Scaffold brain-research + recovery-plan research bases (Phase 0)#1
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APavlov2 wants to merge 90 commits into
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Scaffold brain-research + recovery-plan research bases (Phase 0)#1APavlov2 wants to merge 90 commits into
APavlov2 wants to merge 90 commits into
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Add two parallel literature-graded research scaffolds under docs/: - brain-research/: per the uploaded BRIEF. taxonomy (12 neural channels), rubric (1-4), entry template, status board, and compounds/habits/synthesis directory tree. - recovery-plan/: parallel structure for the metabolic + cardiac plan. Preserves the source PLAN, adds an adapted brief, a 12-channel metabolic-cardiac taxonomy, matching rubric, an entry template with a first-class cardiac_safety overlay, and a status board. Existing files untouched. Phase 0 only - structure ready for review. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ed states) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…evention trials noted) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…preclinical) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…-of-bias noted) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…lagged observational) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…s SB-PS split) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…bias caveats) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…arm signal noted) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…rong but peripheral) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…on trials noted) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ighted, industry-funding caveat) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…s, teratogenicity signal) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…eys) - Adopt 'preclinical' as a 5th population value (documented in _template.md); several entries legitimately needed it for cell/animal-only mechanisms. - Normalize population to the enum, direction to up|down|modulate, and the three safety sub-keys to contraindications/interactions/notable_risks across entries. All 16 frontmatters now parse as valid YAML. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…y + thyroid flags) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…null) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…embedded colon) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ge prevention) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…aphic-bias caveat) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…reclinical) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…t, research-grade) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ian-trial limits) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
… Russian open-label, preclinical BDNF) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…l HACU) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ness, modest rested cognition) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
… of modafinil) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…otoxicity, WADA-banned) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
… addiction caveat central) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…t modest, Schedule II) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…, lipofuscin preclinical) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ss, modest bioavailability edge) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ivalent, status-dependent) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…, glymphatic clearance preclinical) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ic, excluded a retracted paper) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…absent Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…nal, cognition thin) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
… + small RCTs, dose distinction) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ssian/preclinical) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…vidence + bias flags) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…ood signal, sepsis risk noted) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…, Russian/preclinical) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…hemical, no human data, retracted-paper caveat) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…led RCTs null, Schedule I) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
…nds) Add a reproducible generator (generate_matrix.py) that aggregates every entry's channels[] frontmatter into: - channel-matrix.json: the Atlas data source (12 channels, 76 compound agents, channel->mechanism map; duplicate channels merged by max evidence). - channel-briefs.md: per-channel ranked agent tables (by per-channel evidence), coverage-at-a-glance, and honest gap/thin-channel flags. Compounds-only pending Phase 2; convergence flags marked provisional. Re-run the generator after the habit track to finalize. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
New frontmatter fields on every compound entry: - origin: natural | semi-synthetic | synthetic (lab-only) - source: short common/natural source string Breakdown: 57 natural, 4 semi-synthetic, 15 synthetic. Updated _template.md with the controlled vocabulary, extended generate_matrix.py to carry origin + source into channel-matrix.json (per-agent) and meta.by_origin, and regenerated channel-briefs.md with an origin breakdown + per-channel origin column. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm
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Add two parallel literature-graded research scaffolds under docs/:
rubric (1-4), entry template, status board, and compounds/habits/synthesis
directory tree.
Preserves the source PLAN, adds an adapted brief, a 12-channel
metabolic-cardiac taxonomy, matching rubric, an entry template with a
first-class cardiac_safety overlay, and a status board.
Existing files untouched. Phase 0 only - structure ready for review.
Co-Authored-By: Claude Opus 4.8 (1M context) noreply@anthropic.com
Claude-Session: https://claude.ai/code/session_01JizuvoRApjjJ6R5NzVLxBm