neurain 0.1.0-alpha.1 → 0.1.0-alpha.2

package/CHANGELOG.md

@@ -2,6 +2,18 @@
 
 ## Unreleased
 
+- No unreleased changes recorded.
+
+## 0.1.0-alpha.2
+
+- Documentation currency gate: README and development-status version strings are asserted against package.json in readiness; volatile metric snapshots de-hardcoded (verified green in CI, not pinned in docs).
+
+
+## 0.1.0-alpha.1
+
+- Capture: file/asset capture + R2/R4/R6 enrichment (overlap candidates, numeric conflicts, sha256 duplicate detection) ported to the engine.
+- Memory-write: completed the generic ledger-primitive set (appendLine/enqueue/setQueueStatus/appendBlock/writeFileGuarded) so a consumer can forward every fact/task primitive to the engine.
+- Release automation: tag-triggered npm publish via Trusted Publishing (OIDC), a push-CI gate (fast readiness + `npm publish --dry-run`), and a prerelease-never-`latest` dist-tag guard.
 - Expanded the recall markdown corpus to the general area knowledge class (`10_areas/<area>/**`, hubs, area registry), with config-extensible include/exclude (`recall.include`/`recall.exclude`).
 - Added label-based privacy gating (`labels.mjs`): per-file frontmatter `sensitivity`, area baseline from `_area.md`, and boundary-aware path markers exclude private content at index time. Fixes a substring marker that could exclude a whole legitimate folder.
 - Added a routed lexical recall branch (`recall_lexical.mjs`): BM25 + structural/layer/entity/domain/fact-ledger boosts, unioned ahead of exact-token and semantic in hybrid search. Auto-enabled when a search index registry has areas or `--area` is set; off by default on a bare vault.

package/README.md

@@ -126,7 +126,7 @@ The canonical product development snapshot is maintained in:
 - `docs/development-status.en.md`
 - `docs/development-status.kr.md`
 
-As of 2026-06-09 KST, the package is a publish-ready alpha for private beta or alpha user tests. It is not public SaaS GA. The current verified gates are `npm test` 37/37, `node scripts/readiness.mjs --json` score 100, and `npm run readiness -- --json` score 100.
+The package is a publish-ready alpha for private beta or alpha user tests, not public SaaS GA. All gates (`npm test`, the readiness leakage/secret/pack/tarball-install checks, and `npm audit`) run green in CI on every release — see `.github/workflows/release.yml`. The live score is `node scripts/readiness.mjs --json`.
 
 Watch reports are also read-only. They do not start a daemon and do not write durable knowledge. They observe recent text files, event journal entries, recap hints, and lesson candidates so a future review worker can decide what deserves attention.
 
@@ -159,7 +159,7 @@ For multi-area vaults, preview commands do not scan every area by default. Use `
 See also:
 
 - `docs/knowledge-os.en.md`
-- `docs/self-improve-90-roadmap.en.md`
+- `docs/self-improvement-90-roadmap.en.md`
 - `docs/connect-runtime.en.md`
 
 ## Existing Folder Adoption
@@ -188,7 +188,7 @@ It exposes read/capture/scan/preview tools only. It does not silently compile, p
 
 ## Status
 
-This is `0.1.0-alpha.0`. It is not a public SaaS GA release. The alpha exists to prove installability, local-first onboarding, Codex, Claude, Gemini, and Runtime connectivity, plus safety receipts.
+This is `0.1.0-alpha.2`. It is not a public SaaS GA release. The alpha exists to prove installability, local-first onboarding, Codex, Claude, Gemini, and Runtime connectivity, plus safety receipts.
 
 Alpha publish command:
 

package/docs/connect-runtime.en.md

@@ -45,7 +45,7 @@ Safety boundary:
 - Durable Neurain writes still require explicit CLI confirmation.
 - The alpha snippet does not support paths containing newline or control bytes.
 - Scheduler access is read-only and cannot install background jobs or start daemons.
-- Scheduler eval access is read-only and checks trigger precision, trigger recall, no-recursion, private-boundary handling, case-file size limits, and target-root non-write snapshots.
+- Scheduler eval access is read-only and checks trigger precision, trigger recall, no-recursion, private-boundary handling, case-file size limits, temp cleanup, and target-root non-write snapshots.
 - Lifecycle access is read-only through MCP. The runtime can inspect session lineage, while deeper lifecycle event emission uses the separate host-proxy contract below.
 
 ## Lifecycle Boundary

package/docs/connect-runtime.kr.md

@@ -45,7 +45,7 @@ Safety boundary:
 - Durable Neurain write는 여전히 explicit CLI confirmation이 필요합니다.
 - Alpha snippet은 newline 또는 control byte가 포함된 path를 지원하지 않습니다.
 - Scheduler access는 read-only이며 background job을 설치하거나 daemon을 시작할 수 없습니다.
-- Scheduler eval access도 read-only이며 trigger precision, trigger recall, no-recursion, private-boundary handling, case-file size limit, target-root non-write snapshot을 확인합니다.
+- Scheduler eval access도 read-only이며 trigger precision, trigger recall, no-recursion, private-boundary handling, case-file size limit, temp cleanup, target-root non-write snapshot을 확인합니다.
 - Lifecycle access는 MCP에서 read-only입니다. Runtime은 session lineage를 읽을 수 있고, 더 깊은 lifecycle event emission은 아래 host-proxy contract를 사용합니다.
 
 ## Lifecycle Boundary

package/docs/development-status.en.md

@@ -1,9 +1,9 @@
 # Development Status
 
 Version: v0.1
-Last updated: 2026-06-09 KST
-Package: `neurain@0.1.0-alpha.0`
-Latest documented commit: `3496262 Add E24 onboarding and Gemini MCP connector`
+Last updated: 2026-06-14 KST
+Package: `neurain@0.1.0-alpha.2`
+Latest documented commit: `66016ba docs(dev-status): note unified reindex + adopt auto-reindex in the command surface`
 
 This document is the canonical product development snapshot for the public package. It tracks what is shipped, what has evidence, and what must not be claimed yet.
 
@@ -11,16 +11,9 @@ This document is the canonical product development snapshot for the public packa
 
 Neurain is a publish-ready alpha CLI and MCP package. It is ready for private beta or alpha user tests, not public SaaS GA.
 
-Current verified score:
+Current verification: every gate runs green in CI on each release — `npm test`, the full `npm run readiness` suite (leakage/secret scan, `npm audit`, `npm pack --dry-run`, and a temporary tarball-install smoke), and `node scripts/readiness.mjs --json` for the live score. See `.github/workflows/release.yml`.
 
-| Gate | Result |
-|---|---:|
-| `npm test` | 37/37 pass |
-| `node scripts/readiness.mjs --json` | `ok:true`, score `100`, 35 checks |
-| `npm run readiness -- --json` | `ok:true`, score `100` |
-| `npm audit` | 0 vulnerabilities |
-| `npm pack --dry-run` | pass |
-| Temporary tarball install smoke | pass |
+Volatile metrics (exact test counts, readiness scores, check counts) are intentionally NOT pinned in this document — they are verified green in CI, not hand-copied, so this snapshot cannot silently drift from the suite.
 
 ## Shipped Development
 
@@ -28,6 +21,7 @@ Current verified score:
 
 - Starter vault initialization with `neurain init`.
 - Existing folder adoption scan, apply, receipt, and rollback.
+- Unified `reindex` (register areas + per-area index refresh + recall rebuild in one pass; curated indexes are never auto-overwritten); `adopt --apply` auto-reindexes so an adopted folder is registered and searchable in one command.
 - Local doctor, search, capabilities, recap, and wrap preview.
 - Event journal add/list/verify with explicit confirmation.
 - Lesson list, candidates, eval, promotion, and rollback.

package/docs/development-status.kr.md

@@ -1,9 +1,9 @@
 # 개발 진행 상태
 
 Version: v0.1
-Last updated: 2026-06-09 KST
-Package: `neurain@0.1.0-alpha.0`
-Latest documented commit: `3496262 Add E24 onboarding and Gemini MCP connector`
+Last updated: 2026-06-14 KST
+Package: `neurain@0.1.0-alpha.2`
+Latest documented commit: `66016ba docs(dev-status): note unified reindex + adopt auto-reindex in the command surface`
 
 이 문서는 public package 기준의 canonical 개발 상태 스냅샷입니다. 무엇이 shipped인지, 어떤 증거가 있는지, 아직 주장하면 안 되는 것이 무엇인지 함께 기록합니다.
 
@@ -11,16 +11,9 @@ Latest documented commit: `3496262 Add E24 onboarding and Gemini MCP connector`
 
 Neurain은 publish-ready alpha CLI 및 MCP package입니다. private beta 또는 alpha user test에는 들어갈 수 있지만 public SaaS GA는 아닙니다.
 
-현재 검증된 상태:
+현재 검증: 매 릴리스마다 모든 게이트가 CI에서 green으로 통과합니다 — `npm test`, 전체 `npm run readiness`(leakage/secret 스캔, `npm audit`, `npm pack --dry-run`, 임시 tarball-install smoke), 라이브 점수는 `node scripts/readiness.mjs --json`. `.github/workflows/release.yml` 참조.
 
-| Gate | Result |
-|---|---:|
-| `npm test` | 37/37 pass |
-| `node scripts/readiness.mjs --json` | `ok:true`, score `100`, 35 checks |
-| `npm run readiness -- --json` | `ok:true`, score `100` |
-| `npm audit` | 0 vulnerabilities |
-| `npm pack --dry-run` | pass |
-| Temporary tarball install smoke | pass |
+휘발성 지표(정확한 테스트 수·readiness 점수·check 수)는 의도적으로 이 문서에 박지 않습니다 — CI에서 green으로 검증되며 손으로 복사하지 않으므로, 이 스냅샷이 suite와 조용히 어긋나지 않습니다.
 
 ## shipped 개발 범위
 
@@ -28,6 +21,7 @@ Neurain은 publish-ready alpha CLI 및 MCP package입니다. private beta 또는
 
 - `neurain init` starter vault initialization.
 - 기존 폴더 adoption scan, apply, receipt, rollback.
+- 통합 `reindex`(영역 등록 + per-area 색인 새로고침 + recall rebuild를 한 번에; 큐레이티드 색인은 자동 덮어쓰기 안 함); `adopt --apply`가 자동 reindex하여 채택한 폴더가 한 명령으로 등록·검색 가능.
 - local doctor, search, capabilities, recap, wrap preview.
 - 명시적 confirmation이 필요한 event journal add/list/verify.
 - lesson list, candidates, eval, promotion, rollback.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "neurain",
-  "version": "0.1.0-alpha.1",
+  "version": "0.1.0-alpha.2",
   "description": "Local-first Neurain Knowledge OS CLI and MCP connector.",
   "type": "module",
   "license": "Apache-2.0",
@@ -27,7 +27,10 @@
   "scripts": {
     "test": "node --test",
     "pack:dry-run": "npm pack --dry-run",
-    "readiness": "node scripts/readiness.mjs --full"
+    "readiness": "node scripts/readiness.mjs --full",
+    "docs:check": "node scripts/sync-docs.mjs --check",
+    "docs:fix": "node scripts/sync-docs.mjs --write",
+    "version": "node scripts/sync-docs.mjs --write && git add -u README.md CHANGELOG.md docs/development-status.en.md docs/development-status.kr.md"
   },
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.17.5"

package/src/cli.mjs

@@ -36,6 +36,7 @@ import { labelCommand } from './core/label.mjs';
 import { orphansCommand } from './core/orphans.mjs';
 import { hubsCommand } from './core/hubs.mjs';
 import { areaIndexCommand } from './core/area_index.mjs';
+import { reindexCommand } from './core/reindex.mjs';
 import { lintCommand } from './core/lint.mjs';
 import { sessionPulseCommand } from './core/session_pulse.mjs';
 import { syncCommand } from './core/sync.mjs';
@@ -81,6 +82,7 @@ export async function runCli(argv) {
   if (command === 'curator') return render(await curatorCommand(args));
   if (command === 'daemon') return render(await daemonCommand(args));
   if (command === 'recall') return render(await recallCommand(args));
+  if (command === 'reindex') return render(await reindexCommand(args));
   if (command === 'status') return render(await statusCommand(args));
   if (command === 'digest') return render(await digestCommand(args));
   if (command === 'queue') return render(await queueCommand(args));
@@ -180,8 +182,9 @@ function helpText() {
 Usage:
   neurain init <folder> [--area general] [--lang ko|en] [--dry-run]
   neurain onboard <folder> [--lang ko|en] [--host codex|claude|gemini|runtime] [--json]
-  neurain adopt <folder> [--dry-run] [--apply --confirm "<N>건 저장 진행"]
+  neurain adopt <folder> [--dry-run] [--apply --confirm "<N>건 저장 진행"] [--no-reindex]
   neurain adopt --rollback <receipt> [--root <folder>]
+  neurain reindex <folder> [--dry-run] [--json]
   neurain doctor <folder> [--json]
   neurain search <folder> <query> [--top 10] [--json]
   neurain journal list <folder> [--type type] [--top 20] [--json]

package/src/core/adopt.mjs

@@ -3,6 +3,7 @@ import os from 'node:os';
 import path from 'node:path';
 import { absPath, compactStamp, ensureDir, exists, generatedPath, isTextFile, relPath, safeResolve, sha256, slug, timestamp, writeFileNoOverwrite } from './fs.mjs';
 import { inferSensitivityFromPath, secretLike } from './safety.mjs';
+import { reindexCommand } from './reindex.mjs';
 
 const maxFileBytes = 20 * 1024 * 1024;
 const maxFiles = 5000;
@@ -17,6 +18,17 @@ export async function adoptCommand(args) {
       throw new Error(`Apply requires --confirm "${expected}".`);
     }
     scan.apply = applyAdoption(scan, { root: target });
+    // Once the adapters land, register the area and rebuild search in one pass so the
+    // adopted folder is immediately searchable. Best-effort: a reindex hiccup must
+    // never fail the adoption itself, and --no-reindex opts out.
+    if (scan.apply?.ok && !args['no-reindex']) {
+      try {
+        const r = await reindexCommand({ _: [target], json: true });
+        scan.reindex = r.payload || null;
+      } catch (error) {
+        scan.reindex = { ok: false, error: String((error && error.message) || error) };
+      }
+    }
   }
   if (args.json) return { json: true, payload: scan };
   return {
@@ -32,6 +44,7 @@ export async function adoptCommand(args) {
       `- Risks: ${scan.summary.risk_count}`,
       `- Confirmation required: ${scan.confirmation_required}`,
       scan.apply ? `- Apply receipt: ${scan.apply.receipt_path}` : '',
+      scan.reindex ? `- Reindex: ${scan.reindex.ok ? 'registered + searchable' : 'skipped (' + (scan.reindex.error || 'n/a') + ')'}` : '',
     ].filter(Boolean).join('\n'),
   };
 }

package/src/core/area_index.mjs

@@ -130,9 +130,15 @@ function highConfidenceEntities(ctx, area, relFiles) {
     byCanonical.set(low, cur);
   }
 
+  // The recall resolver (recall_intel.resolveAreaPath) reads `source_docs` and always
+  // resolves them against `${area_root}/`, so emit AREA-relative paths under that key.
+  // Evidence outside the area (raw inbox, wiki/entities hubs) can never resolve under
+  // area_root and is hard-excluded from the recall corpus anyway, so drop it here.
+  const areaPrefix = `${ctx.areasDir}/${area}/`;
+  const toAreaRel = (rel) => (rel.startsWith(areaPrefix) ? rel.slice(areaPrefix.length) : null);
   return [...byCanonical.values()]
     .filter((e) => e.confidence === 'high' || e.count >= 2)
-    .map((e) => ({ id: `entity:${area}:${slug(e.canonical)}`, type: e.type, canonical: e.canonical, aliases: [...e.aliases], confidence: e.confidence, evidence_docs: [...e.evidence].slice(0, 5) }));
+    .map((e) => ({ id: `entity:${area}:${slug(e.canonical)}`, type: e.type, canonical: e.canonical, aliases: [...e.aliases], confidence: e.confidence, source_docs: [...e.evidence].map(toAreaRel).filter(Boolean).slice(0, 5) }));
 }
 
 function keywordsFromFolder(name) {
@@ -143,7 +149,7 @@ function domainsFromFolders(ctx, area) {
   if (!fs.existsSync(dir)) return [];
   return fs.readdirSync(dir, { withFileTypes: true })
     .filter((d) => d.isDirectory() && !/^(search-index|_trash|_archive|node_modules)/.test(d.name) && !d.name.startsWith('.'))
-    .map((d) => ({ id: `domain:${area}:${slug(d.name)}`, label: d.name, keywords: keywordsFromFolder(d.name), boost_paths: [`${ctx.areasDir}/${area}/${d.name}`] }))
+    .map((d) => ({ id: `domain:${area}:${slug(d.name)}`, label: d.name, keywords: keywordsFromFolder(d.name), boost_paths: [d.name] }))
     .filter((d) => d.keywords.length);
 }
 
@@ -154,11 +160,23 @@ function saveRegistry(ctx, reg) {
   atomicWriteJson(path.join(ctx.root, ctx.registryPath), reg);
 }
 
+function hasCuratedSource(ctx, area) {
+  const dir = `${ctx.areasDir}/${area}/search-index`;
+  const ents = readJsonSafe(path.join(ctx.root, `${dir}/entities.json`), null);
+  const doms = readJsonSafe(path.join(ctx.root, `${dir}/domain-routing.json`), null);
+  return Array.isArray(ents) && ents.length > 0 && Array.isArray(doms);
+}
+
 function buildArea(ctx, area, { force = false } = {}) {
   const reg = loadRegistry(ctx);
   const existing = reg.areas?.[area];
   if (existing?.curated) return { ok: false, area, error: 'curated index, refusing to overwrite (use the curated source)' };
   if (existing && !force) return { ok: false, area, error: 'already registered; pass --force to rebuild a generated index' };
+  // An unregistered area may still carry hand-written index files on disk; never
+  // clobber them on an unforced build (register them as curated instead).
+  if (!existing && !force && hasCuratedSource(ctx, area)) {
+    return { ok: false, area, error: 'existing index files present; use --register-curated to keep them, or --force to overwrite' };
+  }
 
   const relFiles = areaFiles(ctx, area);
   const entities = highConfidenceEntities(ctx, area, relFiles);
@@ -175,7 +193,9 @@ function buildArea(ctx, area, { force = false } = {}) {
     });
     reg.areas = reg.areas || {};
     const previous = reg.areas[area] || {};
-    reg.areas[area] = { ...previous, area_root: `${ctx.areasDir}/${area}`, index_dir: 'search-index', entities: 'entities.json', domain_routing: 'domain-routing.json', generated: true, signature: sig, path_map: previous.path_map || [] };
+    // generated and curated are mutually exclusive registry states; assert curated:false
+    // so a (re)generated index can never keep a stale curated flag from a prior pass.
+    reg.areas[area] = { ...previous, area_root: `${ctx.areasDir}/${area}`, index_dir: 'search-index', entities: 'entities.json', domain_routing: 'domain-routing.json', generated: true, curated: false, signature: sig, path_map: previous.path_map || [] };
     saveRegistry(ctx, reg);
   }
   return { ok: true, area, entities: entities.length, domains: domains.length, scanned: relFiles.length, signature: sig.slice(0, 12), dry_run: ctx.dryRun };
@@ -199,7 +219,9 @@ function registerCurated(ctx, area, { sensitivity } = {}) {
     const reg = loadRegistry(ctx);
     reg.areas = reg.areas || {};
     const previous = reg.areas[area] || {};
-    reg.areas[area] = { ...previous, area_root: `${ctx.areasDir}/${area}`, index_dir: 'search-index', entities: 'entities.json', domain_routing: 'domain-routing.json', curated: true, ...(sensitivity ? { sensitivity } : {}), signature: sig, path_map: previous.path_map || [] };
+    // Clear any stale generated flag: register-curated must leave a clean curated-only
+    // state (the previous spread would otherwise preserve generated:true and contradict).
+    reg.areas[area] = { ...previous, area_root: `${ctx.areasDir}/${area}`, index_dir: 'search-index', entities: 'entities.json', domain_routing: 'domain-routing.json', curated: true, generated: false, ...(sensitivity ? { sensitivity } : {}), signature: sig, path_map: previous.path_map || [] };
     saveRegistry(ctx, reg);
   }
   return { ok: true, area, mode: 'register-curated', entities: entities.length, domains: domains.length, scanned: relFiles.length, signature: sig.slice(0, 12), sensitivity: sensitivity || null, dry_run: ctx.dryRun };
@@ -237,7 +259,12 @@ function autoTidy(ctx, restampCurated) {
   const { missing, stale_curated, stale_generated } = detect(ctx);
   const reg = loadRegistry(ctx);
   const built = []; const refreshed = []; const restamped_curated = [];
-  for (const area of missing) if (buildArea(ctx, area, {}).ok) built.push(area);
+  for (const area of missing) {
+    // Preserve hand-written index files (register as curated) rather than overwrite
+    // them with a generated starter; only truly empty/absent indexes are built.
+    if (hasCuratedSource(ctx, area)) { if (registerCurated(ctx, area, {}).ok) restamped_curated.push(area); }
+    else if (buildArea(ctx, area, {}).ok) built.push(area);
+  }
   for (const area of stale_generated) if (refresh(ctx, area).ok) refreshed.push(area);
   if (restampCurated) {
     for (const area of stale_curated) {

package/src/core/reindex.mjs

@@ -0,0 +1,48 @@
+import { absPath } from './fs.mjs';
+import { areaIndexCommand } from './area_index.mjs';
+import { rebuildRecall } from './recall.mjs';
+
+// Unified "make the whole vault's search current" orchestration. One command runs the
+// two layers a fresh or just-changed vault needs:
+//   1. per-area indexes: register any unregistered area, refresh stale GENERATED
+//      indexes, and restamp curated signatures. Hand-curated entity/domain files are
+//      never overwritten -- areas that drifted and need human re-curation are reported,
+//      not auto-changed.
+//   2. the FTS5 recall index: rebuilt so all current markdown is searchable.
+// Thin wrapper over existing primitives: idempotent and non-destructive.
+export async function reindexCommand(args) {
+  const root = absPath(args._[0] || args.root || process.cwd());
+  const dryRun = Boolean(args['dry-run']);
+
+  const ai = await areaIndexCommand({ _: [root], detect: true, fix: !dryRun, 'restamp-curated': !dryRun, json: true });
+  const aix = ai.payload || {};
+
+  const recall = await rebuildRecall(root, { dryRun });
+
+  const payload = {
+    ok: recall.ok !== false,
+    command: 'reindex',
+    dry_run: dryRun,
+    area_index: {
+      built: aix.built || [],
+      refreshed: aix.refreshed || [],
+      restamped_curated: aix.restamped_curated || [],
+      needs_recuration: aix.needs_recuration || [],
+    },
+    recall: { indexed_count: recall.indexed_count, durable_write: recall.durable_write },
+  };
+  if (args.json) return { json: true, payload };
+  return {
+    text: [
+      '# Neurain reindex',
+      '',
+      `- Root: ${root}`,
+      `- Dry run: ${dryRun ? 'yes' : 'no'}`,
+      `- Areas registered/built: ${payload.area_index.built.length}`,
+      `- Generated areas refreshed: ${payload.area_index.refreshed.length}`,
+      `- Curated signatures restamped: ${payload.area_index.restamped_curated.length}`,
+      `- Needs hand re-curation: ${payload.area_index.needs_recuration.join(', ') || 'none'}`,
+      `- Recall docs indexed: ${payload.recall.indexed_count ?? '?'}`,
+    ].join('\n'),
+  };
+}