@djolex999/vir-cli 0.5.0 → 0.6.1

package/dist/pipeline/writer.js

@@ -1,7 +1,8 @@
 import chalk from "chalk";
 import { appendFileSync, existsSync, mkdirSync, readFileSync, readdirSync, writeFileSync, } from "node:fs";
-import { join } from "node:path";
+import { join, relative } from "node:path";
 import { embeddingForNote, isOllamaAvailableCached, } from "../search/embedder.js";
+import { ARTICLES_SUBDIR, articleRelPath, buildArticleFrontmatter, } from "./articleDistiller.js";
 const CATEGORY_DIR = {
     pattern: "patterns",
     gotcha: "gotchas",
@@ -14,7 +15,7 @@ export class VaultWriter {
     constructor(cfg, db = null) {
         this.root = join(cfg.vaultPath, cfg.outputDir);
         this.db = db;
-        for (const sub of Object.values(CATEGORY_DIR)) {
+        for (const sub of [...Object.values(CATEGORY_DIR), ARTICLES_SUBDIR]) {
             const p = join(this.root, sub);
             if (!existsSync(p))
                 mkdirSync(p, { recursive: true });
@@ -71,23 +72,91 @@ export class VaultWriter {
         }
         return [fullPath];
     }
+    // Write a distilled web article into articles/<slug>.md. Parallel to write()
+    // but uses the article taxonomy + frontmatter, and always preserves the
+    // source URL as a clickable backlink. Returns the note's absolute path.
+    async writeArticle(article, distilled, mode = "append") {
+        const relPath = articleRelPath(article);
+        const fullPath = join(this.root, relPath);
+        const frontmatter = buildArticleFrontmatter(article, distilled);
+        const sourceLine = article.url
+            ? `Source: [${article.title.replace(/[[\]]/g, "")}](${article.url})\n`
+            : "";
+        const header = sourceLine + `Category: [[${distilled.classification.category}]]\n\n`;
+        const body = wikilinkRelated(distilled.markdown);
+        const finalContent = frontmatter + header + body + "\n";
+        writeFileSync(fullPath, finalContent);
+        await this.maybeEmbedArticle(article, finalContent);
+        const indexProject = article.author ?? "web";
+        if (mode === "append") {
+            this.appendIndex({
+                date: (article.publishedAt ?? new Date().toISOString()).slice(0, 10),
+                topic: article.title,
+                category: distilled.classification.category,
+                project: indexProject,
+                relPath,
+            });
+            this.appendLog({
+                ts: new Date().toISOString().slice(0, 16).replace("T", " "),
+                category: distilled.classification.category,
+                topic: article.title,
+                project: indexProject,
+            });
+        }
+        return fullPath;
+    }
+    // Best-effort article embedding — mirrors maybeEmbed() but keyed by the
+    // article's source path in the articles table. Failure never fails a write.
+    async maybeEmbedArticle(article, fileContent) {
+        if (!this.db)
+            return;
+        try {
+            if (!(await isOllamaAvailableCached()))
+                return;
+            const vec = await embeddingForNote(fileContent);
+            if (!vec)
+                return;
+            this.db.storeArticleEmbedding(article.filePath, vec);
+        }
+        catch {
+            // never crash the writer on embedding failure
+        }
+    }
     // Rebuild index.md from scratch off the distilled rows in SQLite, sorted by
     // date descending. Used by the --rewrite-only run so re-rendering notes never
     // appends duplicate index rows. Never touches log.md. No-op without a db.
     regenerateIndex() {
         if (!this.db)
             return;
-        const rows = [...this.db.listDistilled()].sort((a, b) => (b.startedAt ?? "").localeCompare(a.startedAt ?? ""));
+        const entries = [];
+        for (const r of this.db.listDistilled()) {
+            const relPath = join(CATEGORY_DIR[r.category], `${makeSlug(r.topic, r.sessionId)}.md`);
+            entries.push({
+                date: (r.startedAt ?? "").slice(0, 10),
+                topic: r.topic,
+                category: r.category,
+                project: r.project,
+                link: `[[${relPath.replace(/\.md$/, "")}|${r.topic}]]`,
+            });
+        }
+        for (const a of this.db.listArticles()) {
+            if (!a.notePath)
+                continue;
+            const rel = relative(this.root, a.notePath).replace(/\.md$/, "");
+            entries.push({
+                date: (a.published ?? a.distilledAt ?? "").slice(0, 10),
+                topic: a.title,
+                category: a.category,
+                project: a.author ?? "web",
+                link: `[[${rel}|${a.title}]]`,
+            });
+        }
+        entries.sort((x, y) => y.date.localeCompare(x.date));
         const header = "# vir — Distilled Knowledge\n\n" +
             "| Date | Topic | Category | Project | Link |\n" +
             "|------|-------|----------|---------|------|\n";
-        const body = rows
-            .map((r) => {
-            const date = (r.startedAt ?? "").slice(0, 10);
-            const relPath = join(CATEGORY_DIR[r.category], `${makeSlug(r.topic, r.sessionId)}.md`);
-            const link = `[[${relPath.replace(/\.md$/, "")}|${r.topic}]]`;
-            return `| ${date} | ${r.topic} | ${r.category} | ${r.project} | ${link} |`;
-        })
+        const body = entries
+            .map((e) => `| ${e.date} | ${e.topic} | ${e.category} | ${e.project} | ${e.link} |`)
             .join("\n");
         writeFileSync(join(this.root, "index.md"), body.length > 0 ? `${header}${body}\n` : header);
     }
@@ -172,7 +241,7 @@ export class VaultWriter {
     }
     noteCount() {
         let n = 0;
-        for (const sub of Object.values(CATEGORY_DIR)) {
+        for (const sub of [...Object.values(CATEGORY_DIR), ARTICLES_SUBDIR]) {
             const dir = join(this.root, sub);
             if (!existsSync(dir))
                 continue;

package/dist/pipeline/writer.js.map

@@ -1 +1 @@
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package/dist/search/retriever.js

@@ -37,7 +37,9 @@ async function searchByEmbedding(cfg, db, query, topK) {
         return [];
     }
     const root = vaultRoot(cfg);
-    const rows = db.getEmbeddings(root);
+    // Sessions and articles are embedded into the same vector space; concat both
+    // so semantic search (and the type filter in vir_query) covers articles too.
+    const rows = [...db.getEmbeddings(root), ...db.getArticleEmbeddings()];
     if (rows.length === 0)
         return [];
     // Read each candidate's content once, here, so the verified boost can be
@@ -61,19 +63,67 @@ async function searchByEmbedding(cfg, db, query, topK) {
         const score = isVerified(content) ? s + VERIFIED_BOOST : s;
         enriched.push({ row: r, content, score });
     }
-    enriched.sort((a, b) => b.score - a.score);
-    const hits = [];
-    for (const { row, content, score } of enriched.slice(0, topK)) {
-        const rel = relative(root, row.filePath);
-        hits.push({
-            filePath: row.filePath,
+    // MMR reranks the relevance-sorted pool to balance relevance against diversity
+    // so results cover different facets of the query, not 5 near-duplicates. The
+    // candidate has the embedding it needs to diversify; docId carries the file
+    // path through so the hit can be reconstructed. (TF-IDF stays score-only —
+    // too sparse for MMR to help.)
+    const candidates = enriched.map((e) => ({
+        docId: e.row.filePath,
+        score: e.score,
+        embedding: e.row.embedding,
+        content: e.content,
+    }));
+    // `retrievalDiversity` is user-facing (1.0 = pure diversity) so the config
+    // number reads naturally as "how much diversity". mmrRerank uses the standard
+    // MMR convention where lambda is the *relevance* weight, so invert here.
+    const ranked = mmrRerank(candidates, topK, 1 - cfg.retrievalDiversity);
+    return ranked.map((c) => {
+        const rel = relative(root, c.docId);
+        return {
+            filePath: c.docId,
             title: rel.replace(/\.md$/, ""),
-            content,
-            score: Math.round(score * 10000) / 10000,
+            content: c.content,
+            score: Math.round(c.score * 10000) / 10000,
             method: "embedding",
-        });
+        };
+    });
+}
+// Maximal Marginal Relevance: greedily reranks a candidate pool to trade off
+// relevance against diversity. lambda is the relevance weight — 1.0 is pure
+// relevance (MMR collapses to a score sort), 0.0 is pure diversity. The first
+// pick is always pure top relevance; each subsequent pick maximizes
+// `lambda*relevance - (1-lambda)*maxSimToSelected`. O(N*topK) over the pool.
+export function mmrRerank(candidates, topK, lambda = 0.7) {
+    if (candidates.length === 0 || topK <= 0)
+        return [];
+    // Sort a copy so top-1 and the shortcut below are deterministic regardless of
+    // input order; the caller's array is left untouched.
+    const pool = [...candidates].sort((a, b) => b.score - a.score);
+    // Nothing to diversify: fewer candidates than slots, or only one slot.
+    if (pool.length <= topK || topK === 1)
+        return pool.slice(0, topK);
+    const selected = [pool.shift()];
+    while (selected.length < topK && pool.length > 0) {
+        let bestIdx = 0;
+        let bestMmr = -Infinity;
+        for (let i = 0; i < pool.length; i += 1) {
+            const c = pool[i];
+            let maxSim = 0;
+            for (const sel of selected) {
+                const sim = cosineSimilarity(c.embedding, sel.embedding);
+                if (sim > maxSim)
+                    maxSim = sim;
+            }
+            const mmr = lambda * c.score - (1 - lambda) * maxSim;
+            if (mmr > bestMmr) {
+                bestMmr = mmr;
+                bestIdx = i;
+            }
+        }
+        selected.push(pool.splice(bestIdx, 1)[0]);
     }
-    return hits;
+    return selected;
 }
 function searchByTfIdf(cfg, query, topK) {
     const docs = loadIndex(cfg);

package/dist/search/retriever.js.map

@@ -1 +1 @@
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package/dist/state/db.js

@@ -60,6 +60,24 @@ export class StateDb {
         error TEXT
       );
       CREATE INDEX IF NOT EXISTS idx_sessions_hash ON sessions(hash);
+      CREATE TABLE IF NOT EXISTS articles (
+        path TEXT PRIMARY KEY,
+        hash TEXT NOT NULL,
+        processed_at TEXT NOT NULL,
+        skipped INTEGER NOT NULL DEFAULT 0,
+        note_path TEXT,
+        error TEXT,
+        content TEXT,
+        category TEXT,
+        title TEXT,
+        url TEXT,
+        author TEXT,
+        published TEXT,
+        confidence REAL,
+        distilled_at TEXT,
+        embedding TEXT
+      );
+      CREATE INDEX IF NOT EXISTS idx_articles_hash ON articles(hash);
     `);
         this.migrate();
     }
@@ -297,6 +315,121 @@ export class StateDb {
     reset() {
         this.db.exec("DELETE FROM sessions");
     }
+    // ── articles ────────────────────────────────────────────────────────────
+    // Articles live in their own table so the article taxonomy
+    // (concept/technique/reference/opinion) never pollutes session listings,
+    // stats, or the rewrite path. Read methods guard against a missing table:
+    // the read-only MCP path skips migrations, so an install that upgraded but
+    // never ran a writable pass won't have the articles table yet.
+    hasArticlesTable() {
+        try {
+            const r = this.db
+                .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='articles'")
+                .get();
+            return r !== undefined;
+        }
+        catch {
+            return false;
+        }
+    }
+    isArticleProcessed(path, hash) {
+        if (!this.hasArticlesTable())
+            return false;
+        const row = this.db
+            .prepare("SELECT hash FROM articles WHERE path = ?")
+            .get(path);
+        return row !== undefined && row.hash === hash;
+    }
+    recordArticle(opts) {
+        this.db
+            .prepare(`INSERT INTO articles (
+           path, hash, processed_at, skipped, note_path, error,
+           content, category, title, url, author, published,
+           confidence, distilled_at
+         )
+         VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+         ON CONFLICT(path) DO UPDATE SET
+           hash = excluded.hash,
+           processed_at = excluded.processed_at,
+           skipped = excluded.skipped,
+           error = excluded.error,
+           note_path = COALESCE(excluded.note_path, articles.note_path),
+           content = COALESCE(excluded.content, articles.content),
+           category = COALESCE(excluded.category, articles.category),
+           title = COALESCE(excluded.title, articles.title),
+           url = COALESCE(excluded.url, articles.url),
+           author = COALESCE(excluded.author, articles.author),
+           published = COALESCE(excluded.published, articles.published),
+           confidence = COALESCE(excluded.confidence, articles.confidence),
+           distilled_at = COALESCE(excluded.distilled_at, articles.distilled_at)`)
+            .run(opts.path, opts.hash, new Date().toISOString(), opts.skipped ? 1 : 0, opts.notePath ?? null, opts.error ?? null, opts.content ?? null, opts.category ?? null, opts.title ?? null, opts.url ?? null, opts.author ?? null, opts.published ?? null, opts.confidence ?? null, opts.distilledAt ?? null);
+    }
+    listArticles() {
+        if (!this.hasArticlesTable())
+            return [];
+        const rows = this.db
+            .prepare(`SELECT path, note_path, title, url, author, published,
+                category, confidence, distilled_at, content
+         FROM articles
+         WHERE skipped = 0 AND error IS NULL AND content IS NOT NULL`)
+            .all();
+        return rows.map((r) => ({
+            path: r.path,
+            notePath: r.note_path,
+            title: r.title ?? "",
+            url: r.url,
+            author: r.author,
+            published: r.published,
+            category: r.category ?? "",
+            confidence: r.confidence ?? 0,
+            distilledAt: r.distilled_at,
+            content: r.content,
+        }));
+    }
+    storeArticleEmbedding(path, embedding) {
+        this.db
+            .prepare("UPDATE articles SET embedding = ? WHERE path = ?")
+            .run(JSON.stringify(embedding), path);
+    }
+    // Article embeddings, shaped like session EmbeddingRow so the retriever can
+    // concat both lists. filePath is the stored note path; project is empty
+    // (articles have no project), category is the article taxonomy.
+    getArticleEmbeddings() {
+        if (!this.hasArticlesTable())
+            return [];
+        const rows = this.db
+            .prepare(`SELECT note_path, embedding, title, category
+         FROM articles
+         WHERE skipped = 0
+           AND error IS NULL
+           AND embedding IS NOT NULL
+           AND note_path IS NOT NULL`)
+            .all();
+        const out = [];
+        for (const r of rows) {
+            let vec;
+            try {
+                const parsed = JSON.parse(r.embedding);
+                if (!Array.isArray(parsed))
+                    continue;
+                vec = parsed.map((x) => Number(x));
+                if (vec.some((n) => !Number.isFinite(n)))
+                    continue;
+            }
+            catch {
+                continue;
+            }
+            out.push({
+                sessionId: deriveSessionId(r.note_path),
+                topic: r.title ?? "",
+                category: r.category ?? "",
+                project: "",
+                filePath: r.note_path,
+                embedding: vec,
+            });
+        }
+        return out;
+    }
     close() {
         this.db.close();
     }

package/dist/state/db.js.map

@@ -1 +1 @@
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package/dist/ui/display.js

@@ -14,6 +14,11 @@ export const colorForCategory = {
     gotcha: errorColor,
     decision: info,
     tool: warn,
+    // article taxonomy
+    concept: info,
+    technique: success,
+    reference: muted,
+    opinion: accent,
 };
 // ─── glyphs ─────────────────────────────────────────────────────────────────
 export const BULLET = "·";

package/dist/ui/display.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@djolex999/vir-cli",
-  "version": "0.5.0",
+  "version": "0.6.1",
   "description": "An LLM Wiki for Claude Code, in your Obsidian vault.",
   "author": "Djordje Marković <djordje@growthq.rs>",
   "license": "MIT",