daftari 1.10.0 → 1.12.0

package/dist/server.js.map

@@ -1 +1 @@
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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

@@ -0,0 +1 @@
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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/curation.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"curation.d.ts","sourceRoot":"","sources":["../../src/tools/curation.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,KAAK,aAAa,EAAc,MAAM,mBAAmB,CAAC;AACnE,OAAO,EAAe,KAAK,aAAa,EAAE,KAAK,WAAW,EAAW,MAAM,qBAAqB,CAAC;AACjG,OAAO,EAAE,KAAK,eAAe,EAAqB,MAAM,2BAA2B,CAAC;AACpF,OAAO,EAAc,KAAK,YAAY,EAAE,MAAM,wBAAwB,CAAC;AACvE,OAAO,EAAM,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAC1D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,WAAW,CAAC;AAkBhD,wBAAsB,eAAe,CACnC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,KAAK,CAAC,CAAC,CAoCtC;AAMD,MAAM,WAAW,eAAe;IAC9B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,GAAG,IAAI,CAAC;IAC7B,MAAM,EAAE,OAAO,CAAC,MAAM,CAAC,aAAa,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC;IACtD,aAAa,EAAE,MAAM,CAAC;CACvB;AAED,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,EACjB,IAAI,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,EAClC,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,eAAe,EAAE,KAAK,CAAC,CAAC,CAqCzC;AAMD,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,eAAe,EAAE,CAAC;CAC5B;AAID,wBAAsB,eAAe,CACnC,SAAS,EAAE,MAAM,EACjB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,MAAM,CAAC,EAAE,aAAa,GACrB,OAAO,CAAC,MAAM,CAAC,qBAAqB,EAAE,KAAK,CAAC,CAAC,CAiB/C;AAMD,eAAO,MAAM,aAAa,EAAE,cAAc,EAsFzC,CAAC"}

package/dist/tools/curation.js

@@ -124,6 +124,8 @@ export async function vaultProvenance(vaultRoot, args, access) {
 export const curationTools = [
     {
         name: "vault_tension_log",
+        title: "Log a contradiction",
+        annotations: { destructiveHint: true },
         description: "Record a tension — a contradiction or unresolved pull between two " +
             "vault documents — to the advisory tension log. Records the tension; " +
             "does not resolve it. Entries are logged with status 'unresolved'.",
@@ -162,6 +164,8 @@ export const curationTools = [
     },
     {
         name: "vault_lint",
+        title: "Run curation checks",
+        annotations: { readOnlyHint: true },
         description: "Run the advisory curation checks across the vault: stale files past " +
             "TTL, orphan files with no inbound links, old drafts, stagnant " +
             "low-confidence files, deprecated files still linked from canonical " +
@@ -182,6 +186,8 @@ export const curationTools = [
     },
     {
         name: "vault_provenance",
+        title: "View document write history",
+        annotations: { readOnlyHint: true },
         description: "Return the write history of a single document from the provenance " +
             "log: every create, update, append, promote, and deprecate recorded " +
             "for it, oldest first.",

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package/dist/tools/read.d.ts

@@ -2,10 +2,18 @@ import { type AccessContext } from "../access/rbac.js";
 import { type DecayState } from "../curation/decay.js";
 import { type ProvenanceEntry } from "../curation/provenance.js";
 import { type Frontmatter, type Result, type ValidationReport } from "../frontmatter/types.js";
+export interface ToolAnnotations {
+    readOnlyHint?: boolean;
+    destructiveHint?: boolean;
+    idempotentHint?: boolean;
+    openWorldHint?: boolean;
+}
 export interface ToolDefinition {
     name: string;
+    title?: string;
     description: string;
     inputSchema: Record<string, unknown>;
+    annotations?: ToolAnnotations;
     handler: (vaultRoot: string, args: Record<string, unknown>, access?: AccessContext) => Promise<Result<unknown, Error>>;
 }
 export interface VaultReadResult {

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

@@ -1 +1 @@
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package/dist/tools/read.js

@@ -218,6 +218,8 @@ function asStringArray(v) {
 export const readTools = [
     {
         name: "vault_read",
+        title: "Read a vault document",
+        annotations: { readOnlyHint: true },
         description: "Read a single vault document. Returns its markdown body, parsed " +
             "frontmatter, a validation report, a decay assessment (null when " +
             "healthy; otherwise level, reasons, and an optional banner), and a " +
@@ -239,6 +241,8 @@ export const readTools = [
     },
     {
         name: "vault_index",
+        title: "List vault documents",
+        annotations: { readOnlyHint: true },
         description: "List vault documents with their metadata, including each document's " +
             "questions_answered / questions_raised. Optionally filter by collection, " +
             "status, domain, tags (conjunctive), or has_unanswered.",
@@ -279,6 +283,8 @@ export const readTools = [
     },
     {
         name: "vault_status",
+        title: "Vault health dashboard",
+        annotations: { readOnlyHint: true },
         description: "Vault health dashboard: total file count, per-collection counts, " +
             "count of documents with invalid frontmatter, a staleness distribution " +
             "(fresh/aging/stale), unresolved tensions, and recent write history.",