causantic 0.2.0

package/dist/cli/utils.js

@@ -0,0 +1,105 @@
+/**
+ * Shared CLI utilities.
+ */
+/** Magic bytes for encrypted archives */
+export const ENCRYPTED_MAGIC = Buffer.from('CST\x00');
+/**
+ * Prompt for password with hidden input.
+ * Falls back to visible input if raw mode is not available.
+ */
+export async function promptPassword(prompt) {
+    const readline = await import('node:readline');
+    return new Promise((resolve) => {
+        const rl = readline.createInterface({
+            input: process.stdin,
+            output: process.stdout,
+        });
+        // Check if we can use raw mode for hidden input
+        if (process.stdin.isTTY && typeof process.stdin.setRawMode === 'function') {
+            process.stdout.write(prompt);
+            process.stdin.setRawMode(true);
+            process.stdin.resume();
+            let password = '';
+            const onData = (char) => {
+                const c = char.toString();
+                if (c === '\n' || c === '\r') {
+                    process.stdin.setRawMode(false);
+                    process.stdin.removeListener('data', onData);
+                    process.stdin.pause();
+                    console.log(''); // newline
+                    rl.close();
+                    resolve(password);
+                }
+                else if (c === '\u0003') {
+                    // Ctrl+C
+                    process.stdin.setRawMode(false);
+                    process.exit(0);
+                }
+                else if (c === '\u007F' || c === '\b') {
+                    // Backspace
+                    password = password.slice(0, -1);
+                }
+                else if (c.charCodeAt(0) >= 32) {
+                    // Printable character
+                    password += c;
+                }
+            };
+            process.stdin.on('data', onData);
+        }
+        else {
+            // Fallback to visible input (non-TTY environments)
+            rl.question(prompt, (answer) => {
+                rl.close();
+                resolve(answer);
+            });
+        }
+    });
+}
+/**
+ * Prompt the user for text input.
+ */
+export async function promptUser(message) {
+    const readline = await import('node:readline');
+    return new Promise((resolve) => {
+        const rl = readline.createInterface({
+            input: process.stdin,
+            output: process.stdout,
+        });
+        rl.question(message, (answer) => {
+            rl.close();
+            resolve(answer);
+        });
+    });
+}
+/**
+ * Prompt the user for a yes/no answer.
+ * @param message - The prompt message (bracket hint is appended automatically)
+ * @param defaultYes - Whether "yes" is the default (affects prompt hint and empty input)
+ * @returns true if the user answered yes
+ */
+export async function promptYesNo(message, defaultYes = false) {
+    const hint = defaultYes ? '[Y/n]' : '[y/N]';
+    const answer = await promptUser(`${message} ${hint} `);
+    const normalized = answer.toLowerCase().trim();
+    if (normalized === '') {
+        return defaultYes;
+    }
+    return normalized === 'y' || normalized === 'yes';
+}
+/**
+ * Check if a file is an encrypted Causantic archive.
+ */
+export async function isEncryptedArchive(filePath) {
+    const fs = await import('node:fs');
+    try {
+        const fd = fs.openSync(filePath, 'r');
+        const header = Buffer.alloc(4);
+        fs.readSync(fd, header, 0, 4, 0);
+        fs.closeSync(fd);
+        return header.equals(ENCRYPTED_MAGIC);
+    }
+    catch {
+        return false;
+    }
+}
+//# sourceMappingURL=utils.js.map

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package/dist/clusters/cluster-manager.d.ts

@@ -0,0 +1,96 @@
+/**
+ * Cluster management: HDBSCAN clustering and chunk assignment.
+ */
+import type { StoredCluster } from '../storage/types.js';
+/**
+ * Result of clustering operation.
+ */
+export interface ClusteringResult {
+    /** Number of clusters created */
+    numClusters: number;
+    /** Number of chunks assigned to clusters */
+    assignedChunks: number;
+    /** Number of noise points (unassigned) */
+    noiseChunks: number;
+    /** Noise ratio */
+    noiseRatio: number;
+    /** Cluster sizes */
+    clusterSizes: number[];
+    /** Number of noise points reassigned to clusters via threshold pass */
+    reassignedNoise: number;
+    /** Time taken in milliseconds */
+    durationMs: number;
+}
+/**
+ * Options for clustering.
+ */
+export interface ClusteringOptions {
+    /** Minimum cluster size for HDBSCAN. Default: from config. */
+    minClusterSize?: number;
+    /** Angular distance threshold for assignment. Default: from config. */
+    clusterThreshold?: number;
+    /** Clear existing clusters before reclustering. Default: true. */
+    clearExisting?: boolean;
+}
+/**
+ * Cluster manager for running HDBSCAN and managing cluster assignments.
+ */
+export declare class ClusterManager {
+    private config;
+    /**
+     * Run HDBSCAN on all chunks and create clusters.
+     */
+    recluster(options?: ClusteringOptions): Promise<ClusteringResult>;
+    /**
+     * Assign a new chunk to existing clusters based on angular distance.
+     * Returns IDs of clusters the chunk was assigned to.
+     */
+    assignChunkToClusters(chunkId: string, embedding: number[], options?: {
+        threshold?: number;
+    }): Promise<string[]>;
+    /**
+     * Assign multiple new chunks to existing clusters.
+     */
+    assignNewChunks(chunks: Array<{
+        id: string;
+        embedding: number[];
+    }>, options?: {
+        threshold?: number;
+    }): Promise<{
+        assigned: number;
+        total: number;
+    }>;
+    /**
+     * Reassign noise points (unassigned chunks) to clusters within threshold.
+     * Runs only the threshold pass without HDBSCAN — useful for threshold experimentation.
+     */
+    reassignNoisePoints(options?: {
+        threshold?: number;
+    }): Promise<{
+        reassigned: number;
+        total: number;
+    }>;
+    /**
+     * Update cluster centroids based on current membership.
+     */
+    updateCentroids(): Promise<number>;
+    /**
+     * Get cluster statistics.
+     */
+    getStats(): Promise<{
+        numClusters: number;
+        totalAssignments: number;
+        avgClusterSize: number;
+        largestCluster: number;
+        smallestCluster: number;
+    }>;
+    /**
+     * Find clusters similar to a query embedding.
+     */
+    findSimilarClusters(queryEmbedding: number[], limit?: number): Promise<Array<{
+        cluster: StoredCluster;
+        distance: number;
+    }>>;
+}
+export declare const clusterManager: ClusterManager;
+//# sourceMappingURL=cluster-manager.d.ts.map

package/dist/clusters/cluster-manager.d.ts.map

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package/dist/clusters/cluster-manager.js

@@ -0,0 +1,321 @@
+/**
+ * Cluster management: HDBSCAN clustering and chunk assignment.
+ */
+import { HDBSCAN } from './hdbscan.js';
+import { vectorStore } from '../storage/vector-store.js';
+import { upsertCluster, assignChunksToClusters, getAllClusters, clearAllClusters, getClusterChunkIds, computeMembershipHash, } from '../storage/cluster-store.js';
+import { angularDistance } from '../utils/angular-distance.js';
+import { getConfig } from '../config/memory-config.js';
+import { generateId } from '../storage/db.js';
+/**
+ * Cluster manager for running HDBSCAN and managing cluster assignments.
+ */
+export class ClusterManager {
+    config = getConfig();
+    /**
+     * Run HDBSCAN on all chunks and create clusters.
+     */
+    async recluster(options = {}) {
+        const startTime = Date.now();
+        const { minClusterSize = this.config.minClusterSize, clearExisting = true, } = options;
+        // Clear existing clusters if requested
+        if (clearExisting) {
+            clearAllClusters();
+        }
+        // Get all vectors
+        const vectors = await vectorStore.getAllVectors();
+        if (vectors.length === 0) {
+            return {
+                numClusters: 0,
+                assignedChunks: 0,
+                noiseChunks: 0,
+                noiseRatio: 0,
+                clusterSizes: [],
+                reassignedNoise: 0,
+                durationMs: Date.now() - startTime,
+            };
+        }
+        // Run HDBSCAN
+        const embeddings = vectors.map((v) => v.embedding);
+        const hdbscan = new HDBSCAN({
+            minClusterSize,
+            minSamples: minClusterSize,
+        });
+        const labels = hdbscan.fitSync(embeddings);
+        // Group by cluster
+        const clusterMembers = new Map();
+        for (let i = 0; i < labels.length; i++) {
+            const label = labels[i];
+            if (label < 0)
+                continue; // Skip noise
+            if (!clusterMembers.has(label)) {
+                clusterMembers.set(label, []);
+            }
+            clusterMembers.get(label).push(vectors[i]);
+        }
+        // Create clusters and assignments
+        const assignments = [];
+        const clusterSizes = [];
+        for (const [label, members] of clusterMembers) {
+            // Compute centroid
+            const centroid = computeCentroid(members.map((m) => m.embedding));
+            // Select exemplars (closest to centroid)
+            const withDistances = members.map((m) => ({
+                ...m,
+                distance: angularDistance(m.embedding, centroid),
+            }));
+            withDistances.sort((a, b) => a.distance - b.distance);
+            const exemplarIds = withDistances.slice(0, 3).map((m) => m.id);
+            // Compute membership hash
+            const memberIds = members.map((m) => m.id);
+            const membershipHash = computeMembershipHash(memberIds);
+            // Create cluster
+            const clusterId = generateId();
+            upsertCluster({
+                id: clusterId,
+                name: `Cluster ${label}`,
+                centroid,
+                exemplarIds,
+                membershipHash,
+            });
+            // Create assignments
+            for (const m of withDistances) {
+                assignments.push({
+                    chunkId: m.id,
+                    clusterId,
+                    distance: m.distance,
+                });
+            }
+            clusterSizes.push(members.length);
+        }
+        // Batch insert assignments
+        if (assignments.length > 0) {
+            assignChunksToClusters(assignments);
+        }
+        const rawNoiseCount = labels.filter((l) => l < 0).length;
+        // Noise reassignment pass: assign noise points to clusters within threshold
+        const clusterThreshold = options.clusterThreshold ?? this.config.clusterThreshold;
+        const noiseAssignments = [];
+        const reassignedNoiseIds = new Set();
+        if (rawNoiseCount > 0 && clusterMembers.size > 0) {
+            const clusters = getAllClusters();
+            const noisePoints = vectors.filter((_, i) => labels[i] < 0);
+            for (const point of noisePoints) {
+                for (const cluster of clusters) {
+                    if (!cluster.centroid)
+                        continue;
+                    const distance = angularDistance(point.embedding, cluster.centroid);
+                    if (distance < clusterThreshold) {
+                        noiseAssignments.push({
+                            chunkId: point.id,
+                            clusterId: cluster.id,
+                            distance,
+                        });
+                        reassignedNoiseIds.add(point.id);
+                    }
+                }
+            }
+            if (noiseAssignments.length > 0) {
+                assignChunksToClusters(noiseAssignments);
+                await this.updateCentroids();
+            }
+        }
+        const noiseCount = rawNoiseCount - reassignedNoiseIds.size;
+        return {
+            numClusters: clusterMembers.size,
+            assignedChunks: assignments.length + noiseAssignments.length,
+            noiseChunks: noiseCount,
+            noiseRatio: vectors.length > 0 ? noiseCount / vectors.length : 0,
+            clusterSizes: clusterSizes.sort((a, b) => b - a),
+            reassignedNoise: reassignedNoiseIds.size,
+            durationMs: Date.now() - startTime,
+        };
+    }
+    /**
+     * Assign a new chunk to existing clusters based on angular distance.
+     * Returns IDs of clusters the chunk was assigned to.
+     */
+    async assignChunkToClusters(chunkId, embedding, options = {}) {
+        const threshold = options.threshold ?? this.config.clusterThreshold;
+        const clusters = getAllClusters();
+        const assigned = [];
+        const assignments = [];
+        for (const cluster of clusters) {
+            if (!cluster.centroid)
+                continue;
+            const distance = angularDistance(embedding, cluster.centroid);
+            if (distance < threshold) {
+                assignments.push({
+                    chunkId,
+                    clusterId: cluster.id,
+                    distance,
+                });
+                assigned.push(cluster.id);
+            }
+        }
+        if (assignments.length > 0) {
+            assignChunksToClusters(assignments);
+        }
+        return assigned;
+    }
+    /**
+     * Assign multiple new chunks to existing clusters.
+     */
+    async assignNewChunks(chunks, options = {}) {
+        let assignedCount = 0;
+        for (const chunk of chunks) {
+            const assigned = await this.assignChunkToClusters(chunk.id, chunk.embedding, options);
+            if (assigned.length > 0) {
+                assignedCount++;
+            }
+        }
+        return { assigned: assignedCount, total: chunks.length };
+    }
+    /**
+     * Reassign noise points (unassigned chunks) to clusters within threshold.
+     * Runs only the threshold pass without HDBSCAN — useful for threshold experimentation.
+     */
+    async reassignNoisePoints(options = {}) {
+        const threshold = options.threshold ?? this.config.clusterThreshold;
+        const clusters = getAllClusters();
+        if (clusters.length === 0) {
+            return { reassigned: 0, total: 0 };
+        }
+        // Collect all currently-assigned chunk IDs
+        const assignedIds = new Set();
+        for (const cluster of clusters) {
+            for (const id of getClusterChunkIds(cluster.id)) {
+                assignedIds.add(id);
+            }
+        }
+        // Get all vectors and filter to unassigned
+        const allVectors = await vectorStore.getAllVectors();
+        const unassigned = allVectors.filter((v) => !assignedIds.has(v.id));
+        if (unassigned.length === 0) {
+            return { reassigned: 0, total: 0 };
+        }
+        // Threshold pass
+        const assignments = [];
+        const reassignedIds = new Set();
+        for (const point of unassigned) {
+            for (const cluster of clusters) {
+                if (!cluster.centroid)
+                    continue;
+                const distance = angularDistance(point.embedding, cluster.centroid);
+                if (distance < threshold) {
+                    assignments.push({
+                        chunkId: point.id,
+                        clusterId: cluster.id,
+                        distance,
+                    });
+                    reassignedIds.add(point.id);
+                }
+            }
+        }
+        if (assignments.length > 0) {
+            assignChunksToClusters(assignments);
+            await this.updateCentroids();
+        }
+        return { reassigned: reassignedIds.size, total: unassigned.length };
+    }
+    /**
+     * Update cluster centroids based on current membership.
+     */
+    async updateCentroids() {
+        const clusters = getAllClusters();
+        let updated = 0;
+        for (const cluster of clusters) {
+            const chunkIds = getClusterChunkIds(cluster.id);
+            if (chunkIds.length === 0)
+                continue;
+            // Get embeddings for all chunks
+            const embeddings = [];
+            for (const id of chunkIds) {
+                const embedding = await vectorStore.get(id);
+                if (embedding) {
+                    embeddings.push(embedding);
+                }
+            }
+            if (embeddings.length === 0)
+                continue;
+            // Compute new centroid
+            const centroid = computeCentroid(embeddings);
+            // Update cluster
+            upsertCluster({
+                id: cluster.id,
+                centroid,
+                membershipHash: computeMembershipHash(chunkIds),
+            });
+            updated++;
+        }
+        return updated;
+    }
+    /**
+     * Get cluster statistics.
+     */
+    async getStats() {
+        const clusters = getAllClusters();
+        let totalAssignments = 0;
+        let largest = 0;
+        let smallest = Infinity;
+        for (const cluster of clusters) {
+            const size = getClusterChunkIds(cluster.id).length;
+            totalAssignments += size;
+            largest = Math.max(largest, size);
+            smallest = Math.min(smallest, size);
+        }
+        return {
+            numClusters: clusters.length,
+            totalAssignments,
+            avgClusterSize: clusters.length > 0 ? totalAssignments / clusters.length : 0,
+            largestCluster: largest,
+            smallestCluster: smallest === Infinity ? 0 : smallest,
+        };
+    }
+    /**
+     * Find clusters similar to a query embedding.
+     */
+    async findSimilarClusters(queryEmbedding, limit = 5) {
+        const clusters = getAllClusters();
+        const results = [];
+        for (const cluster of clusters) {
+            if (!cluster.centroid)
+                continue;
+            const distance = angularDistance(queryEmbedding, cluster.centroid);
+            results.push({ cluster, distance });
+        }
+        results.sort((a, b) => a.distance - b.distance);
+        return results.slice(0, limit);
+    }
+}
+/**
+ * Compute centroid of embeddings (mean vector, normalized).
+ */
+function computeCentroid(embeddings) {
+    if (embeddings.length === 0) {
+        return [];
+    }
+    const dim = embeddings[0].length;
+    const sum = new Array(dim).fill(0);
+    for (const emb of embeddings) {
+        for (let i = 0; i < dim; i++) {
+            sum[i] += emb[i];
+        }
+    }
+    // Normalize
+    let norm = 0;
+    for (let i = 0; i < dim; i++) {
+        sum[i] /= embeddings.length;
+        norm += sum[i] * sum[i];
+    }
+    norm = Math.sqrt(norm);
+    if (norm > 0) {
+        for (let i = 0; i < dim; i++) {
+            sum[i] /= norm;
+        }
+    }
+    return sum;
+}
+// Singleton instance
+export const clusterManager = new ClusterManager();
+//# sourceMappingURL=cluster-manager.js.map

package/dist/clusters/cluster-manager.js.map

@@ -0,0 +1 @@
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package/dist/clusters/cluster-refresh.d.ts

@@ -0,0 +1,56 @@
+/**
+ * LLM-based cluster description refresh.
+ * Uses Claude API to generate human-readable descriptions for clusters.
+ */
+/**
+ * Result of cluster refresh.
+ */
+export interface RefreshResult {
+    clusterId: string;
+    name: string;
+    description: string;
+    durationMs: number;
+}
+/**
+ * Options for cluster refresh.
+ */
+export interface RefreshOptions {
+    /** Model to use. Default: from config. */
+    model?: string;
+    /** Max exemplar chunks to include in prompt. Default: 3. */
+    maxExemplars?: number;
+    /** Max tokens per chunk in prompt. Default: 500. */
+    maxTokensPerChunk?: number;
+    /** Progress callback, called after each cluster is labeled. */
+    onProgress?: (current: number, total: number) => void;
+}
+/**
+ * Cluster refresher for generating descriptions using Claude.
+ */
+export declare class ClusterRefresher {
+    private client;
+    private rateLimiter;
+    private config;
+    constructor();
+    /**
+     * Initialize the Anthropic client.
+     * Checks keychain for API key if not set in environment.
+     */
+    private getClient;
+    /**
+     * Refresh a single cluster's description.
+     */
+    refreshCluster(clusterId: string, options?: RefreshOptions): Promise<RefreshResult>;
+    /**
+     * Refresh all stale clusters.
+     */
+    refreshStaleClusters(options?: RefreshOptions & {
+        maxAgeMs?: number;
+    }): Promise<RefreshResult[]>;
+    /**
+     * Refresh all clusters (force refresh).
+     */
+    refreshAllClusters(options?: RefreshOptions): Promise<RefreshResult[]>;
+}
+export declare const clusterRefresher: ClusterRefresher;
+//# sourceMappingURL=cluster-refresh.d.ts.map

package/dist/clusters/cluster-refresh.d.ts.map

@@ -0,0 +1 @@
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