lumina-wiki 1.6.2 → 1.7.1

package/CHANGELOG.md

@@ -5,6 +5,57 @@ Format follows [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [1.7.1] - 2026-07-02
+
+### Added
+
+- `wiki.mjs init --pack learning` now creates `wiki/reflections/`, matching the
+  learning pack's entity schema. Valid `--pack` values are derived from the
+  schema instead of hardcoded, so future packs stay in sync automatically.
+
+### Fixed
+
+- `/lumi-research-topic` previously failed every `add-edge` call with "Unknown
+  edge type" because the topic-organization edges it relies on
+  (`includes_source`/`included_in_topic`, `covers_concept`/`covered_by_topic`)
+  were missing from the schema. Added all four to `EDGE_TYPES`.
+- Corrected skill-prompt and documentation drift: the reset skill's dry-run
+  output format, the internal lint-check reference table (was missing
+  L10-L12), and the documented behavior of ingest phase checkpoints (keyed
+  by file basename, not slug, since the checkpoint exists before slug
+  generation; the checkpoint JSON's `slug` field, written once the slug
+  phase completes, is now documented as the way other skills match a
+  checkpoint to its wiki entry).
+
+## [1.7.0] - 2026-06-16
+
+### Added
+
+- **Advanced paper ranking** via the new research-pack skill
+  `/lumi-research-rank`. It scores an already-ingested paper and records the
+  results on its source page, both as a machine-readable `ranking:` frontmatter
+  block and a human-readable `## Ranking` scorecard. Re-running refreshes the
+  ranking and preserves any notes inside `<!-- user-edited -->` markers.
+- **Citation influence signal**: surfaces Semantic Scholar's influential-citation
+  count alongside the raw citation count (reuses the existing `fetch_s2.py`; no
+  new key required).
+- **4C qualitative rubric** (Correctness, Clarity, Contribution, Context, each
+  scored 1-5) produced with a three-pass reading method to keep the assessment
+  efficient. Scores are explicitly recorded as LLM-assessed with a timestamp.
+- **Venue prestige** recorded from the agent's own knowledge and explicitly
+  flagged as an estimate (`venue_source: llm-estimated`) — no live API or
+  bundled dataset.
+- **Optional, key-gated influence fetchers** `fetch_scite.py` (Scite.ai Smart
+  Citation tallies) and `fetch_altmetric.py` (Altmetric attention score). Both
+  degrade gracefully: with no key set they exit with a clear message and the
+  skill simply skips that signal. New `.env` keys `SCITE_API_KEY` and
+  `ALTMETRIC_API_KEY`.
+
+### Changed
+
+- Source page schema gains an optional `ranking` frontmatter object (no change
+  required for existing un-ranked pages).
+
 ## [1.6.2] - 2026-06-15
 
 ### Fixed

package/README.md

@@ -185,6 +185,7 @@ These are the commands you can use when chatting with your AI agent.
 | | `/lumi-research-survey` | Create a survey or summary from existing knowledge. |
 | | `/lumi-research-prefill` | Seed foundational concepts to avoid duplicates. |
 | | `/lumi-research-topic` | Create a topic page at `wiki/topics/<slug>.md` by gathering related concepts and sources already in your wiki. The AI proposes what to include and you confirm before anything is written. Use this after several `/lumi-ingest` runs when you want to give a theme its own page. |
+| | `/lumi-research-rank` | Score a paper you have already ingested so you know what to read first. It looks up how influential the paper is (citation signals), estimates how respected its venue is, and rates its quality on four points — Correctness, Clarity, Contribution, and Context — then adds a clear scorecard to the paper's page. Measured numbers and the AI's own estimates are always kept separate. |
 | | `/lumi-research-setup` | Help configure API keys for research tools. |
 | | `/lumi-research-watch-run` | Run one scheduled-discovery pass over your watchlist (topics + RSS / Atom feeds). Polls only when you ask. |
 | **Reading** | `/lumi-reading-chapter-ingest` | Ingest a book chapter by chapter. |
@@ -209,7 +210,7 @@ Lumina-Wiki is evolving rapidly. Here is our user-facing roadmap:
 - [x] **Improved CI/CD:** Native support for Bun and Node 22 environments. *(shipped in v1.2)*
 - [x] **Global Source Expansion:** Direct integration with OpenAlex, CORE, and Unpaywall for reliable DOI-to-PDF resolution. *(shipped in v1.6)*
 - [x] **RSS & Blog Monitoring:** Automatically surface new papers from your favorite lab blogs and journals via `type: feed` watchlist items. *(shipped in v1.6)*
-- [ ] **Advanced Paper Ranking:** See influence scores and quality signals for your research papers.
+- [x] **Advanced Paper Ranking:** See influence scores and quality signals for your research papers via `/lumi-research-rank`. *(shipped in v1.7)*
 
 **Long-term (Deep Research & Integration)**
 - [ ] **Image OCR & Scanned PDFs:** Ingest screenshots and scanned PDFs into your wiki.

package/README.vi.md

@@ -185,6 +185,7 @@ Xem [Hướng dẫn Nâng cao](docs/user-guide/advanced-qmd.vi.md) để biết
 | | `/lumi-research-survey` | Tạo một bài tổng quan/khảo sát từ kiến thức hiện có. |
 | | `/lumi-research-prefill` | Tạo trước các khái niệm nền tảng để tránh trùng lặp. |
 | | `/lumi-research-topic` | Gom các khái niệm và nguồn liên quan trong wiki thành một trang chủ đề tại `wiki/topics/<slug>.md`. AI đề xuất danh sách để bạn xem và xác nhận trước khi trang được tạo. Dùng sau khi đã nạp nhiều tài liệu và muốn tổng hợp một nhóm ý tưởng thành trang riêng. |
+| | `/lumi-research-rank` | Chấm điểm một bài báo bạn đã nạp để biết nên đọc gì trước. Nó tra mức độ ảnh hưởng của bài (tín hiệu trích dẫn), ước lượng uy tín nơi công bố, và đánh giá chất lượng theo bốn tiêu chí — Tính đúng đắn, Sự rõ ràng, Đóng góp, và Bối cảnh — rồi thêm một bảng điểm rõ ràng vào trang của bài báo. Các con số đo được và ước lượng của AI luôn được tách bạch. |
 | | `/lumi-research-setup` | Giúp cấu hình API key cho các công cụ nghiên cứu. |
 | | `/lumi-research-watch-run` | Chạy một lượt khám phá theo lịch dựa trên watchlist (chủ đề + nguồn RSS / Atom). Chỉ chạy khi bạn yêu cầu. |
 | **Reading** | `/lumi-reading-chapter-ingest`| Nạp kiến thức sách theo từng chương. |
@@ -209,7 +210,7 @@ Lumina-Wiki đang phát triển nhanh chóng. Dưới đây là lộ trình hư
 - [x] **Cải thiện CI/CD:** Hỗ trợ chính thức cho môi trường Bun và Node 22. *(đã phát hành trong v1.2)*
 - [x] **Mở rộng nguồn dữ liệu toàn cầu:** Tích hợp trực tiếp với OpenAlex, CORE và Unpaywall để tra cứu DOI-to-PDF đáng tin cậy. *(ra mắt trong v1.6)*
 - [x] **Theo dõi RSS & Blog:** Tự động phát hiện bài báo mới từ các blog phòng thí nghiệm và tạp chí yêu thích qua các mục `type: feed` trong watchlist. *(ra mắt trong v1.6)*
-- [ ] **Xếp hạng bài báo nâng cao:** Xem điểm số ảnh hưởng và tín hiệu chất lượng cho các nghiên cứu của bạn.
+- [x] **Xếp hạng bài báo nâng cao:** Xem điểm số ảnh hưởng và tín hiệu chất lượng cho các nghiên cứu của bạn qua `/lumi-research-rank`. *(ra mắt ở v1.7)*
 
 **Dài hạn (Nghiên cứu sâu & Tích hợp)**
 - [ ] **OCR ảnh & PDF scan:** Nạp ảnh chụp màn hình và PDF dạng scan vào wiki.

package/README.zh.md

@@ -186,6 +186,7 @@ npx skills add https://github.com/tobi/qmd --skill qmd
 | | `/lumi-research-survey` | 从现有知识创建综述/调研。 |
 | | `/lumi-research-prefill` | 预先生成基础概念，避免重复。 |
 | | `/lumi-research-topic` | 把 wiki 中已有的相关概念和来源汇聚成一个主题页，保存在 `wiki/topics/<slug>.md`。AI 会提议收录哪些内容，由你确认后再生成页面。多次 `/lumi-ingest` 之后，用它把一组相关想法整理成独立的主题页。 |
+| | `/lumi-research-rank` | 给已经纳入的论文打分，帮你决定先读哪一篇。它会查询论文的影响力（引用信号）、估计发表场所的声望，并从四个方面评估质量——正确性、清晰度、贡献、背景——然后在论文页面上加上一份清晰的评分卡。实测数据与 AI 的估计始终分开标注。 |
 | | `/lumi-research-setup` | 帮助配置研究工具的 API key。 |
 | | `/lumi-research-watch-run` | 基于 watchlist 运行一次计划式发现（主题 + RSS / Atom 源）。仅在你要求时才运行。 |
 | **Reading** | `/lumi-reading-chapter-ingest`| 按章节导入书籍知识。 |
@@ -210,7 +211,7 @@ Lumina-Wiki 正在快速演进。这是我们的用户路线图：
 - [x] **改进的 CI/CD：** 正式支持 Bun 和 Node 22 环境。*（v1.2 已发布）*
 - [x] **全球数据源扩展：** 直接集成 OpenAlex、CORE 和 Unpaywall，实现可靠的 DOI-to-PDF 解析。*（在 v1.6 中发布）*
 - [x] **RSS 与博客监控：** 通过 watchlist 中的 `type: feed` 项，自动从您喜爱的实验室博客和期刊中发现新论文。*（在 v1.6 中发布）*
-- [ ] **高级论文排名：** 查看研究论文的影响力评分和质量信号。
+- [x] **高级论文排名：** 通过 `/lumi-research-rank` 查看研究论文的影响力评分和质量信号。*（在 v1.7 中发布）*
 
 **长期计划（深度研究与集成）**
 - [ ] **图片 OCR 与扫描 PDF：** 将截图与扫描版 PDF 导入维基。

package/package.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/package.json",
   "name": "lumina-wiki",
-  "version": "1.6.2",
+  "version": "1.7.1",
   "description": "Domain-agnostic, multi-IDE wiki scaffolder — Karpathy's LLM-Wiki vision, cross-platform and pack-based.",
   "keywords": [
     "llm-wiki",
@@ -69,6 +69,8 @@
     "src/tools/fetch_core.py",
     "src/tools/resolve_pdf.py",
     "src/tools/fetch_rss.py",
+    "src/tools/fetch_scite.py",
+    "src/tools/fetch_altmetric.py",
     "src/tools/id_utils.py",
     "src/tools/requirements.txt",
     "CHANGELOG.md",

package/src/installer/commands.js

@@ -131,7 +131,7 @@ const RESEARCH_TOOL_FILES = [
   '_env.py', '_cache.py', 'discover.py', 'init_discovery.py', 'prepare_source.py',
   'fetch_arxiv.py', 'fetch_wikipedia.py', 'fetch_s2.py', 'fetch_deepxiv.py',
   'fetch_openalex.py', 'fetch_unpaywall.py', 'fetch_core.py', 'resolve_pdf.py',
-  'fetch_rss.py',
+  'fetch_rss.py', 'fetch_scite.py', 'fetch_altmetric.py',
 ];
 
 async function findEnclosingWorkspace(startDir) {
@@ -1234,6 +1234,7 @@ function getSkillDefs(packs) {
       { name: 'prefill',  canonicalId: 'lumi-research-prefill',  displayName: '/lumi-research-prefill' },
       { name: 'setup',    canonicalId: 'lumi-research-setup',    displayName: '/lumi-research-setup' },
       { name: 'topic',     canonicalId: 'lumi-research-topic',     displayName: '/lumi-research-topic' },
+      { name: 'rank',      canonicalId: 'lumi-research-rank',      displayName: '/lumi-research-rank' },
       { name: 'watchlist', canonicalId: 'lumi-research-watchlist', displayName: '/lumi-research-watchlist' },
       { name: 'watch-run', canonicalId: 'lumi-research-watch-run', displayName: '/lumi-research-watch-run' },
     ];
@@ -1322,6 +1323,10 @@ async function renderEnvExample(projectRoot) {
       `OPENALEX_API_KEY=\n\n` +
       `# DeepXiv token (optional; enables full-text PDF access)\n` +
       `DEEPXIV_TOKEN=\n\n` +
+      `# Scite.ai API key (optional; enables Smart Citation tallies in /lumi-research-rank)\n` +
+      `SCITE_API_KEY=\n\n` +
+      `# Altmetric API key (optional; enables attention scores in /lumi-research-rank)\n` +
+      `ALTMETRIC_API_KEY=\n\n` +
       `# arXiv does not require an API key in v0.1\n`;
   }
   await atomicWrite(destPath, content);

package/src/scripts/schemas.mjs

@@ -215,6 +215,12 @@ export const EDGE_TYPES = [
   { name: 'part_of',            from: 'concepts', to: 'concepts', reverse: 'has_part',        symmetric: false, pack: 'core' },
   { name: 'has_part',           from: 'concepts', to: 'concepts', reverse: 'part_of',         symmetric: false, pack: 'core' },
 
+  // --- research pack: topic organization edges -----------------------------
+  { name: 'includes_source',    from: 'topics',   to: 'sources',  reverse: 'included_in_topic', symmetric: false, pack: 'research' },
+  { name: 'included_in_topic',  from: 'sources',  to: 'topics',   reverse: 'includes_source',   symmetric: false, pack: 'research' },
+  { name: 'covers_concept',     from: 'topics',   to: 'concepts', reverse: 'covered_by_topic',  symmetric: false, pack: 'research' },
+  { name: 'covered_by_topic',   from: 'concepts', to: 'topics',   reverse: 'covers_concept',    symmetric: false, pack: 'research' },
+
   // --- terminal edges (no reverse) — exempt-only rule applies -------------
   // Any entity -> foundations/** (research pack)
   { name: 'grounded_in',        from: '*', to: 'foundations', reverse: null, terminal: true, pack: 'research' },
@@ -283,6 +289,7 @@ export const REQUIRED_FRONTMATTER = {
     { key: 'findings',     type: 'array', required: false },
     { key: 'external_ids', type: 'object', required: false },
     { key: 'sources',      type: 'array',  required: false },
+    { key: 'ranking',      type: 'object', required: false },
   ],
 
   // Concept page

package/src/scripts/wiki.mjs

@@ -1179,26 +1179,33 @@ const CORE_WIKI_DIRS = [
   'wiki/graph',
 ];
 
-/** Research pack additional wiki dirs */
-const RESEARCH_WIKI_DIRS = [
-  'wiki/foundations',
-  'wiki/topics',
-];
+/**
+ * Installable (non-core) pack names, derived from ENTITY_DIRS so a new pack
+ * added to schemas.mjs becomes selectable via `init --pack` without touching
+ * this file.
+ * @type {string[]}
+ */
+const INSTALLABLE_PACKS = [...new Set(Object.values(ENTITY_DIRS).map(e => e.pack))]
+  .filter(pack => pack !== 'core');
 
-/** Reading pack additional wiki dirs */
-const READING_WIKI_DIRS = [
-  'wiki/chapters',
-  'wiki/characters',
-  'wiki/themes',
-  'wiki/plot',
-];
+/**
+ * Additional wiki dirs owned by a given pack, derived from ENTITY_DIRS.
+ * Preserves ENTITY_DIRS declaration order.
+ * @param {string} pack
+ * @returns {string[]}
+ */
+function wikiDirsForPack(pack) {
+  return Object.values(ENTITY_DIRS)
+    .filter(e => e.pack === pack)
+    .map(e => `wiki/${e.dir}`.replace(/\/$/, ''));
+}
 
 /**
  * Initialize a workspace skeleton.
  * Idempotent: re-running on an existing workspace is a no-op.
  * @param {string} projectRoot
  * @param {object} [opts]
- * @param {string} [opts.pack] - 'research' | 'reading' | undefined
+ * @param {string} [opts.pack] - one of INSTALLABLE_PACKS | undefined
  * @returns {Promise<{created: string[], skipped: string[]}>}
  */
 async function initWorkspace(projectRoot, opts = {}) {
@@ -1206,10 +1213,8 @@ async function initWorkspace(projectRoot, opts = {}) {
   const skipped = [];
 
   let dirs = [...CORE_WIKI_DIRS];
-  if (opts.pack === 'research') {
-    dirs = [...dirs, ...RESEARCH_WIKI_DIRS];
-  } else if (opts.pack === 'reading') {
-    dirs = [...dirs, ...READING_WIKI_DIRS];
+  if (opts.pack && INSTALLABLE_PACKS.includes(opts.pack)) {
+    dirs = [...dirs, ...wikiDirsForPack(opts.pack)];
   }
 
   // Add _lumina/_state dir
@@ -1506,7 +1511,7 @@ async function main(argv) {
       'Usage: node wiki.mjs <subcommand> [flags]',
       '',
       'Subcommands:',
-      '  init [--pack research|reading]  Create workspace skeleton',
+      `  init [--pack ${INSTALLABLE_PACKS.join('|')}]  Create workspace skeleton`,
       '  slug <title>                    Emit kebab-case slug',
       '  log <skill> <details...>        Append to wiki/log.md',
       '  read-meta <slug>                Read entity frontmatter as JSON',
@@ -1539,8 +1544,8 @@ async function main(argv) {
         // init does not require an existing workspace; it creates one
         const projectRoot = process.cwd();
         const pack = flags.pack && typeof flags.pack === 'string' ? flags.pack : undefined;
-        if (pack && pack !== 'research' && pack !== 'reading') {
-          emitError(`Invalid --pack value: ${pack}. Must be research or reading.`, 2);
+        if (pack && !INSTALLABLE_PACKS.includes(pack)) {
+          emitError(`Invalid --pack value: ${pack}. Must be one of: ${INSTALLABLE_PACKS.join(', ')}.`, 2);
           process.exit(2);
         }
         const result = await initWorkspace(projectRoot, { pack });

package/src/skills/core/ask/SKILL.md

@@ -127,6 +127,16 @@ Do not ingest the file yourself. The user decides whether to proceed.
 
 If the user asks to save the answer:
 
+First check whether the target page already exists:
+
+```bash
+node _lumina/scripts/wiki.mjs read-meta outputs/<slug>
+```
+
+Exit 0 means the page exists. If it does, ask the user whether to overwrite
+it or pick a new slug — do not silently overwrite. Exit 2 ("Entity not
+found") means the slug is free; proceed.
+
 Ask for confirmation before writing. Then write
 `wiki/outputs/<slug>.md` or `wiki/summary/<slug>.md` with:
 ```yaml
@@ -232,5 +242,6 @@ Before reporting done, verify:
 
 (a) Every cited page in the answer exists in `wiki/` (readable)
 (b) If a page was filed: `wiki/log.md` has a new `## [YYYY-MM-DD] ask | ...` entry
-(c) If a page was filed: running `/lumi-ask` again with the same question does not
-    create a second output page (confirm with user or check for existing slug)
+(c) If a page was filed: the Step 6 existence check (`read-meta outputs/<slug>`)
+    ran before writing, so running `/lumi-ask` again with the same question
+    does not silently create or overwrite a second output page

package/src/skills/core/check/SKILL.md

@@ -99,7 +99,9 @@ node _lumina/scripts/lint.mjs --fix --json
 
 The `--fix` pass:
 - Applies the supported auto-fixes listed in `references/lint-checks.md`
-- Leaves L02, L05, and L08 for manual correction
+  (L01, L03, L06, L07, L09)
+- Leaves every other check (L02, L04, L05, L08, L10, L11, L12, L13, L14, L16)
+  for manual correction
 
 ### Step 4 — Self-check re-run
 
@@ -117,8 +119,10 @@ If errors remain, do not report done. Address each remaining error specifically:
   ```bash
   node _lumina/scripts/wiki.mjs set-meta <slug> <key> "<value>"
   ```
-- If L02, L05, or L08 remain, report the exact fields, wikilinks, or edges that
-  need manual correction.
+- If L02, L05, L08, or L10 remain, report the exact fields, wikilinks, edges,
+  or alias conflicts that need manual correction.
+- If L13 or L16 persist, suggest `/lumi-migrate-legacy --backfill-ids` — these
+  are not fixed by `lint.mjs --fix`.
 
 Repeat until `summary.errors === 0`. Do not loop more than 3 times — if errors
 persist, surface them to the user as needing manual attention.
@@ -137,12 +141,12 @@ Present findings in a structured list. Group errors first, then warnings.
 Lint check: <scanned_files> files scanned
 
 Errors (N):
-  [L06] concepts/positional-encoding.md:18 — Missing reverse edge to sources/attention-revisited
-  [L05] summary/transformers-overview.md:42 — Broken link [[flash-decoding]] (page not found)
+  concepts/positional-encoding.md:18 — a return link is missing, pointing back to sources/attention-revisited (L06)
+  summary/transformers-overview.md:42 — a link points to a page that does not exist: [[flash-decoding]] (L05)
 
 Warnings (M, advisory):
-  [L04] concepts/rotary-embeddings.md — Orphan page (no inbound links)
-  [L09] wiki/index.md — Index catalog is stale
+  concepts/rotary-embeddings.md — this page has no inbound or outbound links yet (L04)
+  wiki/index.md — the page catalog is out of date (L09)
 
 Fixes available: L06, L09 (N total). Apply? [yes/no]
 ```

package/src/skills/core/check/references/lint-checks.md

@@ -14,8 +14,16 @@ output in `/lumi-check`.
 | L05 | Broken wikilink | error | No — user must correct or create target |
 | L06 | Missing reverse edge | error | Yes — writes the reverse edge |
 | L07 | Duplicate symmetric edge | warning | Yes — deduplicates |
-| L08 | Missing required confidence field | error | No — user must add confidence |
+| L08 | Missing required confidence field on an edge | error | No — user must add confidence |
 | L09 | Index out of sync | warning | Yes — rebuilds the index catalog |
+| L10 | Foundation alias conflict | error | No — user must rename or merge the colliding title/alias |
+| L11 | Missing `confidence` field on a source/concept page | warning | No — user must set a value |
+| L12 | `raw_paths` entry missing, unsafe, or parked in `raw/tmp/` | warning | No — user must move or fix the file, then update `raw_paths` |
+| L13 | `external_ids` missing a namespace derivable from `urls[]` | warning | No — run `/lumi-migrate-legacy --backfill-ids` |
+| L14 | `external_ids` value fails validation for its namespace | error | No — user must correct or remove the value |
+| L16 | `external_ids` value disagrees with the value derived from `urls[]` | warning | No — run `/lumi-migrate-legacy --backfill-ids` to reconcile |
+
+(L15 is intentionally unassigned — reserved for a future collision check.)
 
 ## Classification
 
@@ -26,13 +34,19 @@ Errors that must be resolved before done:
 - L03: non-kebab slugs
 - L05: broken wikilinks
 - L06: missing reverse edges
-- L08: missing required confidence fields
+- L08: missing required confidence field on an edge
+- L10: foundation alias conflicts
+- L14: invalid `external_ids` values
 
 Advisories to surface to the user:
 
 - L04: orphan pages
 - L07: duplicate symmetric edges
 - L09: index out of sync
+- L11: missing `confidence` on a source/concept page
+- L12: `raw_paths` missing, unsafe, or transient
+- L13: `external_ids` missing a derivable namespace
+- L16: `external_ids` disagrees with `urls[]`
 
 ## Fix Behavior
 
@@ -44,9 +58,11 @@ Advisories to surface to the user:
 - L07 deduplicates symmetric edges.
 - L09 regenerates the `<!-- lumina:index --> ... <!-- /lumina:index -->` block.
 
-L02, L05, and L08 require manual correction. If L06 remains after `--fix`, the
-target page may not exist; identify it and suggest `/lumi-ingest` or
-`/lumi-edit`.
+L02, L04, L05, L08, L10, L11, L12, L13, L14, and L16 require manual
+correction — none of them are touched by `--fix`. If L06 remains after
+`--fix`, the target page may not exist; identify it and suggest
+`/lumi-ingest` or `/lumi-edit`. For L13 and L16, the fix path is
+`/lumi-migrate-legacy --backfill-ids`, not `lint.mjs --fix`.
 
 The linter reads `_lumina/config/lumina.config.yaml` for exemption globs.
 `foundations/**`, `outputs/**`, and external URL targets are exempt from L06.

package/src/skills/core/edit/SKILL.md

@@ -123,6 +123,10 @@ manual follow-up.
 node _lumina/scripts/wiki.mjs log edit "Updated <slug>: <brief description>"
 ```
 
+After logging, suggest the user run `/lumi-check` in a fresh session or via a
+sub-agent. Blank context catches bias from the reasoning chain that just made
+this edit.
+
 ## Output Format
 
 Report to the user:
@@ -135,7 +139,7 @@ Example:
 Edited concepts/softmax-temperature.md:
 - Added definition paragraph in ## Overview
 - Linked back to sources/attention-revisited (used_in edge added)
-Lint: 0 errors, 1 warning (L04: orphan page — advisory)
+Links check out — one advisory note: this page has no inbound links yet (L04)
 ```
 
 ## Examples

package/src/skills/core/ingest/SKILL.md

@@ -58,7 +58,7 @@ This is the only logic in this body — everything else lives in step files. The
    | `drafted` | → `./references/step-02-lint.md` |
    | `linted` | → `./references/step-03-verify.md` |
    | `verified` | → `./references/step-04-finalize.md` |
-   | `finalized` | HALT, ask "this entry is already finalized; restart from scratch?" On `[Q]` (decline): exit cleanly, exit 0 — declining is not an error. On confirm, do these in order before re-entering step-01: (1) `set-meta sources/<slug> ingest_status drafted` (so a session crash mid-restart leaves the entry in a coherent stage, not a stale-finalized one), (2) delete the phase checkpoint at `_lumina/_state/ingest-<file-basename>.json`, (3) → `./references/step-01-draft.md`. |
+   | `finalized` | HALT, ask "this entry is already finalized; restart from scratch?" On `[Q]` (decline): exit cleanly, exit 0 — declining is not an error. On confirm, do these in order before re-entering step-01: (1) `set-meta sources/<slug> ingest_status drafted` (so a session crash mid-restart leaves the entry in a coherent stage, not a stale-finalized one), (2) delete the phase checkpoint at `_lumina/_state/ingest-<file-basename>.json` — at this point you may only know the slug, not the file basename, so derive it first: read `raw_paths[0]` via `read-meta sources/<slug>` and take its basename; if `raw_paths` is empty or unavailable, list `_lumina/_state/ingest-*.json` and read each one to find the checkpoint whose `slug` field equals `sources/<slug>`; if no checkpoint matches either way, there is nothing to delete — simply proceed, (3) → `./references/step-01-draft.md`. |
 
 ## Examples
 

package/src/skills/core/ingest/references/step-01-draft.md

@@ -88,7 +88,22 @@ node _lumina/scripts/wiki.mjs slug "<Title>"
 
 If `wiki/sources/<slug>.md` already exists: re-ingest — confirm with user before overwriting.
 
-Write checkpoint: `phase: "slug"`.
+The phase checkpoint is keyed by file basename (`ingest-<file-basename>.json`)
+because it is written before the slug exists. Now that the slug is known,
+merge it into the checkpoint so later skills (e.g. `/lumi-migrate-legacy`) can
+match a checkpoint to a wiki entry by reading its content instead of guessing
+the filename:
+
+```bash
+# 1) Read current state
+node _lumina/scripts/wiki.mjs checkpoint-read ingest <file-basename>
+# 2) Merge {"phase":"slug","slug":"sources/<slug>","source_basename":"<file-basename>"}
+#    into the JSON above (preserve all other fields).
+# 3) Write back via stdin:
+echo '<merged-json>' | node _lumina/scripts/wiki.mjs checkpoint-write ingest <file-basename>
+```
+
+Write checkpoint: `phase: "slug"` (already included in the merge above).
 
 ### Phase 3 — Write source page
 

package/src/skills/core/ingest/references/step-04-finalize.md

@@ -4,7 +4,7 @@
 
 - All frontmatter writes go through `wiki.mjs set-meta`.
 - `wiki/log.md` is append-only. Use `wiki.mjs log` — never edit the file directly.
-- The phase-level checkpoint at `_lumina/_state/ingest-<slug>.json` ends here; mark it `phase: "done"`.
+- The phase-level checkpoint at `_lumina/_state/ingest-<file-basename>.json` ends here; mark it `phase: "done"`.
 
 ## Why this step exists
 

package/src/skills/core/init/SKILL.md

@@ -69,6 +69,11 @@ For reading pack (if installed):
 node _lumina/scripts/wiki.mjs init --pack reading
 ```
 
+For learning pack (if installed):
+```bash
+node _lumina/scripts/wiki.mjs init --pack learning
+```
+
 Each call returns `{ ok: true, created: [...], skipped: [...] }`. Report which
 directories were newly created and which already existed.
 
@@ -168,6 +173,8 @@ node _lumina/scripts/lint.mjs --json
 node _lumina/scripts/wiki.mjs log init "Wiki initialized. Packs: core, research. Created: 8 dirs."
 ```
 Additional dirs created: `wiki/foundations/`, `wiki/topics/`, `raw/discovered/`
+(research pack). The learning pack (`init --pack learning`) additionally
+creates `wiki/reflections/`.
 </example>
 
 <example>

package/src/skills/core/migrate-legacy/SKILL.md

@@ -178,11 +178,22 @@ Use the following inference order. Stop at the first tier that yields a result.
 
 **Tier 1 (authoritative): read the ingest checkpoint.**
 
+Ingest checkpoints are keyed by the source file's basename
+(`_lumina/_state/ingest-<file-basename>.json`), not by slug — there is no
+direct `<slug>` lookup. List every ingest checkpoint and match by content:
+
 ```bash
-node _lumina/scripts/wiki.mjs checkpoint-read ingest <slug>
+ls _lumina/_state/ingest-*.json 2>/dev/null
 ```
 
-If a checkpoint exists with a `source_path` field:
+Read each match with the Read tool and check its `slug` field. Newer ingests
+(post-checkpoint-slug-merge) store `"slug": "sources/<slug>"` directly in the
+checkpoint — match the checkpoint whose `slug` equals the entry being
+migrated. Older checkpoints predate this field and won't have it; if no
+checkpoint's `slug` matches (including the case where none carry the field at
+all), fall through to Tier 2.
+
+If a matching checkpoint is found and has a `source_path` field:
 - If `source_path` is under `raw/tmp/*`: do NOT write `raw_paths`. Tell the user:
   "`<slug>` was ingested from a transient location (`<source_path>`). Move the
   file to `raw/sources/` or `raw/download/<resource>/` and re-run
@@ -308,13 +319,14 @@ URL=$(node _lumina/scripts/wiki.mjs read-meta sources/<slug> | node -e "process.
 
 # Step 2 — write urls array
 node _lumina/scripts/wiki.mjs set-meta sources/<slug> urls "[\"$URL\"]" --json-value
-
-# Step 3 — remove legacy url key (set-meta with empty string removes the key)
-node _lumina/scripts/wiki.mjs set-meta sources/<slug> url --remove
 ```
 
-If `set-meta --remove` is not supported by the installed wiki.mjs version, use `Edit` to
-remove the `url:` line directly after confirming `urls:` was written successfully.
+`set-meta` cannot remove a frontmatter key today — there is no `--remove`
+flag. After confirming `urls:` was written successfully, remove the legacy
+`url:` line with the `Edit` tool directly. This is the one sanctioned
+exception to "never hand-edit wiki frontmatter" in this skill, and it is
+limited strictly to deleting the obsolete `url:` key — do not use `Edit` for
+any other frontmatter change.
 
 After backfilling all entries, proceed immediately to Phase 4.
 
@@ -402,7 +414,7 @@ Report to the user:
 2. Entries updated — count and slugs grouped by field.
 3. Inferred values — the inference table from Phase 2 (so the user can review).
 4. Lint result after backfill — must show 0 errors.
-5. Whether `legacyMigrationNeeded` was cleared in the manifest.
+5. Whether the upgrade cleanup is finished.
 
 ## Examples
 
@@ -464,7 +476,10 @@ Re-running this skill on a clean wiki produces zero file changes.
 - Never modify files in `raw/`. Read-only.
 - Never hand-edit `wiki/graph/edges.jsonl` or `wiki/graph/citations.jsonl`.
 - `set-meta` is the only permitted write path for frontmatter changes in this
-  skill. Do not use Edit or Write on wiki pages directly.
+  skill, with one sanctioned exception: deleting the obsolete `url:` key
+  during the `url` → `urls` schema-shape upgrade (Phase 3), since `set-meta`
+  has no key-removal flag. Do not use Edit or Write on wiki pages for
+  anything else.
 - Do not clear `legacyMigrationNeeded` until lint confirms 0 errors.
 - If the CHANGELOG has no `### Migration` section for the detected version gap,
   rely entirely on the L01/L11 finding messages to identify which fields need