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atom-concepts-backfill

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UpdatedJune 12, 2026 at 18:09

Bridge an upstream gap: extract_atoms never stamps `frontmatter.concepts` on page-derived atoms, but synthesize_concepts consumes ONLY that field — so concept synthesis is permanently skipped ("no atoms with concept refs"). This script batch-labels atoms lacking the field with 1-3 kebab-case shared-vocabulary topic labels (sonnet) and stamps them, so upstream synthesize_concepts can tier + materialize concepts/<label> pages. Idempotent: only touches atoms WITHOUT `concepts`; safe to rerun after each extract_atoms drain. Retires when the upstream fix lands.

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ChenyqThu

ChenyqThu/jarvis-knowledge-os-v2

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name	atom-concepts-backfill
version	1.0.0
description	Bridge an upstream gap: extract_atoms never stamps `frontmatter.concepts` on page-derived atoms, but synthesize_concepts consumes ONLY that field — so concept synthesis is permanently skipped ("no atoms with concept refs"). This script batch-labels atoms lacking the field with 1-3 kebab-case shared-vocabulary topic labels (sonnet) and stamps them, so upstream synthesize_concepts can tier + materialize concepts/<label> pages. Idempotent: only touches atoms WITHOUT `concepts`; safe to rerun after each extract_atoms drain. Retires when the upstream fix lands.
triggers	["atom concepts backfill","backfill atom concepts","concepts backfill"]
mutating	true

atom-concepts-backfill — bridge for the extract_atoms → synthesize_concepts gap

上游断点（2026-06-11 定位，gbrain v0.42.37.0/v0.42.38.0）

src/core/cycle/synthesize-concepts.ts 头注释（设计意图）："when the Haiku 3-check from extract_atoms decides 'this atom is about concept X', it stamps the field" — :92 只消费 frontmatter.concepts。
src/core/cycle/extract-atoms.ts 的 page 提取路径从不写该字段（只写 type/atom_type/lesson/source_hash/source_quote/virality_score/ emotional_register）。
结果：所有 page-derived atoms 永远进不了 concept 合成（生产实证：696 atoms / 0 含 concepts / synthesize_concepts 连续 skip）。
上游 issue 已起草（见 TODO）；本脚本为 fork 侧桥接，上游修复后自动退场（届时新 atoms 自带 concepts，本脚本查询恒为空集）。

用法

# 必须从 repo root 跑（bun 自动加载 .env.local 的 crs 代理 key/base）。
# Claude Code shell 注入的 ANTHROPIC_BASE_URL 会覆盖 .env.local 并破坏
# key/base 配对 —— 先 unset（见 memory: pitfall-anthropic-base-url）。
unset ANTHROPIC_BASE_URL

bun run skills/kos-jarvis/atom-concepts-backfill/run.ts              # dry-run（只打标签分布，不写库）
bun run skills/kos-jarvis/atom-concepts-backfill/run.ts --limit 60 --apply   # 试点
bun run skills/kos-jarvis/atom-concepts-backfill/run.ts --apply     # 全量

默认 dry-run；--apply 才写库（jsonb merge concepts + concepts_by 审计标记，不动 body/chunks/embedding，无 re-embed 开销）。
--limit N / --batch N（默认 40/批）；KOS_CONCEPTS_MAX_SPEND 花费上限（默认 $5）；KOS_CONCEPTS_MODEL 模型覆盖（默认 claude-sonnet-4-6，按 Lucien 2026-06-09 路由：上游设计的 Haiku 档 → sonnet）。
词表跨批次累积并从已 stamp 的 atoms 预热，保证标签聚类（ synthesize_concepts 需要 ≥2 atoms 同标签才物化 T3 concept 页）。

验证回路

--limit 60 --apply 试点 → 看输出的 "cluster(s) with >=2 atoms"。
unset ANTHROPIC_BASE_URL && ~/.bun/bin/gbrain dream --phase synthesize_concepts --dir ~/brain → 确认 concepts/<label> 页出现（SELECT slug FROM pages WHERE frontmatter->>'synthesized_by' LIKE 'synthesize_concepts%'）。
全量 --apply；每次 extract_atoms drain 推进后重跑一次补新增。

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name	atom-concepts-backfill
version	1.0.0
description	Bridge an upstream gap: extract_atoms never stamps `frontmatter.concepts` on page-derived atoms, but synthesize_concepts consumes ONLY that field — so concept synthesis is permanently skipped ("no atoms with concept refs"). This script batch-labels atoms lacking the field with 1-3 kebab-case shared-vocabulary topic labels (sonnet) and stamps them, so upstream synthesize_concepts can tier + materialize concepts/<label> pages. Idempotent: only touches atoms WITHOUT `concepts`; safe to rerun after each extract_atoms drain. Retires when the upstream fix lands.
triggers	["atom concepts backfill","backfill atom concepts","concepts backfill"]
mutating	true

atom-concepts-backfill — bridge for the extract_atoms → synthesize_concepts gap

上游断点（2026-06-11 定位，gbrain v0.42.37.0/v0.42.38.0）

src/core/cycle/synthesize-concepts.ts 头注释（设计意图）："when the Haiku 3-check from extract_atoms decides 'this atom is about concept X', it stamps the field" — :92 只消费 frontmatter.concepts。
src/core/cycle/extract-atoms.ts 的 page 提取路径从不写该字段（只写 type/atom_type/lesson/source_hash/source_quote/virality_score/ emotional_register）。
结果：所有 page-derived atoms 永远进不了 concept 合成（生产实证：696 atoms / 0 含 concepts / synthesize_concepts 连续 skip）。
上游 issue 已起草（见 TODO）；本脚本为 fork 侧桥接，上游修复后自动退场（届时新 atoms 自带 concepts，本脚本查询恒为空集）。

用法

# 必须从 repo root 跑（bun 自动加载 .env.local 的 crs 代理 key/base）。
# Claude Code shell 注入的 ANTHROPIC_BASE_URL 会覆盖 .env.local 并破坏
# key/base 配对 —— 先 unset（见 memory: pitfall-anthropic-base-url）。
unset ANTHROPIC_BASE_URL

bun run skills/kos-jarvis/atom-concepts-backfill/run.ts              # dry-run（只打标签分布，不写库）
bun run skills/kos-jarvis/atom-concepts-backfill/run.ts --limit 60 --apply   # 试点
bun run skills/kos-jarvis/atom-concepts-backfill/run.ts --apply     # 全量

默认 dry-run；--apply 才写库（jsonb merge concepts + concepts_by 审计标记，不动 body/chunks/embedding，无 re-embed 开销）。
--limit N / --batch N（默认 40/批）；KOS_CONCEPTS_MAX_SPEND 花费上限（默认 $5）；KOS_CONCEPTS_MODEL 模型覆盖（默认 claude-sonnet-4-6，按 Lucien 2026-06-09 路由：上游设计的 Haiku 档 → sonnet）。
词表跨批次累积并从已 stamp 的 atoms 预热，保证标签聚类（ synthesize_concepts 需要 ≥2 atoms 同标签才物化 T3 concept 页）。

验证回路

--limit 60 --apply 试点 → 看输出的 "cluster(s) with >=2 atoms"。
unset ANTHROPIC_BASE_URL && ~/.bun/bin/gbrain dream --phase synthesize_concepts --dir ~/brain → 确认 concepts/<label> 页出现（SELECT slug FROM pages WHERE frontmatter->>'synthesized_by' LIKE 'synthesize_concepts%'）。
全量 --apply；每次 extract_atoms drain 推进后重跑一次补新增。