lumina-wiki 1.6.1 → 1.7.0

package/CHANGELOG.md

@@ -5,6 +5,55 @@ Format follows [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [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
+
+- Repaired stale Claude skill links during upgrades by validating their real
+  targets instead of trusting the previously recorded link strategy.
+- Made POSIX skill links relative so copied, moved, or renamed workspaces can
+  be upgraded without retaining links to their old absolute location.
+- Reconciled removed packs and IDE targets by deleting obsolete
+  installer-managed skills, tools, links, and unchanged generated stubs while
+  preserving modified or user-owned files.
+- Made `npx lumina-wiki install` detect and upgrade an enclosing workspace when
+  invoked from a nested directory, while explicit `--directory` and `--cwd`
+  targets remain exact.
+- Fixed interactive locale switching for existing and legacy workspaces,
+  including default-language cascading and confirmation binding to the final
+  resolved locale.
+- Made installation fail clearly when required Claude skill links cannot be
+  created instead of writing successful state for a partial install.
+
 ## [1.6.1] - 2026-05-18
 
 ### Fixed

package/README.md

@@ -93,6 +93,8 @@ The agent will help you check the research tools and save keys to a local `.env`
 
 If you reinstall Lumina-Wiki on a project that already has a `wiki/` from an earlier version, just run `npx lumina-wiki install` again. The installer updates scripts, schemas, and skills; **your content in `wiki/`, `raw/`, and `log.md` is not modified**.
 
+You can run the command from the project root or one of its subfolders. If you remove a pack or AI tool from the setup, Lumina removes its old managed commands and unchanged setup files. Files you edited are kept with a warning. If the whole project was copied, moved, or renamed, Lumina repairs its managed links during the upgrade.
+
 If the installer warns that older entries are missing newer frontmatter fields, you have two ways to backfill them:
 
 - **Recommended:** open your AI chat and run `/lumi-migrate-legacy`.
@@ -183,6 +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. |
@@ -207,7 +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

@@ -93,6 +93,8 @@ Agent sẽ hướng dẫn bạn kiểm tra công cụ nghiên cứu và lưu key
 
 Nếu bạn cài lại Lumina-Wiki trên một dự án đã có `wiki/` từ phiên bản trước, cứ chạy lại `npx lumina-wiki install`. Installer cập nhật scripts, schemas và skills; **nội dung của bạn trong `wiki/`, `raw/`, `log.md` không bị chỉnh sửa**.
 
+Bạn có thể chạy lệnh tại thư mục gốc hoặc một thư mục con của dự án. Nếu bỏ một gói hoặc công cụ AI khỏi thiết lập, Lumina sẽ dọn các lệnh cũ và những tệp thiết lập chưa được bạn sửa. Tệp đã chỉnh sửa được giữ lại kèm cảnh báo. Nếu toàn bộ dự án được sao chép, di chuyển hoặc đổi tên, Lumina sẽ sửa lại các liên kết do hệ thống quản lý khi nâng cấp.
+
 Nếu installer cảnh báo entry cũ thiếu frontmatter mới, có hai cách backfill:
 
 - **Khuyến nghị:** mở chat AI và chạy `/lumi-migrate-legacy`.
@@ -183,6 +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. |
@@ -207,7 +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

@@ -93,6 +93,8 @@ Agent 会引导您检查研究工具，并在需要时把 key 保存到本地 `.
 
 如果您在已经有旧版 `wiki/` 的项目上重新安装 Lumina-Wiki，直接再次运行 `npx lumina-wiki install` 即可。安装器会更新 scripts、schemas 和 skills；**您在 `wiki/`、`raw/`、`log.md` 中的内容不会被修改**。
 
+您可以在项目根目录或其子目录中运行该命令。如果从设置中移除某个包或 AI 工具，Lumina 会清理旧命令和未经您修改的设置文件。您修改过的文件会保留，并显示警告。如果整个项目被复制、移动或重命名，Lumina 会在升级时修复由系统管理的链接。
+
 如果安装器提示旧条目缺少新的 frontmatter 字段，可以用两种方式回填：
 
 - **推荐：** 打开 AI 对话并运行 `/lumi-migrate-legacy`。
@@ -184,6 +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。 |
@@ -208,7 +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/bin/lumina.js

@@ -199,6 +199,12 @@ program
   .option('--force-locale-switch', 'allow switching installer locale during upgrade')
   .action(async (cmdOpts) => {
     const globalOpts = program.opts();
+    const hasExplicitDirectory = (
+      cmdOpts.directory != null
+      || cmdOpts.cwd != null
+      || globalOpts.directory != null
+      || globalOpts.cwd != null
+    );
     const mergedDir      = cmdOpts.directory ?? cmdOpts.cwd ?? globalOpts.directory ?? globalOpts.cwd ?? process.cwd();
     const mergedYes      = cmdOpts.yes      ?? globalOpts.yes      ?? false;
     const mergedReLink   = cmdOpts.reLink   ?? globalOpts.reLink   ?? false;
@@ -220,6 +226,7 @@ program
         documentOutputLang: cmdOpts.documentOutputLanguage,
         lang: cmdOpts.lang,
         forceLocaleSwitch: Boolean(cmdOpts.forceLocaleSwitch),
+        searchParents: !hasExplicitDirectory,
       });
     } catch (err) {
       // Top-level catch: locale may not be resolved yet (pre-loadLocale path).

package/package.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/package.json",
   "name": "lumina-wiki",
-  "version": "1.6.1",
+  "version": "1.7.0",
   "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",
@@ -88,7 +90,8 @@
   "devDependencies": {},
   "scripts": {
     "test": "npm run test:installer",
-    "test:installer": "node --test bin/lumina.flags.test.js bin/lumina.deprecations.test.js bin/lumina.cancel.test.js src/installer/commands.test.js src/installer/fs.test.js src/installer/locales.test.js src/installer/manifest.test.js src/installer/prompts.test.js src/installer/readme-templates.test.js src/installer/template-engine.test.js src/installer/update-check.test.js",
+    "test:installer": "npm run test:installer:commands && node --test bin/lumina.flags.test.js bin/lumina.deprecations.test.js bin/lumina.cancel.test.js src/installer/fs.test.js src/installer/locales.test.js src/installer/manifest.test.js src/installer/prompts.test.js src/installer/readme-templates.test.js src/installer/template-engine.test.js src/installer/update-check.test.js",
+    "test:installer:commands": "node src/installer/commands.test.js",
     "test:scripts": "node --test src/scripts/lint.test.mjs src/scripts/reset.test.mjs src/scripts/wiki.test.mjs src/scripts/discover-runner.test.mjs src/scripts/external-ids.test.mjs src/scripts/parse-ids.test.mjs src/scripts/merge-ids.test.mjs src/scripts/build-source.test.mjs src/scripts/wiki-yaml-object.test.mjs src/scripts/schemas.test.mjs",
     "test:python": "node scripts/run-pytest.mjs",
     "test:all": "npm run test:installer && npm run test:scripts && npm run test:python",

package/src/installer/commands.js

@@ -127,6 +127,37 @@ const LUMINA_DIRS = [
 
 const VALID_PACKS = new Set(['core', 'research', 'reading', 'learning']);
 const VALID_IDE_TARGETS = new Set(['claude_code', 'codex', 'cursor', 'gemini_cli', 'qwen', 'iflow', 'generic']);
+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_scite.py', 'fetch_altmetric.py',
+];
+
+async function findEnclosingWorkspace(startDir) {
+  let current = resolve(startDir);
+  while (true) {
+    try {
+      await access(join(current, '_lumina', 'manifest.json'), fsConstants.F_OK);
+      return current;
+    } catch (err) {
+      if (err.code !== 'ENOENT' && err.code !== 'ENOTDIR') throw err;
+    }
+    const parent = dirname(current);
+    if (parent === current) return null;
+    current = parent;
+  }
+}
+
+async function readManifestForInstall(projectRoot) {
+  try {
+    return await readManifest(projectRoot);
+  } catch (err) {
+    const e = new Error(`MANIFEST_READ_FAILED: ${err.message} (path: ${projectRoot}/_lumina/manifest.json)`);
+    e.code = 2;
+    throw e;
+  }
+}
 
 // ---------------------------------------------------------------------------
 // install command
@@ -144,32 +175,24 @@ const VALID_IDE_TARGETS = new Set(['claude_code', 'codex', 'cursor', 'gemini_cli
  * @param {string} [opts.projectName]  - Hidden escape hatch; default = basename(directory)
  * @param {string} [opts.communicationLang]
  * @param {string} [opts.documentOutputLang]
+ * @param {boolean} [opts.searchParents] - Find an enclosing Lumina workspace when no directory flag was used
  */
 export async function installCommand(opts = {}) {
   const { yes = false, reLink = false } = opts;
   const initialDir = opts.directory ?? opts.cwd ?? process.cwd();
-  let projectRoot = resolve(initialDir);
+  const requestedRoot = resolve(initialDir);
+  let projectRoot = opts.searchParents
+    ? (await findEnclosingWorkspace(requestedRoot) ?? requestedRoot)
+    : requestedRoot;
   const colors = await getColorFns();
 
   // 1. Read existing manifest at the initial path (upgrade detection)
   // Distinguish ENOENT (fresh install) from real I/O errors. Real errors must
   // bail loud — silently treating them as "fresh install" would let a transient
   // permission failure quietly nuke an existing install.
-  let existingManifest = null;
-  try {
-    existingManifest = await readManifest(projectRoot);
-  } catch (err) {
-    if (err.code === 'ENOENT') {
-      existingManifest = null;
-    } else {
-      // Pre-loadLocale path — intentionally EN-only and machine-readable.
-      const e = new Error(`MANIFEST_READ_FAILED: ${err.message} (path: ${projectRoot}/_lumina/manifest.json)`);
-      e.code = 2;
-      throw e;
-    }
-  }
+  let existingManifest = await readManifestForInstall(projectRoot);
 
-  const isUpgrade = existingManifest !== null;
+  let isUpgrade = existingManifest !== null;
 
   // 2. Collect answers (locale not yet loaded; prompts use EN fallback literals)
   let answers;
@@ -182,13 +205,27 @@ export async function installCommand(opts = {}) {
       cwd: projectRoot,
       existingManifest,
       defaultLocale: opts.lang ?? 'en',
+      resolveDestination: async (directory) => {
+        const manifest = await readManifestForInstall(directory);
+        if (!manifest) return null;
+        return {
+          existingManifest: manifest,
+          answers: await readAnswersFromConfig(directory, manifest),
+        };
+      },
     });
     // Re-resolve projectRoot from the directory the user typed.
     if (answers.directory) {
       projectRoot = resolve(answers.directory);
     }
+    existingManifest = await readManifestForInstall(projectRoot);
+    isUpgrade = existingManifest !== null;
   }
   answers = applyInstallOverrides(answers, opts);
+  const previousSkillRows = isUpgrade
+    ? previousManagedSkillRows(await readSkillsManifest(projectRoot), existingManifest)
+    : [];
+  const previousFileRows = isUpgrade ? await readFilesManifest(projectRoot) : [];
 
   // 2b. Load locale module ONCE after applyInstallOverrides resolves locale.
   const localeMod = await loadLocale(answers.locale ?? 'en');
@@ -209,7 +246,11 @@ export async function installCommand(opts = {}) {
         ?? migrateManifest(existingManifest, MANIFEST_SCHEMA_VERSION).locale
         ?? 'en'
     );
-    if (installedLocale !== answers.locale && !opts.forceLocaleSwitch) {
+    if (
+      installedLocale !== answers.locale
+      && !opts.forceLocaleSwitch
+      && answers.localeSwitchConfirmedFor !== answers.locale
+    ) {
       const e = new Error(
         `LOCALE_SWITCH_REFUSED: installed locale '${installedLocale}' differs from resolved locale '${answers.locale}'. ` +
         `Pass --force-locale-switch to confirm (this will rewrite README.md and IDE stubs in the new locale).`,
@@ -223,6 +264,9 @@ export async function installCommand(opts = {}) {
   const hasResearch = packs.includes('research');
   const hasReading  = packs.includes('reading');
   const hasLearning = packs.includes('learning');
+  const previousProjectRoot = existingManifest?.resolvedPaths?.projectRoot;
+  const relocated = Boolean(previousProjectRoot && resolve(previousProjectRoot) !== projectRoot);
+  const effectiveReLink = reLink || relocated;
 
   console.log('');
   if (isUpgrade) {
@@ -230,6 +274,9 @@ export async function installCommand(opts = {}) {
   } else {
     console.log(colors.bold(t('progress.installing', { dir: projectRoot })));
   }
+  if (relocated) {
+    console.log(colors.yellow(t('warn.relocated', { from: previousProjectRoot, to: projectRoot })));
+  }
 
   // 3. Scaffold directories
   const dirsToCreate = [
@@ -252,6 +299,20 @@ export async function installCommand(opts = {}) {
     await ensureDir(join(projectRoot, dir));
   }
 
+  await reconcileRemovedIdeTargets({
+    projectRoot,
+    previousIdeTargets: existingManifest?.ideTargets ?? [],
+    currentIdeTargets: ideTargets,
+    previousFileRows,
+    previousSkillRows,
+    colors,
+    t,
+  });
+
+  if (isUpgrade && existingManifest?.packs?.research && !hasResearch) {
+    await cleanupRemovedResearchPack(projectRoot, previousFileRows, colors, t);
+  }
+
   // 4. Template variables
   const templateVars = {
     project_name:             projectName,
@@ -282,7 +343,10 @@ export async function installCommand(opts = {}) {
   await copyChangelog(projectRoot);
 
   // 9. Copy skills
-  const skillRows = await copySkills(projectRoot, packs);
+  const skillRows = await copySkills(projectRoot, packs, {
+    claudeCode: ideTargets.includes('claude_code'),
+  });
+  await reconcileRemovedSkills(projectRoot, previousSkillRows, skillRows);
 
   // 10. Copy Python tools (core: extract_pdf; research pack: discovery/fetchers)
   await copyTools(projectRoot, { research: hasResearch });
@@ -307,10 +371,18 @@ export async function installCommand(opts = {}) {
   // 15. Create per-skill symlinks (.claude/skills/lumi-*) for Claude Code
   const symlinkStrategies = {};
   if (ideTargets.includes('claude_code')) {
-    const { strategies } = await createSkillSymlinks(
-      projectRoot, skillRows, existingManifest, reLink, colors, t
+    const { strategies, errors } = await createSkillSymlinks(
+      projectRoot, skillRows, existingManifest, effectiveReLink, colors, t
     );
     Object.assign(symlinkStrategies, strategies);
+    if (errors.length > 0) {
+      const e = new Error(
+        `SKILL_LINKS_INCOMPLETE: ${errors.length} of ${skillRows.length} Claude skill links failed: ` +
+        errors.map(item => `${item.skill}: ${item.error.message}`).join('; '),
+      );
+      e.code = 2;
+      throw e;
+    }
   }
 
   // 16. Build files-manifest rows
@@ -677,7 +749,9 @@ function applyInstallOverrides(answers, opts) {
   const next = { ...answers };
   const priorLocale = answers.locale ?? null;
 
-  // Locale: --lang flag overrides; case-insensitive normalize.
+  // Locale: --lang overrides the interactive selector. Keep the installed
+  // locale in answers.locale until this point so default language values can
+  // cascade correctly when an existing destination is selected.
   // Pre-loadLocale error → EN-only string (chicken-and-egg, machine-readable).
   if (opts.lang !== undefined && opts.lang !== null && opts.lang !== '') {
     const normalized = String(opts.lang).toLowerCase().trim();
@@ -687,9 +761,12 @@ function applyInstallOverrides(answers, opts) {
       throw e;
     }
     next.locale = normalized;
+  } else if (next.selectedLocale) {
+    next.locale = next.selectedLocale;
   } else if (!next.locale) {
     next.locale = 'en';
   }
+  delete next.selectedLocale;
 
   // Cascade: if --lang changed locale and user didn't explicitly pass language
   // overrides, refresh the language defaults to match the new locale.
@@ -929,6 +1006,113 @@ function ideTargetStubFiles(ideTargets) {
     .filter(Boolean);
 }
 
+async function removeManagedFileIfUnchanged(projectRoot, relPath, previousFileRows, colors, t) {
+  const absPath = safePath(projectRoot, relPath);
+  try {
+    await access(absPath, fsConstants.F_OK);
+  } catch (err) {
+    if (err.code === 'ENOENT') return;
+    throw err;
+  }
+
+  const previous = previousFileRows.find(row => row.relative_path === relPath);
+  if (previous?.sha256) {
+    try {
+      if (await fileHash(absPath) === previous.sha256) {
+        await unlink(absPath);
+        return;
+      }
+    } catch (_) {}
+  }
+
+  console.log(colors.yellow(t('warn.preserved_modified_file', { path: relPath })));
+}
+
+function previousManagedSkillRows(previousSkillRows, existingManifest) {
+  const rowsById = new Map(previousSkillRows.map(row => [row.canonical_id, row]));
+  const previousStrategies = existingManifest?.symlinkStrategies ?? {};
+  const claudeWasSelected = existingManifest?.ideTargets?.includes('claude_code') ?? false;
+  const previousPacks = Object.keys(existingManifest?.packs ?? {});
+  for (const skill of getSkillDefs(previousPacks)) {
+    if (!rowsById.has(skill.canonicalId)) {
+      rowsById.set(skill.canonicalId, {
+        canonical_id: skill.canonicalId,
+        relative_path: join('.agents', 'skills', skill.canonicalId),
+        target_link_path: existingManifest?.ideTargets?.includes('claude_code')
+          ? join('.claude', 'skills', skill.canonicalId)
+          : '',
+      });
+    }
+  }
+  for (const canonicalId of Object.keys(previousStrategies)) {
+    if (!rowsById.has(canonicalId)) {
+      rowsById.set(canonicalId, {
+        canonical_id: canonicalId,
+        relative_path: join('.agents', 'skills', canonicalId),
+        target_link_path: join('.claude', 'skills', canonicalId),
+      });
+    }
+  }
+  return [...rowsById.values()].map(row => ({
+    ...row,
+    managed_link: claudeWasSelected
+      || Object.prototype.hasOwnProperty.call(previousStrategies, row.canonical_id),
+  }));
+}
+
+async function removeManagedSkillLink(projectRoot, skill) {
+  if (skill.managed_link === false) return;
+  const relPath = skill.target_link_path || join('.claude', 'skills', skill.canonical_id);
+  await rm(safePath(projectRoot, relPath), { recursive: true, force: true });
+}
+
+async function reconcileRemovedIdeTargets({
+  projectRoot,
+  previousIdeTargets,
+  currentIdeTargets,
+  previousFileRows,
+  previousSkillRows,
+  colors,
+  t,
+}) {
+  const removedTargets = previousIdeTargets.filter(target => !currentIdeTargets.includes(target));
+  for (const target of removedTargets) {
+    if (target === 'claude_code') {
+      await Promise.all(previousSkillRows.map(skill => removeManagedSkillLink(projectRoot, skill)));
+    }
+
+    const relPath = ideTargetStubFiles([target])[0];
+    if (relPath) {
+      await removeManagedFileIfUnchanged(projectRoot, relPath, previousFileRows, colors, t);
+    }
+  }
+}
+
+async function reconcileRemovedSkills(projectRoot, previousSkillRows, currentSkillRows) {
+  const currentIds = new Set(currentSkillRows.map(row => row.canonical_id));
+  const obsolete = previousSkillRows.filter(row => !currentIds.has(row.canonical_id));
+
+  for (const skill of obsolete) {
+    if (skill.relative_path) {
+      await rm(safePath(projectRoot, skill.relative_path), { recursive: true, force: true });
+    }
+    await removeManagedSkillLink(projectRoot, skill);
+  }
+}
+
+async function cleanupRemovedResearchPack(projectRoot, previousFileRows, colors, t) {
+  await Promise.all(RESEARCH_TOOL_FILES.map(file => (
+    rm(safePath(projectRoot, join('_lumina', 'tools', file)), { force: true })
+  )));
+  await removeManagedFileIfUnchanged(
+    projectRoot,
+    '.env.example',
+    previousFileRows,
+    colors,
+    t,
+  );
+}
+
 function buildIdeStub(target, vars) {
   const name = vars.project_name || 'this wiki';
   switch (target) {
@@ -983,7 +1167,7 @@ async function copyChangelog(projectRoot) {
   }
 }
 
-async function copySkills(projectRoot, packs) {
+async function copySkills(projectRoot, packs, { claudeCode = false } = {}) {
   const skillRows = [];
   const skillDefs = getSkillDefs(packs);
 
@@ -1003,7 +1187,7 @@ async function copySkills(projectRoot, packs) {
       pack:            skill.pack,
       source:          'built-in',
       relative_path:   `.agents/skills/${skill.canonicalId}`,
-      target_link_path: join('.claude', 'skills', skill.canonicalId),
+      target_link_path: claudeCode ? join('.claude', 'skills', skill.canonicalId) : '',
       version:         PKG.version,
     });
   }
@@ -1050,6 +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' },
     ];
@@ -1085,13 +1270,7 @@ function getSkillDefs(packs) {
 async function copyTools(projectRoot, { research }) {
   const destDir = join(projectRoot, '_lumina', 'tools');
   const coreTools = ['extract_pdf.py', 'fetch_pdf.py', 'id_utils.py'];
-  const researchTools = [
-    '_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',
-  ];
-  const toolFiles = research ? [...coreTools, ...researchTools] : coreTools;
+  const toolFiles = research ? [...coreTools, ...RESEARCH_TOOL_FILES] : coreTools;
   // Parallelize: each copy is independent and destDir already exists.
   // Sequential awaits were the main Windows cold-start regression in v1.4
   // (~30 ms per file × 14 files dominates on NTFS + Defender).
@@ -1144,6 +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);
@@ -1213,6 +1396,7 @@ async function seedWikiFiles(projectRoot) {
 
 async function createSkillSymlinks(projectRoot, skillRows, existingManifest, reLink, colors, t = null) {
   const strategies = {};
+  const errors = [];
 
   for (const skill of skillRows) {
     const target   = resolve(projectRoot, skill.relative_path);
@@ -1227,6 +1411,7 @@ async function createSkillSymlinks(projectRoot, skillRows, existingManifest, reL
         console.log(colors.yellow(`  [warn] ${result.message}`));
       }
     } catch (err) {
+      errors.push({ skill: skill.canonical_id, error: err });
       const msg = t
         ? t('error.symlink', { skill: skill.canonical_id, message: err.message })
         : `  [error] Failed to link ${skill.canonical_id}: ${err.message}`;
@@ -1234,7 +1419,7 @@ async function createSkillSymlinks(projectRoot, skillRows, existingManifest, reL
     }
   }
 
-  return { strategies };
+  return { strategies, errors };
 }
 
 async function buildFilesManifest(projectRoot, packs, pkgVersion) {