@djolex999/vir-cli 0.14.1 → 0.16.0

package/dist/search/queryLog.js

@@ -0,0 +1,123 @@
+import { appendFileSync, existsSync, mkdirSync, readFileSync, renameSync, statSync, writeFileSync, } from "node:fs";
+import { homedir } from "node:os";
+import { dirname, join } from "node:path";
+import { isVerified } from "./retriever.js";
+export const QUERY_LOG_PATH = join(homedir(), ".vir", "queries.jsonl");
+// One rotated generation only: at the cap the live file becomes .1 (replacing
+// any previous .1) and a fresh live file starts. Two generations bound the log
+// at ~2×cap while keeping enough history for `vir queries` to be meaningful.
+export const QUERY_LOG_MAX_BYTES = 5 * 1024 * 1024;
+// Written (best-effort) whenever a log append fails, so doctor can surface
+// "queries are happening but the log isn't being written" — the stderr line
+// alone scrolls away, and a silent best-effort is a blind spot.
+export const QUERY_LOG_FAIL_MARKER_PATH = join(homedir(), ".vir", "queries.failed");
+export function formatQueryRecord(input) {
+    return {
+        ts: input.now.toISOString(),
+        source: input.source,
+        query: input.query,
+        type: input.type,
+        method: input.search.method,
+        degraded: input.search.degraded,
+        degradedReason: input.search.degraded ? input.search.embedError : null,
+        provider: input.search.provider,
+        candidates: input.search.candidates,
+        excludedModel: input.search.excludedMismatched,
+        latencyMs: input.latencyMs,
+        hits: input.hits.map((h, i) => ({
+            slug: h.title,
+            rank: i + 1,
+            score: h.score,
+            verified: isVerified(h.content),
+        })),
+    };
+}
+// The one chokepoint both call sites (CLI query, MCP vir_query) wire through:
+// gate on cfg.logQueries, stamp the time, format, append. `append` is
+// injectable for tests only — production callers pass nothing.
+export function recordQueryEvent(event, append = appendQueryLog) {
+    if (!event.logQueries)
+        return;
+    // Outer guard on the WHOLE logging path (format + append): logging must
+    // never throw into a query, no matter what fails. appendQueryLog already
+    // reports its own failures on stderr; anything else dies silently here
+    // rather than failing the query.
+    try {
+        append(formatQueryRecord({
+            source: event.source,
+            query: event.query,
+            type: event.type,
+            hits: event.hits,
+            search: event.search,
+            latencyMs: event.latencyMs,
+            now: new Date(),
+        }));
+    }
+    catch {
+        // best-effort by contract
+    }
+}
+// Best-effort by contract: a log write failure must never fail a query. But
+// never SILENT — on failure it emits one stderr line (stderr only: on the MCP
+// path stdout is the JSON-RPC channel) and stamps the failure marker for
+// doctor. It never touches stdout.
+export function appendQueryLog(rec, opts = {}) {
+    const logPath = opts.logPath ?? QUERY_LOG_PATH;
+    const maxBytes = opts.maxBytes ?? QUERY_LOG_MAX_BYTES;
+    const stderr = opts.stderr ?? ((line) => process.stderr.write(line));
+    try {
+        mkdirSync(dirname(logPath), { recursive: true });
+        rotateIfNeeded(logPath, maxBytes);
+        appendFileSync(logPath, JSON.stringify(rec) + "\n", "utf8");
+    }
+    catch (err) {
+        stderr(`vir: query log write failed: ${err.message}\n`);
+        try {
+            writeFileSync(opts.failMarkerPath ?? QUERY_LOG_FAIL_MARKER_PATH, `${rec.ts} ${err.message}\n`, "utf8");
+        }
+        catch {
+            // marker is itself best-effort — the stderr line already fired
+        }
+    }
+}
+function rotateIfNeeded(logPath, maxBytes) {
+    let size;
+    try {
+        size = statSync(logPath).size;
+    }
+    catch {
+        return; // no live file yet — nothing to rotate
+    }
+    // rename replaces any existing .1, so exactly one generation survives.
+    if (size >= maxBytes)
+        renameSync(logPath, logPath + ".1");
+}
+// Reads the rotated generation first, then the live file, so records come back
+// in chronological order. Malformed lines and missing files are skipped.
+export function readQueryLog(logPath = QUERY_LOG_PATH) {
+    const records = [];
+    for (const p of [logPath + ".1", logPath]) {
+        if (!existsSync(p))
+            continue;
+        let raw;
+        try {
+            raw = readFileSync(p, "utf8");
+        }
+        catch {
+            continue;
+        }
+        for (const line of raw.split("\n")) {
+            const trimmed = line.trim();
+            if (!trimmed)
+                continue;
+            try {
+                records.push(JSON.parse(trimmed));
+            }
+            catch {
+                // skip malformed lines
+            }
+        }
+    }
+    return records;
+}
+//# sourceMappingURL=queryLog.js.map

package/dist/search/queryLog.js.map

@@ -0,0 +1 @@
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package/dist/search/retriever.js

@@ -1,6 +1,8 @@
 import { existsSync, readFileSync, readdirSync, statSync } from "node:fs";
 import { join, relative } from "node:path";
-import { cosineSimilarity, embed, isOllamaAvailable, } from "./embedder.js";
+import { cosineSimilarity } from "./embedder.js";
+import { resolveEmbeddingProvider, } from "./provider.js";
+import { thresholdsFor } from "./thresholds.js";
 const SKIP_FILES = new Set(["index.md", "log.md"]);
 // Directories the TF-IDF walk must never index: derived period summaries
 // (files-only, never in SQLite), human-rejected notes (`vir review` moves
@@ -8,14 +10,16 @@ const SKIP_FILES = new Set(["index.md", "log.md"]);
 // covered separately — rejected notes' recorded paths no longer exist (the
 // content read skips them) and getEmbeddings gates on `archived`.
 const SKIP_DIRS = new Set(["summaries", ".rejected", "archived"]);
-const MIN_EMBEDDING_SCORE = 0.3;
+// Resolved per-model from thresholds.ts — see MODEL_THRESHOLDS.
 // Notes a user has approved via `vir review` carry `verified: true` in their
 // frontmatter. They get a flat ranking boost so human-verified knowledge floats
 // above unverified auto-distillations of comparable relevance. Applied before
 // the topK slice in both the embedding and TF-IDF paths.
 const VERIFIED_BOOST = 0.2;
 // Cheap frontmatter check — true only when the YAML block has `verified: true`.
-function isVerified(raw) {
+// Exported so the query log records per-hit verified status without a second
+// drift-prone reimplementation (the kebabLite lesson).
+export function isVerified(raw) {
     const m = raw.match(/^---\n([\s\S]*?)\n---/);
     if (!m?.[1])
         return false;
@@ -27,8 +31,9 @@ export async function search(cfg, db, query, topK = 8) {
     return (await searchWithOutcome(cfg, db, query, topK)).hits;
 }
 export async function searchWithOutcome(cfg, db, query, topK = 8) {
-    if (await isOllamaAvailable()) {
-        const attempt = await searchByEmbedding(cfg, db, query, topK);
+    const provider = await resolveEmbeddingProvider(cfg.embeddingProvider);
+    if (provider) {
+        const attempt = await searchByEmbedding(cfg, db, query, topK, provider);
         // If embeddings produced at least one match above the floor, take it.
         // Otherwise fall through to TF-IDF: low cosine on every doc means the
         // query is semantically off; lexical overlap might still find a match.
@@ -38,50 +43,82 @@ export async function searchWithOutcome(cfg, db, query, topK = 8) {
                 method: "embedding",
                 degraded: false,
                 embedError: null,
+                excludedMismatched: attempt.excluded,
+                noProvider: false,
+                candidates: attempt.candidates,
+                provider: {
+                    name: provider.name,
+                    model: provider.modelName,
+                    dim: provider.dimensions,
+                },
             };
         }
+        const fallback = searchByTfIdf(cfg, query, topK);
         return {
-            hits: searchByTfIdf(cfg, query, topK),
+            hits: fallback.hits,
             method: "tfidf",
             degraded: attempt.error !== null,
             embedError: attempt.error,
+            excludedMismatched: attempt.excluded,
+            noProvider: false,
+            candidates: fallback.candidates,
+            provider: null,
         };
     }
+    // TF-IDF is the supported floor, not a degraded state — but the caller must
+    // be able to say "no provider" rather than "embeddings failed".
+    const floor = searchByTfIdf(cfg, query, topK);
     return {
-        hits: searchByTfIdf(cfg, query, topK),
+        hits: floor.hits,
         method: "tfidf",
         degraded: false,
         embedError: null,
+        excludedMismatched: 0,
+        noProvider: true,
+        candidates: floor.candidates,
+        provider: null,
     };
 }
-async function searchByEmbedding(cfg, db, query, topK) {
+// Splits an embedding pool into rows comparable with the active model and a
+// count of refusals. Cosine between vectors from different models (or different
+// dimensionalities) is meaningless, so those rows must never enter the ranking.
+export function partitionByEmbeddingModel(rows, activeModel) {
+    const compatible = rows.filter((r) => r.embeddingModel === activeModel);
+    return { compatible, excluded: rows.length - compatible.length };
+}
+async function searchByEmbedding(cfg, db, query, topK, provider) {
     let queryVec;
     try {
-        queryVec = await embed(query);
+        queryVec = await provider.embedQuery(query);
     }
     catch (err) {
-        return { hits: [], error: err.message };
+        return { hits: [], error: err.message, excluded: 0, candidates: 0 };
     }
     const root = vaultRoot(cfg);
     // Sessions, articles, topics, and PDFs are embedded into the same vector
     // space; concat all four so semantic search covers every layer. No layer gets
     // a ranking boost — they compete on cosine like everything else.
-    const rows = [
+    const allRows = [
         ...db.getEmbeddings(root),
         ...db.getArticleEmbeddings(),
         ...db.getTopicEmbeddings(root, cfg.topicsDir),
         ...db.getPdfEmbeddings(),
     ];
+    // Vectors from another model are geometric nonsense against this query —
+    // refuse to compare them. Excluded rows are counted, never silently dropped;
+    // they re-enter search once re-embedded under the active model.
+    const { compatible: rows, excluded } = partitionByEmbeddingModel(allRows, provider.modelName);
     if (rows.length === 0)
-        return { hits: [], error: null };
+        return { hits: [], error: null, excluded, candidates: 0 };
     // Read each candidate's content once, here, so the verified boost can be
     // applied BEFORE the topK slice — a verified note must be able to outrank an
     // unverified one just outside the window. Reads are bounded to docs above the
     // cosine floor (a personal-scale vault), and the content is reused for hits.
+    const minScore = thresholdsFor(provider.modelName).minEmbeddingScore;
     const enriched = [];
     for (const r of rows) {
         const s = cosineSimilarity(queryVec, r.embedding);
-        if (s < MIN_EMBEDDING_SCORE)
+        if (s < minScore)
             continue;
         let content = "";
         try {
@@ -120,7 +157,7 @@ async function searchByEmbedding(cfg, db, query, topK) {
             method: "embedding",
         };
     });
-    return { hits, error: null };
+    return { hits, error: null, excluded, candidates: enriched.length };
 }
 // Maximal Marginal Relevance: greedily reranks a candidate pool to trade off
 // relevance against diversity. lambda is the relevance weight — 1.0 is pure
@@ -160,15 +197,18 @@ export function mmrRerank(candidates, topK, lambda = 0.7) {
 }
 function searchByTfIdf(cfg, query, topK) {
     const docs = loadIndex(cfg);
-    const scored = searchTfIdf(docs, query, topK);
+    // Score everything, slice here: the full match count is the `candidates`
+    // telemetry for the query log. Same sort, same slice — ranking unchanged.
+    const scored = searchTfIdf(docs, query, docs.length);
     const root = vaultRoot(cfg);
-    return scored.map((d) => ({
+    const hits = scored.slice(0, topK).map((d) => ({
         filePath: join(root, d.relPath),
         title: d.title,
         content: d.raw,
         score: d.score,
         method: "tfidf",
     }));
+    return { hits, candidates: scored.length };
 }
 export function vaultRoot(cfg) {
     return join(cfg.vaultPath, cfg.outputDir);
@@ -229,7 +269,11 @@ export function searchTfIdf(docs, query, topK = 8) {
             const df = dfMap.get(term) ?? 0;
             if (df === 0)
                 continue;
-            const idf = Math.log(totalDocs / df);
+            // Smoothed: log(1 + N/df), never zero. Bare log(N/df) is 0 whenever
+            // df === N — which is EVERY term in a single-note vault, making the
+            // first note a new user creates unfindable. log(1+x) → log(x) for
+            // large x, so established-vault rankings are essentially unchanged.
+            const idf = Math.log(1 + totalDocs / df);
             // Normalize TF by doc length so long docs don't dominate.
             const tfNorm = tf / Math.max(1, d.tokens.length);
             score += tfNorm * idf;

package/dist/search/retriever.js.map

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

@@ -0,0 +1,18 @@
+export const MODEL_THRESHOLDS = {
+    "nomic-embed-text": { minEmbeddingScore: 0.3, relatedMinSim: 0.6 },
+    // Calibrated 2026-07-31 by quantile-matching nomic's floors on a real
+    // 389-note vault (20 queries; 75,466 doc-doc pairs). The two models'
+    // DOC-DOC cosine distributions are nearly identical (p50 0.744 vs 0.741,
+    // p90 0.800 vs 0.795), so relatedMinSim carries over unchanged. QUERY-DOC
+    // scores run ~0.15 hotter on bge (its query instruction prefix): nomic's
+    // 0.3 floor sits ~0.12 below its in-domain minimum (0.416), so bge gets
+    // the same margin below its own minimum (0.456) → 0.35. Remaining unknown:
+    // where garbage/out-of-domain queries score under bge — measuring that
+    // distribution against the vault would pin the floor exactly.
+    "bge-small-en-v1.5": { minEmbeddingScore: 0.35, relatedMinSim: 0.6 },
+};
+const FALLBACK = MODEL_THRESHOLDS["nomic-embed-text"];
+export function thresholdsFor(model) {
+    return MODEL_THRESHOLDS[model] ?? FALLBACK;
+}
+//# sourceMappingURL=thresholds.js.map

package/dist/search/thresholds.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"thresholds.js","sourceRoot":"","sources":["../../src/search/thresholds.ts"],"names":[],"mappings":"AAaA,MAAM,CAAC,MAAM,gBAAgB,GAAoC;IAC/D,kBAAkB,EAAE,EAAE,iBAAiB,EAAE,GAAG,EAAE,aAAa,EAAE,GAAG,EAAE;IAClE,sEAAsE;IACtE,qEAAqE;IACrE,yEAAyE;IACzE,0EAA0E;IAC1E,yEAAyE;IACzE,wEAAwE;IACxE,2EAA2E;IAC3E,uEAAuE;IACvE,8DAA8D;IAC9D,mBAAmB,EAAE,EAAE,iBAAiB,EAAE,IAAI,EAAE,aAAa,EAAE,GAAG,EAAE;CACrE,CAAC;AAEF,MAAM,QAAQ,GAAG,gBAAgB,CAAC,kBAAkB,CAAE,CAAC;AAEvD,MAAM,UAAU,aAAa,CAAC,KAAa;IACzC,OAAO,gBAAgB,CAAC,KAAK,CAAC,IAAI,QAAQ,CAAC;AAC7C,CAAC"}

package/dist/state/db.js

@@ -10,6 +10,13 @@ const GATED_SKIP_REASONS = new Set([
     "sidechain-transcript",
     "agent-transcript",
 ]);
+// Every embedding written before provenance existed came from Ollama's
+// nomic-embed-text (the only embedder any vir binary ever had), so legacy rows
+// backfill to this on migration.
+export const LEGACY_EMBEDDING_PROVENANCE = {
+    model: "nomic-embed-text",
+    dim: 768,
+};
 const ADDED_COLUMNS = [
     { name: "content", ddl: "ALTER TABLE sessions ADD COLUMN content TEXT" },
     { name: "category", ddl: "ALTER TABLE sessions ADD COLUMN category TEXT" },
@@ -148,6 +155,35 @@ export class StateDb {
             if (!existing.has(col.name))
                 this.db.exec(col.ddl);
         }
+        // Embedding provenance, all four embedding-bearing tables. Backfill is safe
+        // and idempotent: rows embedded before provenance existed can only have come
+        // from nomic (the sole embedder in every prior release), and the WHERE
+        // clause never touches rows that already carry provenance.
+        for (const table of ["sessions", "articles", "pdfs", "topics"]) {
+            const cols = new Set(this.db.prepare(`PRAGMA table_info(${table})`).all().map((r) => r.name));
+            if (!cols.has("embedding_model")) {
+                this.db.exec(`ALTER TABLE ${table} ADD COLUMN embedding_model TEXT`);
+            }
+            if (!cols.has("embedding_dim")) {
+                this.db.exec(`ALTER TABLE ${table} ADD COLUMN embedding_dim INTEGER`);
+            }
+            this.db.exec(`UPDATE ${table}
+         SET embedding_model = '${LEGACY_EMBEDDING_PROVENANCE.model}',
+             embedding_dim = ${LEGACY_EMBEDDING_PROVENANCE.dim}
+         WHERE embedding IS NOT NULL AND embedding_model IS NULL`);
+        }
+    }
+    // True when `table` carries the provenance columns. The read-only MCP path
+    // skips migrations, so an upgraded-but-never-written DB may lack them; read
+    // paths must degrade to legacy provenance instead of erroring.
+    provenanceCache = new Map();
+    hasProvenance(table) {
+        const cached = this.provenanceCache.get(table);
+        if (cached !== undefined)
+            return cached;
+        const has = this.db.prepare(`PRAGMA table_info(${table})`).all().some((r) => r.name === "embedding_model");
+        this.provenanceCache.set(table, has);
+        return has;
     }
     getByPath(path) {
         return this.db
@@ -451,14 +487,15 @@ export class StateDb {
     // Embedding storage is keyed by sessionId (the JSONL basename), since callers
     // typically have that handy and not the full path. Match suffix-anchored:
     // `path LIKE '%/<sessionId>.jsonl'`.
-    storeEmbedding(sessionId, embedding) {
+    storeEmbedding(sessionId, embedding, provenance) {
         this.db
-            .prepare("UPDATE sessions SET embedding = ? WHERE path LIKE ?")
-            .run(JSON.stringify(embedding), `%/${sessionId}.jsonl`);
+            .prepare("UPDATE sessions SET embedding = ?, embedding_model = ?, embedding_dim = ? WHERE path LIKE ?")
+            .run(JSON.stringify(embedding), provenance.model, provenance.dim, `%/${sessionId}.jsonl`);
     }
     getEmbeddings(vaultRoot) {
+        const prov = this.hasProvenance("sessions");
         const rows = this.db
-            .prepare(`SELECT path, embedding, topic, category, project
+            .prepare(`SELECT path, embedding, topic, category, project${prov ? ", embedding_model, embedding_dim" : ""}
          FROM sessions
          WHERE skipped = 0
            AND error IS NULL
@@ -491,6 +528,8 @@ export class StateDb {
                 project: r.project ?? "",
                 filePath,
                 embedding: vec,
+                embeddingModel: r.embedding_model ?? LEGACY_EMBEDDING_PROVENANCE.model,
+                embeddingDim: r.embedding_dim ?? vec.length,
             });
         }
         return out;
@@ -505,7 +544,7 @@ export class StateDb {
     // would never heal (the 0.8.2-class blind spot, on the UPDATE path).
     updateContent(path, content) {
         this.db
-            .prepare("UPDATE sessions SET content = ?, embedding = NULL WHERE path = ?")
+            .prepare("UPDATE sessions SET content = ?, embedding = NULL, embedding_model = NULL, embedding_dim = NULL WHERE path = ?")
             .run(content, path);
     }
     reset() {
@@ -604,10 +643,10 @@ export class StateDb {
            AND note_path IS NOT NULL`)
             .all();
     }
-    storeArticleEmbedding(path, embedding) {
+    storeArticleEmbedding(path, embedding, provenance) {
         this.db
-            .prepare("UPDATE articles SET embedding = ? WHERE path = ?")
-            .run(JSON.stringify(embedding), path);
+            .prepare("UPDATE articles SET embedding = ?, embedding_model = ?, embedding_dim = ? WHERE path = ?")
+            .run(JSON.stringify(embedding), provenance.model, provenance.dim, path);
     }
     // Article embeddings, shaped like session EmbeddingRow so the retriever can
     // concat both lists. filePath is the stored note path; project is empty
@@ -615,8 +654,9 @@ export class StateDb {
     getArticleEmbeddings() {
         if (!this.hasArticlesTable())
             return [];
+        const prov = this.hasProvenance("articles");
         const rows = this.db
-            .prepare(`SELECT note_path, embedding, title, category
+            .prepare(`SELECT note_path, embedding, title, category${prov ? ", embedding_model, embedding_dim" : ""}
          FROM articles
          WHERE skipped = 0
            AND error IS NULL
@@ -644,6 +684,8 @@ export class StateDb {
                 project: "",
                 filePath: r.note_path,
                 embedding: vec,
+                embeddingModel: r.embedding_model ?? LEGACY_EMBEDDING_PROVENANCE.model,
+                embeddingDim: r.embedding_dim ?? vec.length,
             });
         }
         return out;
@@ -731,10 +773,10 @@ export class StateDb {
            AND note_path IS NOT NULL`)
             .all();
     }
-    storePdfEmbedding(path, embedding) {
+    storePdfEmbedding(path, embedding, provenance) {
         this.db
-            .prepare("UPDATE pdfs SET embedding = ? WHERE path = ?")
-            .run(JSON.stringify(embedding), path);
+            .prepare("UPDATE pdfs SET embedding = ?, embedding_model = ?, embedding_dim = ? WHERE path = ?")
+            .run(JSON.stringify(embedding), provenance.model, provenance.dim, path);
     }
     // PDF embeddings, shaped like session/article EmbeddingRow so the retriever can
     // concat all sources. filePath is the stored note path; project is empty (PDFs
@@ -742,8 +784,9 @@ export class StateDb {
     getPdfEmbeddings() {
         if (!this.hasPdfsTable())
             return [];
+        const prov = this.hasProvenance("pdfs");
         const rows = this.db
-            .prepare(`SELECT note_path, embedding, title, category
+            .prepare(`SELECT note_path, embedding, title, category${prov ? ", embedding_model, embedding_dim" : ""}
          FROM pdfs
          WHERE skipped = 0
            AND error IS NULL
@@ -771,6 +814,8 @@ export class StateDb {
                 project: "",
                 filePath: r.note_path,
                 embedding: vec,
+                embeddingModel: r.embedding_model ?? LEGACY_EMBEDDING_PROVENANCE.model,
+                embeddingDim: r.embedding_dim ?? vec.length,
             });
         }
         return out;
@@ -784,8 +829,9 @@ export class StateDb {
     getTopicEmbeddings(vaultRoot, topicsDir) {
         if (!this.hasTopicsTable())
             return [];
+        const prov = this.hasProvenance("topics");
         const rows = this.db
-            .prepare(`SELECT id, embedding, title
+            .prepare(`SELECT id, embedding, title${prov ? ", embedding_model, embedding_dim" : ""}
          FROM topics
          WHERE embedding IS NOT NULL`)
             .all();
@@ -810,6 +856,8 @@ export class StateDb {
                 project: "",
                 filePath: join(vaultRoot, topicsDir, `${r.id}.md`),
                 embedding: vec,
+                embeddingModel: r.embedding_model ?? LEGACY_EMBEDDING_PROVENANCE.model,
+                embeddingDim: r.embedding_dim ?? vec.length,
             });
         }
         return out;
@@ -872,10 +920,10 @@ export class StateDb {
     // Future-proofing for v0.7.3 (topic-aware retrieval). Stored now so topics
     // are searchable then without a backfill; the retriever does not read these
     // yet — keeping topics out of `vir query` per the plugin-compat contract.
-    storeTopicEmbedding(id, embedding) {
+    storeTopicEmbedding(id, embedding, provenance) {
         this.db
-            .prepare("UPDATE topics SET embedding = ? WHERE id = ?")
-            .run(JSON.stringify(embedding), id);
+            .prepare("UPDATE topics SET embedding = ?, embedding_model = ?, embedding_dim = ? WHERE id = ?")
+            .run(JSON.stringify(embedding), provenance.model, provenance.dim, id);
     }
     close() {
         this.db.close();