mindlore 0.4.0 → 0.4.2

package/hooks/mindlore-index.cjs

@@ -16,8 +16,10 @@ function main() {
   const filePath = readHookStdin(['path', 'file_path']);
   if (!filePath) return;
 
-  // Only process .md files inside .mindlore/
-  if (!filePath.includes(MINDLORE_DIR) || !filePath.endsWith('.md')) return;
+  // Only process .md files inside .mindlore/ (resolved path check prevents traversal)
+  if (!filePath.endsWith('.md')) return;
+  const resolvedFile = path.resolve(filePath);
+  if (!resolvedFile.includes(path.sep + MINDLORE_DIR + path.sep) && !resolvedFile.includes(path.sep + MINDLORE_DIR)) return;
 
   const fileName = path.basename(filePath);
   if (SKIP_FILES.has(fileName)) return;
@@ -60,18 +62,19 @@ function main() {
     const { meta, body } = parseFrontmatter(content);
     const { slug, description, type, category, title, tags, quality, dateCaptured } = extractFtsMetadata(meta, body, filePath, baseDir);
 
-    // Update FTS5
-    db.prepare('DELETE FROM mindlore_fts WHERE path = ?').run(filePath);
-    insertFtsRow(db, { path: filePath, slug, description, type, category, title, content: body, tags, quality, dateCaptured, project: getProjectName() });
-
-    // Update hash
-    db.prepare(
-      `INSERT INTO file_hashes (path, content_hash, last_indexed)
-       VALUES (?, ?, ?)
-       ON CONFLICT(path) DO UPDATE SET
-         content_hash = excluded.content_hash,
-         last_indexed = excluded.last_indexed`
-    ).run(filePath, hash, new Date().toISOString());
+    // Update FTS5 + hash atomically
+    const updateIndex = db.transaction(() => {
+      db.prepare('DELETE FROM mindlore_fts WHERE path = ?').run(filePath);
+      insertFtsRow(db, { path: filePath, slug, description, type, category, title, content: body, tags, quality, dateCaptured, project: getProjectName() });
+      db.prepare(
+        `INSERT INTO file_hashes (path, content_hash, last_indexed)
+         VALUES (?, ?, ?)
+         ON CONFLICT(path) DO UPDATE SET
+           content_hash = excluded.content_hash,
+           last_indexed = excluded.last_indexed`
+      ).run(filePath, hash, new Date().toISOString());
+    });
+    updateIndex();
   } finally {
     db.close();
   }

package/hooks/mindlore-pre-compact.cjs

@@ -21,8 +21,8 @@ function main() {
   const indexScript = path.join(__dirname, '..', 'scripts', 'mindlore-fts5-index.cjs');
   if (fs.existsSync(indexScript)) {
     try {
-      const { execSync } = require('child_process');
-      execSync(`node "${indexScript}" "${baseDir}"`, {
+      const { spawnSync } = require('child_process');
+      spawnSync('node', [indexScript, baseDir], {
         timeout: 10000,
         stdio: 'pipe',
       });

package/hooks/mindlore-search.cjs

@@ -80,7 +80,9 @@ function searchDb(dbPath, keywords, Database) {
 
       for (const kw of keywords) {
         try {
-          const r = matchStmt.get(row.path, '"' + kw + '"');
+          const sanitized = kw.replace(/["*(){}[\]^~:]/g, '');
+          if (!sanitized) continue;
+          const r = matchStmt.get(row.path, '"' + sanitized + '"');
           if (r) {
             hits++;
             totalRank += r.rank;
@@ -110,7 +112,7 @@ function searchDb(dbPath, keywords, Database) {
  */
 function searchEpisodesFts(db, keywords) {
   try {
-    const ftsQuery = keywords.map(kw => '"' + kw + '"').join(' OR ');
+    const ftsQuery = keywords.map(kw => '"' + kw.replace(/["*(){}[\]^~:]/g, '') + '"').filter(q => q !== '""').join(' OR ');
     const rows = db.prepare(
       "SELECT title, category, slug, tags FROM mindlore_fts WHERE type = 'episode' AND mindlore_fts MATCH ? LIMIT 2"
     ).all(ftsQuery);

package/hooks/mindlore-session-end.cjs

@@ -143,6 +143,9 @@ function main() {
   // v0.4.0: Write bare episode to episodes table
   writeBareEpisode(baseDir, project, commits, changedFiles, reads);
 
+  // Obsidian auto-export (if vault configured)
+  syncObsidian(baseDir);
+
   // Git auto-commit + push for global ~/.mindlore/ only
   syncGlobalRepo();
 }
@@ -220,6 +223,95 @@ function writeBareEpisode(baseDir, project, commits, changedFiles, reads) {
   }
 }
 
+const EXPORT_DIRS = ['analyses', 'decisions', 'diary', 'raw', 'sources', 'domains', 'connections', 'insights', 'learnings'];
+
+/**
+ * Load obsidian-helpers from compiled dist (single source of truth for wikilink conversion).
+ * Returns null if helpers not available (e.g. dev environment without build).
+ */
+function loadObsidianHelpers() {
+  try {
+    // Resolve from package root (hooks/ is sibling to dist/)
+    const hookDir = __dirname;
+    const pkgRoot = path.dirname(hookDir);
+    const helpersPath = path.join(pkgRoot, 'dist', 'scripts', 'lib', 'obsidian-helpers.js');
+    if (!fs.existsSync(helpersPath)) return null;
+    return require(helpersPath);
+  } catch (_err) {
+    return null;
+  }
+}
+
+/**
+ * Export a single .md file to Obsidian vault with wikilink conversion.
+ * Uses obsidian-helpers.convertToWikilinks for consistent behavior.
+ * Returns true if file was exported.
+ */
+function exportMdFile(srcPath, destPath, convertFn) {
+  try {
+    const destStat = fs.statSync(destPath);
+    const srcStat = fs.statSync(srcPath);
+    if (srcStat.mtimeMs <= destStat.mtimeMs) return false;
+  } catch (_err) {
+    // dest doesn't exist — proceed with export
+  }
+  let content = fs.readFileSync(srcPath, 'utf8');
+  content = convertFn(content);
+  fs.writeFileSync(destPath, content, 'utf8');
+  return true;
+}
+
+/**
+ * Auto-export .md files to Obsidian vault if configured.
+ * Skips if no vault configured, vault missing, or nothing changed since last export.
+ */
+function syncObsidian(baseDir) {
+  try {
+    const configPath = path.join(baseDir, 'config.json');
+    if (!fs.existsSync(configPath)) return;
+
+    const config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
+    const vaultPath = config?.obsidian?.vault;
+    if (!vaultPath || typeof vaultPath !== 'string') return;
+    if (!fs.existsSync(vaultPath)) return;
+
+    const helpers = loadObsidianHelpers();
+    // Fallback regex if helpers unavailable (strips path prefixes like the canonical version)
+    const convertFn = helpers?.convertToWikilinks
+      ?? ((c) => c.replace(/\[([^\]]+)\]\((?:\.\.?\/)?(?:[\w-]+\/)*([^/)]+)\.md\)/g, '[[$2]]'));
+
+    const destBase = path.join(vaultPath, 'mindlore');
+    let exported = 0;
+
+    for (const dir of EXPORT_DIRS) {
+      const srcDir = path.join(baseDir, dir);
+      if (!fs.existsSync(srcDir)) continue;
+
+      const destDir = path.join(destBase, dir);
+      if (!fs.existsSync(destDir)) fs.mkdirSync(destDir, { recursive: true });
+
+      for (const file of fs.readdirSync(srcDir).filter(f => f.endsWith('.md') && !f.startsWith('_'))) {
+        if (exportMdFile(path.join(srcDir, file), path.join(destDir, file), convertFn)) exported++;
+      }
+    }
+
+    for (const rootFile of ['INDEX.md', 'log.md']) {
+      const srcPath = path.join(baseDir, rootFile);
+      if (!fs.existsSync(srcPath)) continue;
+      if (!fs.existsSync(destBase)) fs.mkdirSync(destBase, { recursive: true });
+      if (exportMdFile(srcPath, path.join(destBase, rootFile), convertFn)) exported++;
+    }
+
+    if (exported > 0) {
+      config.obsidian.lastExport = new Date().toISOString();
+      config.obsidian.lastExportCount = exported;
+      fs.writeFileSync(configPath, JSON.stringify(config, null, 2), 'utf8');
+    }
+  } catch (err) {
+    process.stderr.write(`[mindlore] obsidian sync failed: ${err?.message ?? err}\n`);
+  }
+}
+
 /**
  * Auto-commit and push ~/.mindlore/ if it has a .git directory.
  * Only runs for the global scope — project .mindlore/ is in the project's own git.

package/hooks/mindlore-session-focus.cjs

@@ -10,13 +10,14 @@
 
 const fs = require('fs');
 const path = require('path');
-const { findMindloreDir, readConfig, openDatabase, hasEpisodesTable, queryRecentEpisodes } = require('./lib/mindlore-common.cjs');
+const { findMindloreDir, readConfig, openDatabase, hasEpisodesTable, queryRecentEpisodes, querySupersededChains, formatSupersededChains, queryMultiSessionEpisodes, formatMultiSessionEpisodes, getAllMdFiles } = require('./lib/mindlore-common.cjs');
 
 function main() {
   const baseDir = findMindloreDir();
   if (!baseDir) return; // No .mindlore/ found, silently skip
 
   const output = [];
+  const config = readConfig(baseDir);
 
   // Inject INDEX.md
   const indexPath = path.join(baseDir, 'INDEX.md');
@@ -41,7 +42,6 @@ function main() {
       }
 
       // Reflect trigger
-      const config = readConfig(baseDir);
       const threshold = config?.reflect?.threshold ?? 5;
       if (diaryFiles.length >= threshold) {
         output.push(`[Mindlore] ${diaryFiles.length} diary entry birikti — \`/mindlore-log reflect\` calistirmayi dusun.`);
@@ -70,7 +70,6 @@ function main() {
     if (db) {
       try {
         if (hasEpisodesTable(db)) {
-          const config = readConfig(baseDir);
           const maxEpisodes = config?.session_focus?.max_episodes ?? 3;
           const project = path.basename(process.cwd());
           const episodes = queryRecentEpisodes(db, { project, limit: maxEpisodes });
@@ -83,6 +82,22 @@ function main() {
             });
             output.push(`[Mindlore Episodes]\n${lines.join('\n')}`);
           }
+
+          // v0.4.1: Enriched multi-session episodes
+          const multiDays = config?.session_focus?.multi_session_days ?? 3;
+          const enriched = queryMultiSessionEpisodes(db, { project, days: multiDays, limit: 20 });
+          if (enriched.length > 0) {
+            const formatted = formatMultiSessionEpisodes(enriched);
+            if (formatted) {
+              output.push(`[Mindlore Recent Activity]\n${formatted}`);
+            }
+          }
+
+          // v0.4.1: Supersedes chain display
+          const chains = querySupersededChains(db, { project, days: 7, limit: 5 });
+          if (chains.length > 0) {
+            output.push(`[Mindlore Supersedes]\n${formatSupersededChains(chains)}`);
+          }
         }
       } finally {
         db.close();
@@ -90,6 +105,18 @@ function main() {
     }
   } catch (_err) { /* graceful skip */ }
 
+  // v0.4.1: Lightweight stale content check (monitors fallback)
+  try {
+    const allFiles = getAllMdFiles(baseDir);
+    const thirtyDaysAgo = Date.now() - (30 * 24 * 60 * 60 * 1000);
+    const staleCount = allFiles.reduce((count, f) => {
+      try { return fs.statSync(f).mtimeMs < thirtyDaysAgo ? count + 1 : count; } catch { return count; }
+    }, 0);
+    if (staleCount > 3) {
+      output.push(`[Mindlore: ${staleCount} dosya 30+ gundur guncellenmemis — \`/mindlore-evolve\` dusun]`);
+    }
+  } catch (_healthErr) { /* skip */ }
+
   if (output.length > 0) {
     process.stdout.write(output.join('\n\n') + '\n');
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "mindlore",
-  "version": "0.4.0",
+  "version": "0.4.2",
   "description": "AI-native knowledge system for Claude Code",
   "type": "commonjs",
   "bin": {

package/plugin.json

@@ -1,42 +1,42 @@
 {
   "name": "mindlore",
   "description": "AI-native knowledge system for Claude Code. Persistent, searchable, evolving knowledge base with FTS5.",
-  "version": "0.3.0",
+  "version": "0.4.2",
   "skills": [
     {
       "name": "mindlore-ingest",
       "path": "skills/mindlore-ingest/SKILL.md",
-      "description": "Add new knowledge sources (URL, text, file, PDF, GitHub repo)"
+      "description": "Add new knowledge sources to .mindlore/ knowledge base. Supports: URL (web page to markdown), text (inline paste), file (local .md/.txt/.pdf), PDF (markitdown extraction), GitHub repo (README + structure analysis). Includes 6-point quality gate: frontmatter validation, slug uniqueness, content length, source_type tagging, quality heuristic assignment, and FTS5 indexing. Auto-generates frontmatter with type, slug, date, tags, and quality fields."
     },
     {
       "name": "mindlore-health",
       "path": "skills/mindlore-health/SKILL.md",
-      "description": "Run 16-point structural health check on .mindlore/ knowledge base"
+      "description": "Run 16-point structural health check on .mindlore/ knowledge base. 12 deterministic script checks: INDEX.md sync, FTS5 row count, frontmatter validation, orphan file detection, slug uniqueness, directory structure, log.md integrity, config.json schema, episodes table health, content-hash dedup status, cross-reference consistency, file naming conventions. 4 LLM-powered checks: domain coverage gaps, stale content detection, tag taxonomy coherence, knowledge graph connectivity."
     },
     {
       "name": "mindlore-query",
       "path": "skills/mindlore-query/SKILL.md",
-      "description": "Search, ask, stats, brief — compounding knowledge pipeline"
+      "description": "Search, ask, stats, brief — compounding knowledge pipeline. Modes: search (FTS5 full-text + episodes recall), ask (LLM-powered Q&A grounded in knowledge base), stats (episode counts, domain coverage, freshness metrics), brief (executive summary of recent activity). Combines FTS5 text search with episodic memory for richer recall. Supports project-scoped and global queries."
     },
     {
       "name": "mindlore-log",
       "path": "skills/mindlore-log/SKILL.md",
-      "description": "Session logging, pattern extraction, wiki updates"
+      "description": "Session logging, pattern extraction, and wiki updates. Modes: diary (LLM session analysis to enriched episodes: decisions, discoveries, frictions, learnings, preferences, events), reflect (scan episodes for recurring patterns, 3-tier confidence assessment, nomination pipeline for rule proposals), status (recent sessions summary with trends), save (structured delta + log.md append + domain wiki update). Episodes-powered since v0.4.0."
     },
     {
       "name": "mindlore-decide",
       "path": "skills/mindlore-decide/SKILL.md",
-      "description": "Record and list decisions with context, alternatives, rationale"
+      "description": "Record and list architectural, tool, format, and strategy decisions with full context. Captures: alternatives considered, rationale, trade-offs, and outcome. Supports supersedes chain — when a decision replaces an older one, links them with reason. Episodes integration: decisions stored as kind:decision episodes with structured body. List mode shows active decisions with supersedes history."
     },
     {
       "name": "mindlore-evolve",
       "path": "skills/mindlore-evolve/SKILL.md",
-      "description": "Knowledge schema co-evolution — scan domains+sources, suggest updates"
+      "description": "Knowledge schema co-evolution — scan domains and sources for inconsistencies, suggest structural updates. Detects: orphaned references, outdated cross-links, missing domain coverage, INDEX.md drift, stale source summaries. Proposes: new domain pages, source updates, INDEX.md reorganization, CLAUDE.md convention changes. Default scope: project + global (--scope project|global|all)."
     },
     {
       "name": "mindlore-explore",
       "path": "skills/mindlore-explore/SKILL.md",
-      "description": "Discover unexpected connections between knowledge sources"
+      "description": "Discover unexpected connections between knowledge sources — undirected exploration mode. Cross-references domains, sources, analyses, and episodes to find non-obvious relationships. Identifies: shared entities across sources, pattern convergence between domains, episodic evidence supporting or contradicting domain claims. Default scope: project + global (--scope project|global|all)."
     }
   ],
   "hooks": [

package/skills/mindlore-evolve/SKILL.md

@@ -11,10 +11,14 @@ Knowledge schema co-evolution. Karpathy's 4th operation (ingest/query/health/**e
 
 ## Scope
 
-Determine target using `getActiveMindloreDir()` logic:
-- Default (no flag): scan project `.mindlore/`
-- `--global`: scan `~/.mindlore/`
-- Never hardcode `.mindlore/` path — always resolve dynamically
+Default: `--scope all` (project + global birlikte taranır).
+Options: `--scope project` | `--scope global` | `--scope all`
+
+1. Determine scope from argument (default: all)
+2. If `all`: scan both project `.mindlore/` and global `~/.mindlore/`
+3. If `project`: scan only project-scoped content (current CWD's `.mindlore/`)
+4. If `global`: scan only global `~/.mindlore/` content
+- Never hardcode `.mindlore/` path — always resolve dynamically via `getActiveMindloreDir()`
 
 ## Trigger
 

package/skills/mindlore-explore/SKILL.md

@@ -11,10 +11,14 @@ Discover unexpected connections between knowledge sources. Undirected exploratio
 
 ## Scope
 
-Determine target using `getActiveMindloreDir()` logic:
-- Default (no flag): explore project `.mindlore/`
-- `--global`: explore `~/.mindlore/` + project cross-reference (most valuable mode)
-- Never hardcode `.mindlore/` path — always resolve dynamically
+Default: `--scope all` (project + global birlikte taranır — en değerli mod).
+Options: `--scope project` | `--scope global` | `--scope all`
+
+1. Determine scope from argument (default: all)
+2. If `all`: explore both project `.mindlore/` and global `~/.mindlore/` + cross-reference
+3. If `project`: explore only project-scoped content (current CWD's `.mindlore/`)
+4. If `global`: explore only global `~/.mindlore/` content
+- Never hardcode `.mindlore/` path — always resolve dynamically via `getActiveMindloreDir()`
 
 ## Trigger
 

package/skills/mindlore-log/SKILL.md

@@ -86,7 +86,16 @@ LLM-driven pattern extraction from episodes → persistent learnings.
    - Recurring frictions (same blocker/error)
    - Discovery patterns (assumptions that keep breaking)
    - Workflow patterns that worked well
-5. **Structured report output:**
+5. **3-Tier Confidence Assessment:**
+   For each detected pattern, count occurrences across episodes:
+
+   | Tekrar | Tier | Aksiyon |
+   |--------|------|---------|
+   | 1x | Note | Sessiz — episode olarak kalır, raporda göster |
+   | 2x | Learning | `kind: learning` episode oluştur, learnings/ dosyasına yaz |
+   | 3x+ | Nomination | `kind: nomination, status: staged, source: reflect` episode oluştur |
+
+6. **Structured report output:**
 
 ```
 ── Reflect Raporu (son {days} gün, {N} episode) ──
@@ -101,25 +110,73 @@ Decisions ({count}):
   - {summary}
 
 Patterns:
-  - "{pattern_description}" → kural adayı
+  - "CO-EVOLUTION sync hatası" → 3x tekrar → NOMINATION (staged)
+  - "ESM import sorunu" → 2x tekrar → LEARNING
+  - "Test mock karmaşıklığı" → 1x → NOTE
 
 Önerilen:
   [ ] {rule} ({repeat_count}x, {confidence} confidence)
 ```
 
-6. User approves → write to `learnings/{topic}.md`
-7. Format: `YAPMA:` / `BEST PRACTICE:` / `KRITIK:` prefixed rules
-8. Update relevant domain page if pattern relates to an existing domain
-9. Mark processed episodes: future reflect skips already-processed timeranges
-10. Append to `log.md`: `| {date} | reflect | {N} episodes processed, {M} learnings written |`
+7. **Nomination oluşturma (3x+ tekrar):**
+   - `kind: nomination`, `status: staged`, `source: reflect`
+   - Body formatı:
+     ```markdown
+     ## Target: learnings
+     ## Rule
+     YAPMA: Schema değişikliğinde tek dosyayı güncelleme — CO-EVOLUTION sync zorunlu
+     ## Evidence
+     - ep-xxx: episodes.ts güncellendi ama common.cjs unutuldu (2026-04-10)
+     - ep-yyy: Aynı hata tekrar (2026-04-12)
+     - ep-zzz: Test'te yakalandı (2026-04-13)
+     ## Confidence
+     3x tekrar, 3 gün içinde
+     ```
+   - Target options: `learnings` | `claude.md` | `domain:{slug}`
+
+8. **Pending nominations check:**
+   Reflect başlarken staged nomination'ları kontrol et:
+   ```sql
+   SELECT id, summary, body, created_at FROM episodes
+   WHERE kind = 'nomination' AND status = 'staged' AND project = ?
+   ORDER BY created_at ASC
+   ```
+   Varsa kullanıcıya sun:
+   ```
+   ── Bekleyen Nomination'lar ({N} adet) ──
+   1. "CO-EVOLUTION sync zorunlu" (staged 2 gün önce)
+      Target: learnings | Confidence: 3x
+   2. "Test before commit" (staged 5 gün önce)
+      Target: claude.md | Confidence: 4x
+
+   Onaylamak istediğin numara(lar)ı seç, veya 'skip' de:
+   ```
+
+9. **Nomination approval flow:**
+   Kullanıcı onaylarsa:
+   - `status: staged → approved`
+   - Target'a göre yaz:
+     - `learnings` → ilgili `learnings/{topic}.md` dosyasına YAPMA/BEST PRACTICE ekle
+     - `claude.md` → ilgili projenin CLAUDE.md'sine kural ekle (kullanıcıya göster, onay al)
+     - `domain:{slug}` → ilgili domain sayfasına ekle
+   Kullanıcı reddederse:
+   - `status: staged → rejected`
+   - Body'ye `## Rejection Reason\n{kullanıcı açıklaması}` ekle
+
+10. User approves new learnings → write to `learnings/{topic}.md`
+11. Format: `YAPMA:` / `BEST PRACTICE:` / `KRITIK:` prefixed rules
+12. Update relevant domain page if pattern relates to an existing domain
+13. Mark processed episodes: future reflect skips already-processed timeranges
+14. Append to `log.md`: `| {date} | reflect | {N} episodes processed, {M} learnings written |`
 
 **Fallback:** Also reads non-archived delta files if episodes table is empty (backward compat with v0.3 deltas).
 
 **Rules:**
-- NEVER write learnings without user approval
+- NEVER write learnings or nominations without user approval
 - Group related patterns into existing topic files (don't create one file per pattern)
 - Reflect scans both project + global diary/ in `--all` mode
 - Deduplication: same pattern found in both episodes and deltas → episodes win
+- Nominations with `status: staged` are hidden from default queries — only reflect sees them
 
 ### status
 

package/templates/config.json

@@ -1,5 +1,5 @@
 {
-  "version": "0.4.0",
+  "version": "0.4.2",
   "models": {
     "ingest": "haiku",
     "evolve": "sonnet",
@@ -10,6 +10,7 @@
     "threshold": 5
   },
   "session_focus": {
-    "max_episodes": 3
+    "max_episodes": 3,
+    "multi_session_days": 3
   }
 }