daftari 1.10.0 → 1.11.0

package/CHANGELOG.md

@@ -7,6 +7,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.11.0] - 2026-05-21
+
+### Added
+
+- **`vault_themes` thematic clustering** (#56). New MCP tool surfaces
+  thematic clusters across the vault. For each document the tool mean-pools
+  its chunk embeddings into one vector, L2-normalises, and clusters the
+  resulting per-document set with hand-rolled k-means (k-means++ init,
+  Lloyd's iterations). Default behaviour sweeps k ∈ {10, 15, 20, 25} and
+  picks the k with the best mean silhouette; an explicit `k` argument
+  skips the sweep. Each theme returns a heuristic label (TF-IDF over
+  titles + tags — no LLM call), a coherence score (mean pairwise cosine
+  inside the cluster — `null` for singleton clusters, where there are no
+  pairs to average), representative documents nearest the centroid, the
+  most frequent tags, and `secondaryDocs`: documents whose primary
+  cluster is elsewhere but whose pooled vector also aligns with this
+  theme's centroid (surfaces cross-cutting documents that the hard
+  one-doc-one-theme partition would otherwise hide). Optional
+  `collection` and `tags` filters scope clustering; RBAC drops documents
+  the caller cannot read. Output is deterministic for the same vault
+  (fixed seed). No new storage — reads the existing `chunks` /
+  `embeddings` tables. v1 is one-doc-one-theme at the partition level
+  (`documentCount` still partitions by primary); true multi-theme
+  membership, HDBSCAN, seeded-search/coverage mode, and LLM labels are
+  deferred.
+
 ## [1.10.0] - 2026-05-21
 
 ### Added

package/README.md

@@ -87,6 +87,7 @@ Daftari exposes 13 tools, grouped by layer.
 |------|-------------|
 | `vault_search` | Hybrid BM25 + vector search across the vault, with tunable ranking weights; each hit carries an inline decay assessment. |
 | `vault_search_related` | Find documents thematically related to a given document. |
+| `vault_themes` | Surface thematic clusters across the vault via k-means over document-pooled embeddings. Heuristic labels (TF-IDF), per-theme coherence, representative docs, secondary docs (cross-cutting documents from other clusters that also align here), deterministic output. |
 | `vault_reindex` | Rebuild the SQLite search index from the markdown files. |
 
 **Write safety**

package/dist/server.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,MAAM,EAAE,MAAM,2CAA2C,CAAC;AAEnE,OAAO,EAAE,KAAK,aAAa,EAAe,MAAM,kBAAkB,CAAC;AAOnE,eAAO,MAAM,WAAW,YAAY,CAAC;AAQrC,eAAO,MAAM,cAAc,QAAmB,CAAC;AAK/C,wBAAgB,YAAY,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,GAAE,aAA6B,GAAG,MAAM,CA2D7F"}

package/dist/server.js

@@ -11,6 +11,7 @@ import { guestAccess } from "./access/rbac.js";
 import { curationTools } from "./tools/curation.js";
 import { readTools } from "./tools/read.js";
 import { searchTools } from "./tools/search.js";
+import { themesTools } from "./tools/themes.js";
 import { writeTools } from "./tools/write.js";
 export const SERVER_NAME = "daftari";
 // The version is read from the package manifest so it never drifts from the
@@ -23,7 +24,13 @@ export const SERVER_VERSION = manifest.version;
 // Absent an explicit context the server falls back to the deny-all guest.
 export function createServer(vaultRoot, access = guestAccess()) {
     const server = new Server({ name: SERVER_NAME, version: SERVER_VERSION }, { capabilities: { tools: {} } });
-    const tools = [...readTools, ...searchTools, ...writeTools, ...curationTools];
+    const tools = [
+        ...readTools,
+        ...searchTools,
+        ...themesTools,
+        ...writeTools,
+        ...curationTools,
+    ];
     const byName = new Map(tools.map((t) => [t.name, t]));
     server.setRequestHandler(ListToolsRequestSchema, async () => ({
         tools: tools.map((t) => ({

package/dist/server.js.map

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package/dist/themes/clustering.d.ts

@@ -0,0 +1,30 @@
+export declare function seededRng(seed: number): () => number;
+export declare function l2Normalize(vec: Float32Array): Float32Array;
+export declare function meanPoolL2(vectors: Float32Array[]): Float32Array | null;
+export declare function kmeansPlusPlusInit(data: Float32Array[], k: number, rng: () => number): number[];
+export interface KMeansResult {
+    assignments: number[];
+    centroids: Float32Array[];
+    iterations: number;
+}
+export declare function kmeans(data: Float32Array[], k: number, rng: () => number, maxIter: number): KMeansResult;
+export declare function silhouetteScore(data: Float32Array[], assignments: number[]): number;
+export declare function clusterCoherence(vectors: Float32Array[]): number;
+export interface PickKResult {
+    k: number;
+    silhouette: number;
+    assignments: number[];
+    centroids: Float32Array[];
+}
+export declare function pickK(data: Float32Array[], candidates: number[], rng: () => number, maxIter: number): PickKResult;
+export interface SecondaryMembership {
+    docIndex: number;
+    sim: number;
+}
+export interface SecondaryOptions {
+    delta: number;
+    minSimilarity: number;
+    maxPerDoc: number;
+}
+export declare function selectSecondaryMemberships(vectors: Float32Array[], assignments: number[], centroids: Float32Array[], options: SecondaryOptions): Map<number, SecondaryMembership[]>;
+//# sourceMappingURL=clustering.d.ts.map

package/dist/themes/clustering.d.ts.map

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package/dist/themes/clustering.js

@@ -0,0 +1,439 @@
+// Clustering primitives for vault_themes.
+//
+// All functions are pure. The k-means implementation is hand-rolled (no
+// new dependency) and seeded by a caller-supplied RNG so the same vault
+// produces the same themes across runs.
+//
+// Input vectors are L2-normalised by the caller, so Euclidean distance on
+// the unit sphere is equivalent to cosine distance (1 - cos θ). We use
+// squared Euclidean inside k-means because it is monotonic with Euclidean
+// distance and avoids per-iteration sqrt work.
+//
+// Two distinct quality scores live here and must not be confused:
+//   - silhouetteScore: the internal k-picker. Mean over all points of
+//     (b - a) / max(a, b) where a is mean intra-cluster distance and b is
+//     mean nearest-other-cluster distance. Higher = better separation.
+//   - clusterCoherence: the per-theme number returned in the tool output.
+//     Mean pairwise cosine similarity inside one cluster. Higher = tighter.
+// --- Seeded RNG ------------------------------------------------------------
+// Mulberry32: a 32-bit, single-state PRNG. Cheap, deterministic, sufficient
+// for clustering's stochastic init. Returns numbers in [0, 1). Seed 0 still
+// produces a valid (constant-free) sequence because the increment 0x6D2B79F5
+// keeps the state moving.
+export function seededRng(seed) {
+    let a = seed | 0;
+    return () => {
+        a = (a + 0x6d2b79f5) | 0;
+        let t = a;
+        t = Math.imul(t ^ (t >>> 15), t | 1);
+        t ^= t + Math.imul(t ^ (t >>> 7), t | 61);
+        return ((t ^ (t >>> 14)) >>> 0) / 4294967296;
+    };
+}
+// --- Vector math -----------------------------------------------------------
+// In-place is tempting but every caller wants a fresh array; allocating
+// here avoids surprise mutations.
+export function l2Normalize(vec) {
+    let norm = 0;
+    for (let i = 0; i < vec.length; i++) {
+        const x = vec[i];
+        norm += x * x;
+    }
+    if (norm === 0)
+        return new Float32Array(vec);
+    const inv = 1 / Math.sqrt(norm);
+    const out = new Float32Array(vec.length);
+    for (let i = 0; i < vec.length; i++) {
+        out[i] = vec[i] * inv;
+    }
+    return out;
+}
+// Mean-pool a document's chunk vectors into one vector, then L2-normalise so
+// the result lives on the unit sphere (cosine semantics).
+// Returns null when there is nothing to pool or the pooled vector is zero.
+export function meanPoolL2(vectors) {
+    if (vectors.length === 0)
+        return null;
+    const dim = vectors[0]?.length ?? 0;
+    if (dim === 0)
+        return null;
+    const sum = new Float32Array(dim);
+    let kept = 0;
+    for (const v of vectors) {
+        if (v.length !== dim)
+            continue;
+        kept += 1;
+        for (let i = 0; i < dim; i++)
+            sum[i] = sum[i] + v[i];
+    }
+    if (kept === 0)
+        return null;
+    for (let i = 0; i < dim; i++)
+        sum[i] = sum[i] / kept;
+    // If the mean is the zero vector, l2Normalize returns zeros — surface that
+    // as null so downstream callers skip the document.
+    let norm = 0;
+    for (let i = 0; i < dim; i++) {
+        const x = sum[i];
+        norm += x * x;
+    }
+    if (norm === 0)
+        return null;
+    return l2Normalize(sum);
+}
+function squaredEuclidean(a, b) {
+    let acc = 0;
+    const n = Math.min(a.length, b.length);
+    for (let i = 0; i < n; i++) {
+        const d = a[i] - b[i];
+        acc += d * d;
+    }
+    return acc;
+}
+function cosineSimilarityNormalized(a, b) {
+    let dot = 0;
+    const n = Math.min(a.length, b.length);
+    for (let i = 0; i < n; i++)
+        dot += a[i] * b[i];
+    return dot;
+}
+// Euclidean distance on the unit sphere is monotonic with cosine distance.
+// We expose it as the public distance for silhouette so the score is on the
+// same scale callers expect.
+function euclideanDistance(a, b) {
+    return Math.sqrt(squaredEuclidean(a, b));
+}
+// --- k-means++ initialisation ---------------------------------------------
+// Picks k initial centroid INDICES from `data` using the k-means++ rule:
+// the first centroid is uniform-random; each subsequent centroid is sampled
+// with probability proportional to D(x)^2, where D(x) is the squared distance
+// from x to the nearest already-chosen centroid.
+//
+// Falls back to a uniform draw if the weighted total is zero (degenerate
+// data with all duplicates) so we always return k distinct indices when
+// k ≤ data.length.
+export function kmeansPlusPlusInit(data, k, rng) {
+    const n = data.length;
+    if (k <= 0 || n === 0)
+        return [];
+    const seeds = [];
+    const taken = new Set();
+    // First centroid: uniform-random.
+    const firstIdx = Math.floor(rng() * n);
+    const first = firstIdx >= n ? n - 1 : firstIdx;
+    seeds.push(first);
+    taken.add(first);
+    // For each remaining slot, compute D(x)^2 for every point against the
+    // closest already-picked centroid and sample one index weighted by D^2.
+    const dSquared = new Float64Array(n);
+    for (let i = 0; i < n; i++) {
+        dSquared[i] = squaredEuclidean(data[i], data[first]);
+    }
+    while (seeds.length < Math.min(k, n)) {
+        let total = 0;
+        for (let i = 0; i < n; i++) {
+            if (!taken.has(i))
+                total += dSquared[i];
+        }
+        let chosen = -1;
+        if (total === 0) {
+            // All untaken points coincide with an existing centroid (or there are
+            // duplicates). Pick the first untaken index uniformly so we still
+            // return k distinct seeds.
+            for (let i = 0; i < n; i++) {
+                if (!taken.has(i)) {
+                    chosen = i;
+                    break;
+                }
+            }
+        }
+        else {
+            let target = rng() * total;
+            for (let i = 0; i < n; i++) {
+                if (taken.has(i))
+                    continue;
+                target -= dSquared[i];
+                if (target <= 0) {
+                    chosen = i;
+                    break;
+                }
+            }
+            if (chosen === -1) {
+                // Numeric drift across the loop; pick the last untaken candidate.
+                for (let i = n - 1; i >= 0; i--) {
+                    if (!taken.has(i)) {
+                        chosen = i;
+                        break;
+                    }
+                }
+            }
+        }
+        if (chosen === -1)
+            break;
+        seeds.push(chosen);
+        taken.add(chosen);
+        // Update each point's D^2 to the nearest of the (now larger) centroid set.
+        const chosenVec = data[chosen];
+        for (let i = 0; i < n; i++) {
+            const d = squaredEuclidean(data[i], chosenVec);
+            if (d < dSquared[i])
+                dSquared[i] = d;
+        }
+    }
+    return seeds;
+}
+// Standard Lloyd's iterations until assignments stabilise or `maxIter` is
+// reached. k is clamped to data.length: clustering 4 documents into 10
+// groups is undefined; instead we just return at most data.length clusters.
+export function kmeans(data, k, rng, maxIter) {
+    const n = data.length;
+    if (n === 0)
+        return { assignments: [], centroids: [], iterations: 0 };
+    const effectiveK = Math.max(1, Math.min(k, n));
+    const dim = data[0].length;
+    const seedIdxs = kmeansPlusPlusInit(data, effectiveK, rng);
+    let centroids = seedIdxs.map((i) => {
+        const src = data[i];
+        const copy = new Float32Array(src.length);
+        for (let j = 0; j < src.length; j++)
+            copy[j] = src[j];
+        return copy;
+    });
+    const assignments = new Array(n).fill(0);
+    let iterations = 0;
+    for (let iter = 0; iter < maxIter; iter++) {
+        iterations = iter + 1;
+        let changed = false;
+        // Assign step.
+        for (let i = 0; i < n; i++) {
+            const point = data[i];
+            let bestC = 0;
+            let bestD = Number.POSITIVE_INFINITY;
+            for (let c = 0; c < centroids.length; c++) {
+                const d = squaredEuclidean(point, centroids[c]);
+                if (d < bestD) {
+                    bestD = d;
+                    bestC = c;
+                }
+            }
+            if (assignments[i] !== bestC) {
+                assignments[i] = bestC;
+                changed = true;
+            }
+        }
+        // Update step.
+        const sums = Array.from({ length: centroids.length }, () => new Float32Array(dim));
+        const counts = new Array(centroids.length).fill(0);
+        for (let i = 0; i < n; i++) {
+            const c = assignments[i];
+            counts[c] = counts[c] + 1;
+            const sum = sums[c];
+            const point = data[i];
+            for (let d = 0; d < dim; d++)
+                sum[d] = sum[d] + point[d];
+        }
+        const newCentroids = [];
+        for (let c = 0; c < centroids.length; c++) {
+            const count = counts[c];
+            if (count === 0) {
+                // Empty cluster: keep the previous centroid in place rather than
+                // re-seeding. Re-seeding mid-run would defeat determinism.
+                newCentroids.push(centroids[c]);
+                continue;
+            }
+            const sum = sums[c];
+            const next = new Float32Array(dim);
+            for (let d = 0; d < dim; d++)
+                next[d] = sum[d] / count;
+            newCentroids.push(next);
+        }
+        centroids = newCentroids;
+        if (!changed)
+            break;
+    }
+    // Final assignment pass on the converged centroids so callers don't see
+    // a stale assignment vector from before the last update step.
+    for (let i = 0; i < n; i++) {
+        const point = data[i];
+        let bestC = 0;
+        let bestD = Number.POSITIVE_INFINITY;
+        for (let c = 0; c < centroids.length; c++) {
+            const d = squaredEuclidean(point, centroids[c]);
+            if (d < bestD) {
+                bestD = d;
+                bestC = c;
+            }
+        }
+        assignments[i] = bestC;
+    }
+    return { assignments, centroids, iterations };
+}
+// --- Silhouette (k-picker) ------------------------------------------------
+// Mean silhouette over all points. For each point i:
+//   a(i) = mean distance from i to other points in the same cluster
+//   b(i) = min over other clusters C of (mean distance from i to points in C)
+//   s(i) = (b - a) / max(a, b)
+// Singleton clusters contribute 0. With only one cluster the score is 0
+// (no contrast).
+export function silhouetteScore(data, assignments) {
+    const n = data.length;
+    if (n === 0 || n !== assignments.length)
+        return 0;
+    const clusters = new Map();
+    for (let i = 0; i < n; i++) {
+        const c = assignments[i];
+        const list = clusters.get(c);
+        if (list)
+            list.push(i);
+        else
+            clusters.set(c, [i]);
+    }
+    if (clusters.size < 2)
+        return 0;
+    let total = 0;
+    for (let i = 0; i < n; i++) {
+        const ci = assignments[i];
+        const own = clusters.get(ci);
+        if (!own || own.length <= 1) {
+            // Singleton: silhouette defined as 0.
+            continue;
+        }
+        // a(i): mean distance to other own-cluster members.
+        let aSum = 0;
+        let aCount = 0;
+        for (const j of own) {
+            if (j === i)
+                continue;
+            aSum += euclideanDistance(data[i], data[j]);
+            aCount += 1;
+        }
+        const a = aSum / aCount;
+        // b(i): min over other clusters of mean distance.
+        let b = Number.POSITIVE_INFINITY;
+        for (const [cj, members] of clusters) {
+            if (cj === ci)
+                continue;
+            let s = 0;
+            for (const j of members) {
+                s += euclideanDistance(data[i], data[j]);
+            }
+            const mean = s / members.length;
+            if (mean < b)
+                b = mean;
+        }
+        const denom = Math.max(a, b);
+        if (denom === 0)
+            continue;
+        total += (b - a) / denom;
+    }
+    return total / n;
+}
+// --- Coherence (per-theme score) ------------------------------------------
+// Mean pairwise cosine similarity inside one cluster. Vectors are assumed
+// L2-normalised, so cosine reduces to a dot product. Range is [-1, 1] in
+// general; for unit-sphere embeddings produced by sentence-transformers it
+// tends to fall in [0, 1].
+export function clusterCoherence(vectors) {
+    if (vectors.length === 0)
+        return 0;
+    if (vectors.length === 1)
+        return 1;
+    let total = 0;
+    let pairs = 0;
+    for (let i = 0; i < vectors.length; i++) {
+        for (let j = i + 1; j < vectors.length; j++) {
+            total += cosineSimilarityNormalized(vectors[i], vectors[j]);
+            pairs += 1;
+        }
+    }
+    if (pairs === 0)
+        return 0;
+    return total / pairs;
+}
+// Runs k-means for each k in `candidates`, computes silhouette, and returns
+// the run with the highest score. Candidates are clamped to data.length and
+// deduped; this is what handles the "tiny vault" edge case — if the user
+// requested k ∈ {10, 15, 20, 25} but only has 8 documents, we end up running
+// k-means at k=8 and stop.
+export function pickK(data, candidates, rng, maxIter) {
+    const n = data.length;
+    const seen = new Set();
+    const ks = [];
+    for (const c of candidates) {
+        const clamped = Math.max(1, Math.min(c, n));
+        if (!seen.has(clamped)) {
+            seen.add(clamped);
+            ks.push(clamped);
+        }
+    }
+    if (ks.length === 0)
+        ks.push(Math.min(1, n));
+    let best = null;
+    for (const k of ks) {
+        const { assignments, centroids } = kmeans(data, k, rng, maxIter);
+        const score = silhouetteScore(data, assignments);
+        if (!best || score > best.silhouette) {
+            best = { k, silhouette: score, assignments, centroids };
+        }
+    }
+    // `best` is non-null because ks has at least one entry.
+    return best;
+}
+// For each doc, finds the clusters (other than its primary) whose centroid
+// is close enough that the doc plausibly belongs there too. Returns a map
+// from cluster index → ordered (by sim desc) list of secondary docs.
+//
+// This implements the "soft reporting" path on top of the hard partition
+// produced by k-means: `documentCount` still partitions by primary, but
+// the secondary list surfaces the cross-cutting documents the partition
+// hides. See `docs/architecture.md` for the rationale.
+export function selectSecondaryMemberships(vectors, assignments, centroids, options) {
+    const out = new Map();
+    const { delta, minSimilarity, maxPerDoc } = options;
+    if (vectors.length === 0 || centroids.length < 2 || maxPerDoc <= 0)
+        return out;
+    for (let i = 0; i < vectors.length; i++) {
+        const vec = vectors[i];
+        const primary = assignments[i];
+        const primaryCentroid = centroids[primary];
+        if (!primaryCentroid)
+            continue;
+        const primarySim = cosineSimilarityNormalized(vec, primaryCentroid);
+        // Score every non-primary cluster; collect those passing both bars.
+        const candidates = [];
+        for (let c = 0; c < centroids.length; c++) {
+            if (c === primary)
+                continue;
+            const cv = centroids[c];
+            if (!cv)
+                continue;
+            const sim = cosineSimilarityNormalized(vec, cv);
+            if (sim < minSimilarity)
+                continue;
+            if (sim < primarySim - delta)
+                continue;
+            candidates.push({ cluster: c, sim });
+        }
+        if (candidates.length === 0)
+            continue;
+        // Take the doc's top `maxPerDoc` secondaries (highest-sim wins ties
+        // first; stable cluster index for a deterministic ordering otherwise).
+        candidates.sort((a, b) => b.sim - a.sim || a.cluster - b.cluster);
+        const top = candidates.slice(0, maxPerDoc);
+        for (const { cluster, sim } of top) {
+            const list = out.get(cluster);
+            const entry = { docIndex: i, sim };
+            if (list)
+                list.push(entry);
+            else
+                out.set(cluster, [entry]);
+        }
+    }
+    // Order each cluster's secondaries by sim desc; stable on docIndex so the
+    // map serialises deterministically across runs.
+    for (const list of out.values()) {
+        list.sort((a, b) => b.sim - a.sim || a.docIndex - b.docIndex);
+    }
+    return out;
+}
+//# sourceMappingURL=clustering.js.map

package/dist/themes/clustering.js.map

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package/dist/tools/search.d.ts

@@ -2,7 +2,10 @@ import { type AccessContext } from "../access/rbac.js";
 import { type Result } from "../frontmatter/types.js";
 import { type HybridSearchResult, type RelatedSearchResult } from "../search/hybrid.js";
 import { type ReindexResult } from "../search/reindex.js";
+import { type IndexDb } from "../storage/index-db.js";
 import type { ToolDefinition } from "./read.js";
+export declare function openIndexForActiveProvider(vaultRoot: string): Result<IndexDb, Error>;
+export declare function ensureIndexReady(vaultRoot: string): Promise<Result<void, Error>>;
 export declare function vaultSearch(vaultRoot: string, args: Record<string, unknown>, access?: AccessContext): Promise<Result<HybridSearchResult, Error>>;
 export declare function vaultSearchRelated(vaultRoot: string, args: Record<string, unknown>, access?: AccessContext): Promise<Result<RelatedSearchResult, Error>>;
 export interface VaultReindexResult extends ReindexResult {

package/dist/tools/search.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/tools/search.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,KAAK,aAAa,EAAW,MAAM,mBAAmB,CAAC;AAChE,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAC/D,OAAO,EAEL,KAAK,kBAAkB,EAGvB,KAAK,mBAAmB,EAEzB,MAAM,qBAAqB,CAAC;AAQ7B,OAAO,EAAE,KAAK,aAAa,EAAgB,MAAM,sBAAsB,CAAC;AAGxE,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,WAAW,CAAC;AA0EhD,wBAAsB,WAAW,CAC/B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CA2B5C;AAMD,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CAAC,CA2B7C;AAMD,MAAM,WAAW,kBAAmB,SAAQ,aAAa;IACvD,KAAK,EAAE,MAAM,CAAC;CACf;AAED,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CAahG;AAgBD,eAAO,MAAM,WAAW,EAAE,cAAc,EA2DvC,CAAC"}
+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/tools/search.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,KAAK,aAAa,EAAW,MAAM,mBAAmB,CAAC;AAChE,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAC/D,OAAO,EAEL,KAAK,kBAAkB,EAGvB,KAAK,mBAAmB,EAEzB,MAAM,qBAAqB,CAAC;AAQ7B,OAAO,EAAE,KAAK,aAAa,EAAgB,MAAM,sBAAsB,CAAC;AAExE,OAAO,EAAiB,KAAK,OAAO,EAAe,MAAM,wBAAwB,CAAC;AAClF,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,WAAW,CAAC;AAShD,wBAAgB,0BAA0B,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAC,OAAO,EAAE,KAAK,CAAC,CAEpF;AAgBD,wBAAsB,gBAAgB,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAsBtF;AA+BD,wBAAsB,WAAW,CAC/B,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CA2B5C;AAMD,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CAAC,CA2B7C;AAMD,MAAM,WAAW,kBAAmB,SAAQ,aAAa;IACvD,KAAK,EAAE,MAAM,CAAC;CACf;AAED,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CAahG;AAgBD,eAAO,MAAM,WAAW,EAAE,cAAc,EA2DvC,CAAC"}

package/dist/tools/search.js

@@ -16,7 +16,10 @@ import { documentCount, openIndexDb } from "../storage/index-db.js";
 // table matches the embeddings the search will query. A read-only tool
 // that opens after a provider switch would otherwise face a vec table
 // sized for the *previous* provider's vectors.
-function openIndexForActiveProvider(vaultRoot) {
+//
+// Exported so other index-backed tools (vault_themes) reuse the same
+// dim-aware open path.
+export function openIndexForActiveProvider(vaultRoot) {
     return openIndexDb(vaultRoot, getProvider().dim);
 }
 // Gate every index-backed tool on the current indexing state.
@@ -30,7 +33,10 @@ function openIndexForActiveProvider(vaultRoot) {
 //   through main(), or a vault whose .daftari directory was wiped) trigger
 //   a synchronous reindex so search still works without an explicit
 //   --reindex step.
-async function ensureIndexReady(vaultRoot) {
+//
+// Exported so other index-backed tools (vault_themes) reuse the same
+// readiness gate.
+export async function ensureIndexReady(vaultRoot) {
     const status = getIndexStatus();
     if (status.status === "indexing") {
         return err(new Error(indexingBusyMessage(status)));

package/dist/tools/search.js.map

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package/dist/tools/themes.d.ts

@@ -0,0 +1,21 @@
+import { type AccessContext } from "../access/rbac.js";
+import { type Result } from "../frontmatter/types.js";
+import type { ToolDefinition } from "./read.js";
+export interface VaultTheme {
+    label: string;
+    documentCount: number;
+    coherence: number | null;
+    representativeDocs: string[];
+    secondaryDocs: string[];
+    relatedTags: string[];
+}
+export interface VaultThemesResult {
+    themes: VaultTheme[];
+    totalDocuments: number;
+    skippedDocuments: number;
+    selectedK: number;
+    clusteredAt: string;
+}
+export declare function vaultThemes(vaultRoot: string, args: Record<string, unknown>, access?: AccessContext): Promise<Result<VaultThemesResult, Error>>;
+export declare const themesTools: ToolDefinition[];
+//# sourceMappingURL=themes.d.ts.map

package/dist/tools/themes.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/themes.js

@@ -0,0 +1,425 @@
+// vault_themes — thematic clustering over document-pooled embeddings.
+//
+// Cluster DOCUMENTS, not chunks: for each document we mean-pool its chunk
+// embeddings into one vector, L2-normalise it, and cluster the resulting
+// ~N-doc set. ~3.5k document vectors instead of ~44k chunk vectors makes
+// every algorithm cheap (silhouette becomes tractable on the full set; no
+// sampling needed at this scale).
+//
+// v1 constraints (locked):
+//   - One-doc-one-theme. Each document lives in exactly one cluster.
+//   - Heuristic labels from TF-IDF over titles + tags. No LLM call.
+//   - No new storage — the tool is read-only against the existing
+//     embeddings / chunks / documents tables.
+//   - Default k-sweep over {10, 15, 20, 25}; an explicit `k` argument
+//     skips the sweep.
+//   - Deterministic via a fixed seed for the k-means RNG.
+import { canRead } from "../access/rbac.js";
+import { err, ok } from "../frontmatter/types.js";
+import { getProvider } from "../search/vector.js";
+import { blobToEmbedding } from "../storage/index-db.js";
+import { clusterCoherence, kmeans, meanPoolL2, pickK, seededRng, selectSecondaryMemberships, } from "../themes/clustering.js";
+import { ensureIndexReady, openIndexForActiveProvider } from "./search.js";
+// Fixed seed for the k-means RNG. The whole point of vault_themes is that
+// the same vault produces the same themes — a random seed would give the
+// user different themes every run and erode trust in the output.
+const THEMES_RNG_SEED = 0x7da17f1; // arbitrary; constant is what matters
+// Default k-sweep range (from the issue dialogue). Each is clamped to the
+// number of clusterable documents inside pickK.
+const DEFAULT_K_CANDIDATES = [10, 15, 20, 25];
+// k-means iteration cap. Documents on the unit sphere converge fast in
+// practice; this is a safety bound for pathological inputs.
+const KMEANS_MAX_ITER = 50;
+// Representative-doc count returned per theme. 5 is enough to be useful in
+// the UI without dragging in marginal members.
+const REPRESENTATIVE_DOCS_PER_THEME = 5;
+// Tag-frequency cutoff per theme. Five most-common tags is enough signal
+// without burying the user in noise.
+const RELATED_TAGS_PER_THEME = 5;
+// Secondary-membership tuning. A doc qualifies as a secondary member of a
+// non-primary cluster when its centroid similarity is BOTH within DELTA of
+// the primary AND above MIN_ABS_SIMILARITY. The cap prevents a centroid-
+// of-mass doc from showing up in every cluster. Defaults are deliberately
+// conservative — secondaries should surface cross-cutting docs, not bury
+// the primary signal.
+const SECONDARY_DELTA = 0.1;
+const SECONDARY_MIN_SIMILARITY = 0.5;
+const SECONDARY_MAX_PER_DOC = 2;
+// Hard cap on secondaries reported per theme. Same UX rationale as
+// REPRESENTATIVE_DOCS_PER_THEME — enough to be useful, bounded enough to
+// not bury the user.
+const SECONDARY_DOCS_PER_THEME = 5;
+// Tokenisation for TF-IDF labels: lowercase, split on non-alphanumeric,
+// drop stopwords. This is deliberately a smaller list than bm25's — the
+// label step doesn't need FTS5 alignment, and we keep "tag-like" tokens.
+const LABEL_STOPWORDS = new Set([
+    "a",
+    "an",
+    "and",
+    "are",
+    "as",
+    "at",
+    "be",
+    "but",
+    "by",
+    "for",
+    "from",
+    "has",
+    "have",
+    "in",
+    "is",
+    "it",
+    "its",
+    "of",
+    "on",
+    "or",
+    "that",
+    "the",
+    "their",
+    "them",
+    "they",
+    "this",
+    "to",
+    "was",
+    "were",
+    "will",
+    "with",
+    "you",
+    "your",
+]);
+function labelTokens(text) {
+    return text
+        .toLowerCase()
+        .split(/[^a-z0-9]+/)
+        .filter((t) => t.length > 1 && !LABEL_STOPWORDS.has(t));
+}
+// Loads every (path, content_hash, embedding) row for the active model, in
+// path-then-chunk-index order, and groups embeddings by document path.
+function loadEmbeddingsByPath(db, model) {
+    const rows = db
+        .prepare(`SELECT c.path AS path, e.embedding AS embedding, e.dim AS dim
+         FROM chunks c
+         LEFT JOIN embeddings e
+           ON e.content_hash = c.content_hash AND e.model = ?
+        ORDER BY c.path, c.chunk_index`)
+        .all(model);
+    const provider = getProvider();
+    const expectedDim = provider.dim;
+    const out = new Map();
+    for (const row of rows) {
+        if (!row.embedding)
+            continue;
+        // Defense-in-depth: skip rows whose stored dim disagrees with the
+        // provider's expected dim — same guard `getAllChunks` applies.
+        const blobOk = row.embedding.length === expectedDim * 4;
+        const dimOk = row.dim === expectedDim;
+        if (!blobOk || !dimOk)
+            continue;
+        const vec = blobToEmbedding(row.embedding);
+        const list = out.get(row.path);
+        if (list)
+            list.push(vec);
+        else
+            out.set(row.path, [vec]);
+    }
+    return out;
+}
+// Applies the scope filter (collection, tags), RBAC, and the doc-has-an-
+// embedded-chunk requirement; returns the clusterable doc set and the count
+// of docs the embedding requirement skipped.
+function buildScopedDocs(documents, embeddingsByPath, filters, access) {
+    const scoped = [];
+    let skipped = 0;
+    for (const doc of documents) {
+        if (filters.collection && doc.collection !== filters.collection)
+            continue;
+        if (filters.tags && filters.tags.length > 0) {
+            const hasAll = filters.tags.every((t) => doc.tags.includes(t));
+            if (!hasAll)
+                continue;
+        }
+        if (access && !canRead(access.role, doc.collection))
+            continue;
+        const chunkVecs = embeddingsByPath.get(doc.path) ?? [];
+        const pooled = meanPoolL2(chunkVecs);
+        if (!pooled) {
+            // No embedded chunks (or an all-zero pool): count as skipped per
+            // the v1 contract.
+            skipped += 1;
+            continue;
+        }
+        scoped.push({
+            path: doc.path,
+            title: doc.title,
+            collection: doc.collection,
+            tags: doc.tags,
+            vector: pooled,
+        });
+    }
+    return { scoped, skipped };
+}
+// Cosine similarity for L2-normalised vectors == dot product. Used for
+// representative-doc ranking against a cluster centroid.
+function dotNormalized(a, b) {
+    let s = 0;
+    const n = Math.min(a.length, b.length);
+    for (let i = 0; i < n; i++)
+        s += a[i] * b[i];
+    return s;
+}
+// TF-IDF over the cluster: term frequency among the cluster's titles +
+// tags, divided by the document-frequency across ALL clusters (so a term
+// that names every theme — e.g. "doc" — doesn't dominate any one of them).
+// Falls back to the most common tags if TF-IDF yields nothing useful, and
+// finally to a generic "theme N" placeholder.
+function buildLabel(clusterDocs, globalDocCount, globalDf, themeIndex) {
+    const tf = new Map();
+    for (const doc of clusterDocs) {
+        const seen = new Set();
+        for (const tok of labelTokens(doc.title))
+            seen.add(tok);
+        for (const tag of doc.tags) {
+            for (const tok of labelTokens(tag))
+                seen.add(tok);
+        }
+        for (const tok of seen)
+            tf.set(tok, (tf.get(tok) ?? 0) + 1);
+    }
+    const scored = [];
+    for (const [term, freq] of tf) {
+        const df = globalDf.get(term) ?? 1;
+        // Standard smoothed IDF.
+        const idf = Math.log((globalDocCount + 1) / (df + 1)) + 1;
+        if (idf <= 0)
+            continue;
+        scored.push({ term, score: freq * idf });
+    }
+    scored.sort((a, b) => b.score - a.score);
+    const top = scored.slice(0, 3).map((s) => s.term);
+    if (top.length > 0)
+        return top.join(" / ");
+    // Fallback: most common tags.
+    const tagFreq = new Map();
+    for (const doc of clusterDocs) {
+        for (const tag of doc.tags)
+            tagFreq.set(tag, (tagFreq.get(tag) ?? 0) + 1);
+    }
+    const topTags = [...tagFreq.entries()]
+        .sort((a, b) => b[1] - a[1])
+        .slice(0, 3)
+        .map(([t]) => t);
+    if (topTags.length > 0)
+        return topTags.join(" / ");
+    return `theme ${themeIndex + 1}`;
+}
+// Builds the global document-frequency map across the clustered set. Used
+// by buildLabel; computed once and shared because every cluster's IDF must
+// agree on the document base.
+function buildGlobalDf(docs) {
+    const df = new Map();
+    for (const doc of docs) {
+        const seen = new Set();
+        for (const tok of labelTokens(doc.title))
+            seen.add(tok);
+        for (const tag of doc.tags) {
+            for (const tok of labelTokens(tag))
+                seen.add(tok);
+        }
+        for (const tok of seen)
+            df.set(tok, (df.get(tok) ?? 0) + 1);
+    }
+    return df;
+}
+function topTagsForCluster(clusterDocs) {
+    const freq = new Map();
+    for (const doc of clusterDocs) {
+        for (const tag of doc.tags)
+            freq.set(tag, (freq.get(tag) ?? 0) + 1);
+    }
+    return [...freq.entries()]
+        .sort((a, b) => b[1] - a[1] || a[0].localeCompare(b[0]))
+        .slice(0, RELATED_TAGS_PER_THEME)
+        .map(([t]) => t);
+}
+function representativesForCluster(clusterDocs, centroid) {
+    return [...clusterDocs]
+        .map((d) => ({ path: d.path, sim: dotNormalized(d.vector, centroid) }))
+        .sort((a, b) => b.sim - a.sim || a.path.localeCompare(b.path))
+        .slice(0, REPRESENTATIVE_DOCS_PER_THEME)
+        .map((d) => d.path);
+}
+function parseArgs(args) {
+    let k;
+    if (args.k !== undefined) {
+        if (typeof args.k !== "number" || !Number.isInteger(args.k) || args.k <= 0) {
+            return err(new Error("vault_themes: 'k' must be a positive integer when provided"));
+        }
+        k = args.k;
+    }
+    const collection = typeof args.collection === "string" && args.collection.length > 0 ? args.collection : undefined;
+    let tags;
+    if (Array.isArray(args.tags)) {
+        const filtered = args.tags.filter((t) => typeof t === "string" && t.length > 0);
+        if (filtered.length > 0)
+            tags = filtered;
+    }
+    return ok({ k, collection, tags });
+}
+export async function vaultThemes(vaultRoot, args, access) {
+    const parsed = parseArgs(args);
+    if (!parsed.ok)
+        return parsed;
+    const ready = await ensureIndexReady(vaultRoot);
+    if (!ready.ok)
+        return ready;
+    const dbResult = openIndexForActiveProvider(vaultRoot);
+    if (!dbResult.ok)
+        return dbResult;
+    const db = dbResult.value;
+    try {
+        const provider = getProvider();
+        const docRows = db
+            .prepare("SELECT path, title, collection, tags FROM documents ORDER BY path")
+            .all();
+        const documents = docRows.map((r) => ({
+            path: r.path,
+            title: r.title,
+            collection: r.collection,
+            domain: "",
+            status: "",
+            confidence: "",
+            updated: "",
+            tags: JSON.parse(r.tags),
+            content: "",
+            tokens: [],
+            ttlDays: null,
+            created: "",
+            supersededBy: null,
+        }));
+        const embeddingsByPath = loadEmbeddingsByPath(db, provider.id);
+        const { scoped, skipped } = buildScopedDocs(documents, embeddingsByPath, parsed.value, access);
+        if (scoped.length === 0) {
+            return ok({
+                themes: [],
+                totalDocuments: 0,
+                skippedDocuments: skipped,
+                selectedK: 0,
+                clusteredAt: new Date().toISOString(),
+            });
+        }
+        const vectors = scoped.map((s) => s.vector);
+        const rng = seededRng(THEMES_RNG_SEED);
+        let selectedK;
+        let assignments;
+        let centroids;
+        if (parsed.value.k !== undefined) {
+            const result = kmeans(vectors, parsed.value.k, rng, KMEANS_MAX_ITER);
+            selectedK = result.centroids.length;
+            assignments = result.assignments;
+            centroids = result.centroids;
+        }
+        else {
+            const result = pickK(vectors, DEFAULT_K_CANDIDATES, rng, KMEANS_MAX_ITER);
+            selectedK = result.centroids.length;
+            assignments = result.assignments;
+            centroids = result.centroids;
+        }
+        // Group docs by cluster.
+        const byCluster = new Map();
+        for (let i = 0; i < scoped.length; i++) {
+            const c = assignments[i];
+            const doc = scoped[i];
+            const list = byCluster.get(c);
+            if (list)
+                list.push(doc);
+            else
+                byCluster.set(c, [doc]);
+        }
+        const globalDf = buildGlobalDf(scoped);
+        // Secondary memberships: for each doc, find non-primary clusters its
+        // pooled vector also aligns with. This is the soft-reporting layer on
+        // top of the hard partition — it does NOT change documentCount, which
+        // still reflects primary membership only.
+        const secondaryByCluster = selectSecondaryMemberships(vectors, assignments, centroids, {
+            delta: SECONDARY_DELTA,
+            minSimilarity: SECONDARY_MIN_SIMILARITY,
+            maxPerDoc: SECONDARY_MAX_PER_DOC,
+        });
+        const themes = [];
+        let themeIndex = 0;
+        for (const [clusterIdx, clusterDocs] of byCluster) {
+            if (clusterDocs.length === 0)
+                continue;
+            const centroid = centroids[clusterIdx];
+            if (!centroid)
+                continue;
+            // Singleton clusters have no pairs to average — return null rather
+            // than the mathematically-trivial 1.0, which would falsely imply
+            // tightness.
+            const coherence = clusterDocs.length < 2 ? null : clusterCoherence(clusterDocs.map((d) => d.vector));
+            const secondaries = (secondaryByCluster.get(clusterIdx) ?? [])
+                .slice(0, SECONDARY_DOCS_PER_THEME)
+                .map((s) => scoped[s.docIndex].path);
+            themes.push({
+                label: buildLabel(clusterDocs, scoped.length, globalDf, themeIndex),
+                documentCount: clusterDocs.length,
+                coherence,
+                representativeDocs: representativesForCluster(clusterDocs, centroid),
+                secondaryDocs: secondaries,
+                relatedTags: topTagsForCluster(clusterDocs),
+            });
+            themeIndex += 1;
+        }
+        themes.sort((a, b) => b.documentCount - a.documentCount || a.label.localeCompare(b.label));
+        return ok({
+            themes,
+            totalDocuments: scoped.length,
+            skippedDocuments: skipped,
+            selectedK,
+            clusteredAt: new Date().toISOString(),
+        });
+    }
+    finally {
+        db.close();
+    }
+}
+// ---------------------------------------------------------------------------
+// MCP tool definition
+// ---------------------------------------------------------------------------
+export const themesTools = [
+    {
+        name: "vault_themes",
+        description: "Surface thematic clusters across the vault using k-means over " +
+            "document-pooled embeddings. Each document's chunk vectors are " +
+            "mean-pooled into one vector, L2-normalised, and clustered. By " +
+            "default the tool sweeps k ∈ {10, 15, 20, 25} and picks the k with " +
+            "the best mean silhouette; pass `k` to skip the sweep. Each theme " +
+            "reports a heuristic label (TF-IDF over titles + tags), a coherence " +
+            "score (mean pairwise cosine inside the cluster), representative " +
+            "documents nearest the centroid, and the most frequent tags. " +
+            "Output is deterministic for the same vault.",
+        inputSchema: {
+            type: "object",
+            properties: {
+                k: {
+                    type: "integer",
+                    description: "Optional explicit cluster count. When omitted, the tool sweeps " +
+                        "k ∈ {10, 15, 20, 25} and picks the k with the best silhouette.",
+                    minimum: 1,
+                },
+                collection: {
+                    type: "string",
+                    description: "Restrict clustering to documents in this collection.",
+                },
+                tags: {
+                    type: "array",
+                    items: { type: "string" },
+                    description: "Restrict to documents that have all of these tags.",
+                },
+            },
+            additionalProperties: false,
+        },
+        handler: (vaultRoot, args, access) => vaultThemes(vaultRoot, args, access),
+    },
+];
+//# sourceMappingURL=themes.js.map

package/dist/tools/themes.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "daftari",
-  "version": "1.10.0",
+  "version": "1.11.0",
   "description": "An open-source, multi-user knowledge vault exposed to AI agents via an MCP server.",
   "license": "MIT",
   "author": "Mihir Wagle / mavaali",