Numbered in order from left to right (1-13):
Intrinsic 2
[spoiler]2, 11, 1, 10, 7, 6[/spoiler]
Intrinsic 3
[spoiler]1, 4, 11, 1, 4, 10[/spoiler]
Intrinsic 4
[spoiler]1, 8, 1, 6[/spoiler]
Secret Boss Fight (Great to get the tonic effect kills for the catalysts):
[spoiler]10, 4, 6, 1, 11, 4, 8, 1[/spoiler]
The Shrine (nobody knows if it has a purpose - in the jumping section):
[spoiler]1, 8, 4, 11, 1, 6, 4, 10[/spoiler]
Other codes that are still a mystery (2/3 have pop-up flavor text):
[spoiler]1,8, 1, 9
1, 8, 1, 11, 9
4, 7, 9, 6, 2, 6, 7, 1[/spoiler]
😇👍💠
Edit: I was more tired than I thought last night, the bonus codes were wrong - just a repeat of the intrinsics...
It's correct now.