_the_Atari_ST
http://www.atari-wiki.com/index.php/Atari_ST_Scancode_diagram_by_Unseen_Menace
http://www.atari-wiki.com/index.php/Keyboard_Protocol