gnosys 4.0.0

package/dist/lib/history.js

@@ -0,0 +1,112 @@
+/**
+ * Gnosys History — Git-backed version history for individual memories.
+ *
+ * Every memory write/update auto-commits to git. This module exposes
+ * that history: view what changed, when, and rollback to prior versions.
+ */
+import { execFileSync } from "child_process";
+import path from "path";
+/** Validate a git commit hash (short or full, hex only). */
+function isValidCommitHash(hash) {
+    return /^[a-f0-9]{4,40}$/i.test(hash);
+}
+/** Validate a relative path has no traversal or shell metacharacters. */
+function isValidRelativePath(p) {
+    const resolved = path.resolve("/fake-root", p);
+    return resolved.startsWith("/fake-root/") && !p.includes("\0");
+}
+/**
+ * Get the commit history for a specific memory file.
+ */
+export function getFileHistory(storePath, relativePath, limit = 20) {
+    if (!isValidRelativePath(relativePath))
+        return [];
+    try {
+        const output = execFileSync("git", ["log", "--follow", `--format=%H|%ai|%s`, `-n`, String(limit), "--", relativePath], { cwd: storePath, stdio: ["pipe", "pipe", "pipe"], encoding: "utf-8" });
+        if (!output.trim())
+            return [];
+        return output
+            .trim()
+            .split("\n")
+            .filter(Boolean)
+            .map((line) => {
+            const [commitHash, date, ...msgParts] = line.split("|");
+            return {
+                commitHash: commitHash.trim(),
+                date: date.trim().split(" ")[0], // Just the date part
+                message: msgParts.join("|").trim(),
+            };
+        });
+    }
+    catch {
+        return [];
+    }
+}
+/**
+ * Get the full file content at a specific commit.
+ */
+export function getFileAtCommit(storePath, relativePath, commitHash) {
+    if (!isValidCommitHash(commitHash))
+        return null;
+    if (!isValidRelativePath(relativePath))
+        return null;
+    try {
+        return execFileSync("git", ["show", `${commitHash}:${relativePath}`], { cwd: storePath, stdio: ["pipe", "pipe", "pipe"], encoding: "utf-8" });
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Get a diff between two commits for a specific file.
+ */
+export function getFileDiff(storePath, relativePath, fromHash, toHash) {
+    if (!isValidCommitHash(fromHash) || !isValidCommitHash(toHash))
+        return null;
+    if (!isValidRelativePath(relativePath))
+        return null;
+    try {
+        return execFileSync("git", ["diff", `${fromHash}..${toHash}`, "--", relativePath], { cwd: storePath, stdio: ["pipe", "pipe", "pipe"], encoding: "utf-8" });
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Rollback a memory to its state at a specific commit.
+ * Creates a new commit with the reverted content (non-destructive).
+ */
+export function rollbackToCommit(storePath, relativePath, commitHash) {
+    if (!isValidCommitHash(commitHash))
+        return false;
+    if (!isValidRelativePath(relativePath))
+        return false;
+    try {
+        // Restore file to its state at the target commit
+        execFileSync("git", ["checkout", commitHash, "--", relativePath], { cwd: storePath, stdio: "pipe" });
+        // Stage the restored file
+        execFileSync("git", ["add", relativePath], { cwd: storePath, stdio: "pipe" });
+        // Commit the rollback as a new commit
+        execFileSync("git", ["commit", "-m", `Rollback ${relativePath} to ${commitHash.substring(0, 7)}`], { cwd: storePath, stdio: "pipe" });
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Check if git is available and the store has history.
+ */
+export function hasGitHistory(storePath) {
+    try {
+        execFileSync("git", ["rev-parse", "--git-dir"], {
+            cwd: storePath,
+            stdio: "pipe",
+        });
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+//# sourceMappingURL=history.js.map

package/dist/lib/history.js.map

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package/dist/lib/hybridSearch.d.ts

@@ -0,0 +1,80 @@
+/**
+ * Gnosys Hybrid Search — Combines FTS5 keyword search with semantic embeddings
+ * using Reciprocal Rank Fusion (RRF).
+ *
+ * Three modes:
+ *   keyword  — FTS5 only (fast, no model needed)
+ *   semantic — embeddings cosine similarity only
+ *   hybrid   — RRF fusion of both (default when embeddings exist)
+ */
+import { GnosysSearch } from "./search.js";
+import { GnosysEmbeddings } from "./embeddings.js";
+import { GnosysResolver } from "./resolver.js";
+import { GnosysDB } from "./db.js";
+export type SearchMode = "keyword" | "semantic" | "hybrid";
+export interface HybridSearchResult {
+    relativePath: string;
+    title: string;
+    snippet: string;
+    score: number;
+    /** Which method(s) found this result */
+    sources: ("keyword" | "semantic" | "archive")[];
+    /** Full memory content (loaded on demand for ask engine) */
+    content?: string;
+    /** The memory frontmatter content field */
+    fullContent?: string;
+    /** Memory ID (used for dearchiving) */
+    memoryId?: string;
+    /** Whether this result came from the archive */
+    fromArchive?: boolean;
+}
+export declare class GnosysHybridSearch {
+    private search;
+    private embeddings;
+    private resolver;
+    private storePath;
+    /** v2.0: When set, hybrid search uses SQLite directly */
+    private dbSearch;
+    constructor(search: GnosysSearch, embeddings: GnosysEmbeddings, resolver: GnosysResolver, storePath: string, gnosysDb?: GnosysDB);
+    /**
+     * Main hybrid search entry point.
+     * Searches active memories first; if results are insufficient, also searches archive.db.
+     */
+    hybridSearch(query: string, limit?: number, mode?: SearchMode): Promise<HybridSearchResult[]>;
+    /**
+     * Search the archive.db for memories.
+     */
+    private searchArchive;
+    /**
+     * Keyword search via existing FTS5.
+     */
+    private keywordSearch;
+    /**
+     * Semantic search via embeddings cosine similarity.
+     */
+    private semanticSearch;
+    /**
+     * Reciprocal Rank Fusion — combines two ranked lists.
+     * RRF score: score(d) = Σ 1/(k + rank_i(d)) for each ranking system i
+     */
+    private rrfFusion;
+    /**
+     * Reindex all embeddings from all stores.
+     * Returns count of files indexed.
+     */
+    reindex(onProgress?: (current: number, total: number, filePath: string) => void): Promise<number>;
+    /**
+     * Load full content for search results (used by Ask engine).
+     * Handles both active memories and archived memories.
+     */
+    loadContent(results: HybridSearchResult[]): Promise<HybridSearchResult[]>;
+    /**
+     * Check if embeddings are available.
+     */
+    hasEmbeddings(): boolean;
+    /**
+     * Get embedding count.
+     */
+    embeddingCount(): number;
+}
+//# sourceMappingURL=hybridSearch.d.ts.map

package/dist/lib/hybridSearch.d.ts.map

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package/dist/lib/hybridSearch.js

@@ -0,0 +1,296 @@
+/**
+ * Gnosys Hybrid Search — Combines FTS5 keyword search with semantic embeddings
+ * using Reciprocal Rank Fusion (RRF).
+ *
+ * Three modes:
+ *   keyword  — FTS5 only (fast, no model needed)
+ *   semantic — embeddings cosine similarity only
+ *   hybrid   — RRF fusion of both (default when embeddings exist)
+ */
+import { GnosysEmbeddings } from "./embeddings.js";
+import { GnosysArchive } from "./archive.js";
+import { GnosysDbSearch } from "./dbSearch.js";
+/** RRF constant k — standard value from Cormack et al. 2009 */
+const RRF_K = 60;
+export class GnosysHybridSearch {
+    search;
+    embeddings;
+    resolver;
+    storePath;
+    /** v2.0: When set, hybrid search uses SQLite directly */
+    dbSearch = null;
+    constructor(search, embeddings, resolver, storePath, gnosysDb) {
+        this.search = search;
+        this.embeddings = embeddings;
+        this.resolver = resolver;
+        this.storePath = storePath;
+        // v2.0: If GnosysDB is migrated, create a DB search adapter
+        if (gnosysDb?.isAvailable() && gnosysDb?.isMigrated()) {
+            this.dbSearch = new GnosysDbSearch(gnosysDb);
+        }
+    }
+    /**
+     * Main hybrid search entry point.
+     * Searches active memories first; if results are insufficient, also searches archive.db.
+     */
+    async hybridSearch(query, limit = 15, mode = "hybrid") {
+        // v2.0 DB-backed fast path: run entirely from gnosys.db
+        if (this.dbSearch) {
+            const embedQuery = this.embeddings.hasEmbeddings()
+                ? (text) => this.embeddings.embed(text)
+                : undefined;
+            return this.dbSearch.hybridSearch(query, limit, mode, embedQuery);
+        }
+        // Auto-downgrade to keyword if no embeddings available
+        if (mode === "hybrid" || mode === "semantic") {
+            if (!this.embeddings.hasEmbeddings()) {
+                if (mode === "semantic") {
+                    return []; // Can't do semantic without embeddings
+                }
+                mode = "keyword"; // Downgrade hybrid to keyword
+            }
+        }
+        let results;
+        if (mode === "keyword") {
+            results = this.keywordSearch(query, limit);
+        }
+        else if (mode === "semantic") {
+            results = await this.semanticSearch(query, limit);
+        }
+        else {
+            // Hybrid: run both and fuse with RRF
+            const [keywordResults, semanticResults] = await Promise.all([
+                this.keywordSearch(query, limit * 2),
+                this.semanticSearch(query, limit * 2),
+            ]);
+            results = this.rrfFusion(keywordResults, semanticResults, limit);
+        }
+        // If active results are insufficient, search archive.db
+        if (results.length < limit) {
+            const archiveResults = this.searchArchive(query, limit - results.length);
+            if (archiveResults.length > 0) {
+                // Deduplicate by title (archive results won't have same relativePath)
+                const existingTitles = new Set(results.map((r) => r.title.toLowerCase()));
+                const newArchiveResults = archiveResults.filter((ar) => !existingTitles.has(ar.title.toLowerCase()));
+                results = [...results, ...newArchiveResults];
+            }
+        }
+        return results.slice(0, limit);
+    }
+    /**
+     * Search the archive.db for memories.
+     */
+    searchArchive(query, limit) {
+        try {
+            const archive = new GnosysArchive(this.storePath);
+            if (!archive.isAvailable())
+                return [];
+            const archiveResults = archive.searchArchive(query, limit);
+            archive.close();
+            return archiveResults.map((ar) => ({
+                relativePath: `archive:${ar.category}/${ar.id}`,
+                title: ar.title,
+                snippet: ar.snippet,
+                score: Math.abs(ar.score) > 0 ? 1 / (RRF_K + Math.abs(ar.score)) : 0.001,
+                sources: ["archive"],
+                memoryId: ar.id,
+                fromArchive: true,
+            }));
+        }
+        catch {
+            return [];
+        }
+    }
+    /**
+     * Keyword search via existing FTS5.
+     */
+    keywordSearch(query, limit) {
+        const results = this.search.search(query, limit);
+        return results.map((r, i) => ({
+            relativePath: r.relative_path,
+            title: r.title,
+            snippet: r.snippet,
+            score: 1 / (RRF_K + i + 1), // RRF score based on rank position
+            sources: ["keyword"],
+        }));
+    }
+    /**
+     * Semantic search via embeddings cosine similarity.
+     */
+    async semanticSearch(query, limit) {
+        // Embed the query
+        const queryEmbedding = await this.embeddings.embed(query);
+        // Get all stored embeddings and compute similarities
+        const allEmbeddings = this.embeddings.getAllEmbeddings();
+        const scored = [];
+        for (const entry of allEmbeddings) {
+            const similarity = GnosysEmbeddings.cosineSimilarity(queryEmbedding, entry.embedding);
+            scored.push({ filePath: entry.filePath, similarity });
+        }
+        // Sort by similarity descending
+        scored.sort((a, b) => b.similarity - a.similarity);
+        const topN = scored.slice(0, limit);
+        // Load memory metadata for results
+        const results = [];
+        for (const item of topN) {
+            const memory = await this.resolver.readMemory(item.filePath);
+            if (memory) {
+                results.push({
+                    relativePath: item.filePath,
+                    title: memory.frontmatter.title,
+                    snippet: memory.content.substring(0, 200),
+                    score: item.similarity,
+                    sources: ["semantic"],
+                });
+            }
+        }
+        return results;
+    }
+    /**
+     * Reciprocal Rank Fusion — combines two ranked lists.
+     * RRF score: score(d) = Σ 1/(k + rank_i(d)) for each ranking system i
+     */
+    rrfFusion(keywordResults, semanticResults, limit) {
+        const scoreMap = new Map();
+        // Score keyword results
+        for (let i = 0; i < keywordResults.length; i++) {
+            const r = keywordResults[i];
+            const rrfScore = 1 / (RRF_K + i + 1);
+            scoreMap.set(r.relativePath, {
+                score: rrfScore,
+                result: r,
+                sources: new Set(["keyword"]),
+            });
+        }
+        // Score semantic results and merge
+        for (let i = 0; i < semanticResults.length; i++) {
+            const r = semanticResults[i];
+            const rrfScore = 1 / (RRF_K + i + 1);
+            const existing = scoreMap.get(r.relativePath);
+            if (existing) {
+                existing.score += rrfScore;
+                existing.sources.add("semantic");
+                // Use semantic snippet if keyword snippet is empty
+                if (!existing.result.snippet && r.snippet) {
+                    existing.result.snippet = r.snippet;
+                }
+            }
+            else {
+                scoreMap.set(r.relativePath, {
+                    score: rrfScore,
+                    result: r,
+                    sources: new Set(["semantic"]),
+                });
+            }
+        }
+        // Sort by combined RRF score descending
+        const fused = Array.from(scoreMap.values())
+            .sort((a, b) => b.score - a.score)
+            .slice(0, limit)
+            .map((entry) => ({
+            ...entry.result,
+            score: entry.score,
+            sources: Array.from(entry.sources),
+        }));
+        return fused;
+    }
+    /**
+     * Reindex all embeddings from all stores.
+     * Returns count of files indexed.
+     */
+    async reindex(onProgress) {
+        // Gather all memories from all stores
+        const allMemories = await this.resolver.getAllMemories();
+        // Clear existing embeddings
+        this.embeddings.clear();
+        let indexed = 0;
+        const total = allMemories.length;
+        // Process in batches for efficiency
+        const batchSize = 32;
+        for (let i = 0; i < allMemories.length; i += batchSize) {
+            const batch = allMemories.slice(i, i + batchSize);
+            // Prepare texts: combine title + relevance + content for embedding
+            const texts = batch.map((m) => {
+                const tags = Array.isArray(m.frontmatter.tags)
+                    ? m.frontmatter.tags.join(" ")
+                    : Object.values(m.frontmatter.tags).flat().join(" ");
+                return `${m.frontmatter.title}\n${m.frontmatter.relevance || ""}\n${tags}\n${m.content}`;
+            });
+            const embeddings = await this.embeddings.embedBatch(texts);
+            for (let j = 0; j < batch.length; j++) {
+                const memory = batch[j];
+                const embedding = embeddings[j];
+                const hash = GnosysEmbeddings.contentHash(texts[j]);
+                // Use the store-prefixed path for multi-store support
+                const indexPath = `${memory.sourceLabel}:${memory.relativePath}`;
+                this.embeddings.storeEmbedding(indexPath, embedding, hash);
+                indexed++;
+                onProgress?.(indexed, total, memory.relativePath);
+            }
+        }
+        return indexed;
+    }
+    /**
+     * Load full content for search results (used by Ask engine).
+     * Handles both active memories and archived memories.
+     */
+    async loadContent(results) {
+        // v2.0 DB-backed fast path
+        if (this.dbSearch) {
+            return this.dbSearch.loadContent(results);
+        }
+        const enriched = [];
+        let archive = null;
+        for (const r of results) {
+            if (r.fromArchive && r.memoryId) {
+                // Load from archive
+                if (!archive) {
+                    archive = new GnosysArchive(this.storePath);
+                }
+                if (archive.isAvailable()) {
+                    const archived = archive.getArchivedMemory(r.memoryId);
+                    if (archived) {
+                        enriched.push({
+                            ...r,
+                            fullContent: archived.content,
+                        });
+                        continue;
+                    }
+                }
+                enriched.push(r);
+            }
+            else {
+                const memory = await this.resolver.readMemory(r.relativePath);
+                if (memory) {
+                    enriched.push({
+                        ...r,
+                        fullContent: memory.content,
+                        memoryId: memory.frontmatter.id,
+                    });
+                }
+                else {
+                    enriched.push(r);
+                }
+            }
+        }
+        archive?.close();
+        return enriched;
+    }
+    /**
+     * Check if embeddings are available.
+     */
+    hasEmbeddings() {
+        if (this.dbSearch)
+            return this.dbSearch.hasEmbeddings();
+        return this.embeddings.hasEmbeddings();
+    }
+    /**
+     * Get embedding count.
+     */
+    embeddingCount() {
+        if (this.dbSearch)
+            return this.dbSearch.embeddingCount();
+        return this.embeddings.count();
+    }
+}
+//# sourceMappingURL=hybridSearch.js.map

package/dist/lib/hybridSearch.js.map

@@ -0,0 +1 @@
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package/dist/lib/import.d.ts

@@ -0,0 +1,52 @@
+/**
+ * Gnosys Bulk Import — Structured data → atomic memories.
+ * Supports CSV, JSON, JSONL formats with LLM or structured ingestion modes.
+ * Shared core used by both the MCP tool and CLI command.
+ */
+import { GnosysIngestion } from "./ingest.js";
+import { GnosysStore } from "./store.js";
+export interface ImportOptions {
+    format: "csv" | "json" | "jsonl";
+    data: string;
+    mapping: Record<string, string>;
+    mode: "llm" | "structured";
+    limit?: number;
+    offset?: number;
+    dryRun?: boolean;
+    skipExisting?: boolean;
+    batchCommit?: boolean;
+    concurrency?: number;
+    author?: "human" | "ai" | "human+ai";
+    authority?: "declared" | "observed" | "imported" | "inferred";
+    onProgress?: (progress: ImportProgress) => void;
+}
+export interface ImportProgress {
+    processed: number;
+    total: number;
+    current: string;
+    stage: "parsing" | "deduplicating" | "ingesting" | "writing" | "committing";
+}
+export interface ImportResult {
+    imported: Array<{
+        title: string;
+        category: string;
+        path: string;
+    }>;
+    skipped: string[];
+    failed: Array<{
+        record: string;
+        error: string;
+    }>;
+    totalProcessed: number;
+    duration: number;
+}
+export declare function performImport(store: GnosysStore, ingestion: GnosysIngestion, options: ImportOptions): Promise<ImportResult>;
+/**
+ * Format a human-readable summary of import results.
+ */
+export declare function formatImportSummary(result: ImportResult): string;
+/**
+ * Estimate import duration for smart threshold guidance.
+ */
+export declare function estimateDuration(recordCount: number, mode: "llm" | "structured", concurrency?: number): string;
+//# sourceMappingURL=import.d.ts.map

package/dist/lib/import.d.ts.map

@@ -0,0 +1 @@
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