gnosys 4.0.0

package/dist/lib/ask.d.ts

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+/**
+ * Gnosys Ask Engine — Freeform natural-language Q&A over the entire vault.
+ * Pipeline: hybridSearch → context assembly → LLM synthesis → cited answer.
+ *
+ * Supports streaming and "deep query" mode (auto follow-up on insufficient context).
+ * Uses the LLM abstraction layer — works with Anthropic, Ollama, or any future provider.
+ */
+import { GnosysHybridSearch } from "./hybridSearch.js";
+import { GnosysConfig } from "./config.js";
+import { GnosysResolver } from "./resolver.js";
+export interface AskResult {
+    answer: string;
+    sources: {
+        relativePath: string;
+        title: string;
+    }[];
+    deepQueryUsed: boolean;
+    searchMode: string;
+    /** Memory IDs that were dearchived (moved from archive → active) during this query */
+    dearchivedIds: string[];
+}
+export interface AskStreamCallbacks {
+    onToken?: (token: string) => void;
+    onSearchComplete?: (count: number, mode: string) => void;
+    onDeepQuery?: (refinedQuery: string) => void;
+    onSourcesReady?: (sources: {
+        relativePath: string;
+        title: string;
+    }[]) => void;
+}
+export declare class GnosysAsk {
+    private provider;
+    private hybridSearch;
+    private config;
+    private promptTemplate;
+    private resolver;
+    private storePath;
+    constructor(hybridSearch: GnosysHybridSearch, config?: GnosysConfig, resolver?: GnosysResolver, storePath?: string);
+    get isLLMAvailable(): boolean;
+    get providerName(): string;
+    get modelName(): string;
+    /**
+     * Load the synthesis prompt template.
+     */
+    private loadPromptTemplate;
+    /**
+     * Format retrieved memories as numbered context blocks.
+     */
+    private formatContext;
+    /**
+     * Extract a refined search query from a partial answer that needs more info.
+     */
+    private extractRefinedQuery;
+    /**
+     * Ask a question and get a synthesized answer with citations.
+     */
+    ask(question: string, options?: {
+        limit?: number;
+        mode?: "keyword" | "semantic" | "hybrid";
+        stream?: boolean;
+        callbacks?: AskStreamCallbacks;
+        /** Additional context to prepend (e.g. from federated search) */
+        additionalContext?: string;
+    }): Promise<AskResult>;
+    /**
+     * Dearchive memories that were used in the synthesis.
+     * Uses deterministic fallback: if cited paths don't match archive results,
+     * falls back to title-matching from the answer text to ensure anything
+     * the answer actually references gets dearchived.
+     */
+    private dearchiveUsedMemories;
+    /**
+     * Extract sources that were actually cited in the answer.
+     */
+    private extractCitedSources;
+}
+//# sourceMappingURL=ask.d.ts.map

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

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package/dist/lib/ask.js

@@ -0,0 +1,316 @@
+/**
+ * Gnosys Ask Engine — Freeform natural-language Q&A over the entire vault.
+ * Pipeline: hybridSearch → context assembly → LLM synthesis → cited answer.
+ *
+ * Supports streaming and "deep query" mode (auto follow-up on insufficient context).
+ * Uses the LLM abstraction layer — works with Anthropic, Ollama, or any future provider.
+ */
+import fs from "fs/promises";
+import path from "path";
+import { fileURLToPath } from "url";
+import { DEFAULT_CONFIG } from "./config.js";
+import { getLLMProvider } from "./llm.js";
+import { GnosysArchive } from "./archive.js";
+import { GnosysMaintenanceEngine } from "./maintenance.js";
+import { auditLog } from "./audit.js";
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
+/**
+ * Phrases that trigger a deep query follow-up.
+ */
+const NEED_MORE_INFO_PHRASES = [
+    "i need more information",
+    "i don't have enough",
+    "insufficient information",
+    "not enough context",
+    "no relevant information",
+    "cannot find",
+    "none of the provided memories",
+    "the provided context does not",
+];
+export class GnosysAsk {
+    provider = null;
+    hybridSearch;
+    config;
+    promptTemplate = null;
+    resolver = null;
+    storePath = null;
+    constructor(hybridSearch, config, resolver, storePath) {
+        this.hybridSearch = hybridSearch;
+        this.config = config || DEFAULT_CONFIG;
+        this.resolver = resolver || null;
+        this.storePath = storePath || null;
+        // Initialize LLM provider via abstraction layer
+        try {
+            this.provider = getLLMProvider(this.config, "synthesis");
+        }
+        catch {
+            // Provider not available (e.g., no API key for Anthropic)
+            this.provider = null;
+        }
+    }
+    get isLLMAvailable() {
+        return this.provider !== null;
+    }
+    get providerName() {
+        return this.provider?.name || "none";
+    }
+    get modelName() {
+        return this.provider?.model || "none";
+    }
+    /**
+     * Load the synthesis prompt template.
+     */
+    async loadPromptTemplate() {
+        if (this.promptTemplate)
+            return this.promptTemplate;
+        // Try loading from the installed package prompts/ directory
+        const candidates = [
+            path.resolve(__dirname, "..", "..", "prompts", "synthesize.md"),
+            path.resolve(__dirname, "..", "prompts", "synthesize.md"),
+            path.resolve(process.cwd(), "prompts", "synthesize.md"),
+        ];
+        for (const candidate of candidates) {
+            try {
+                this.promptTemplate = await fs.readFile(candidate, "utf-8");
+                return this.promptTemplate;
+            }
+            catch {
+                // Try next
+            }
+        }
+        // Fallback inline prompt
+        this.promptTemplate = `You are Gnosys, a knowledge synthesis engine. Answer the question using ONLY the provided context memories. Cite every claim with Obsidian wikilinks [[filename.md]]. If the context is insufficient, say "I need more information to fully answer this question."
+
+## Context Memories
+
+{{CONTEXT}}
+
+## Question
+
+{{QUESTION}}`;
+        return this.promptTemplate;
+    }
+    /**
+     * Format retrieved memories as numbered context blocks.
+     */
+    formatContext(results) {
+        return results
+            .map((r, i) => {
+            const content = r.fullContent || r.snippet;
+            return `### [${i + 1}] ${r.title}\n**File:** ${r.relativePath}\n**Score:** ${r.score.toFixed(4)}\n\n${content}`;
+        })
+            .join("\n\n---\n\n");
+    }
+    /**
+     * Extract a refined search query from a partial answer that needs more info.
+     */
+    extractRefinedQuery(question, _partialAnswer) {
+        // Take the original question but add "related" to broaden the search
+        return `${question} related details`;
+    }
+    /**
+     * Ask a question and get a synthesized answer with citations.
+     */
+    async ask(question, options) {
+        if (!this.provider) {
+            const providerName = this.config.llm.defaultProvider;
+            throw new Error(providerName === "anthropic"
+                ? "No ANTHROPIC_API_KEY set. gnosys_ask requires an LLM for synthesis. " +
+                    "Set the ANTHROPIC_API_KEY environment variable or switch to Ollama: gnosys config set provider ollama"
+                : `LLM provider "${providerName}" is not available. Check your configuration.`);
+        }
+        const limit = options?.limit || 15;
+        const mode = options?.mode || "hybrid";
+        const callbacks = options?.callbacks;
+        // Step 1: Hybrid search for relevant memories
+        let results = await this.hybridSearch.hybridSearch(question, limit, mode);
+        callbacks?.onSearchComplete?.(results.length, mode);
+        if (results.length === 0) {
+            return {
+                answer: "No relevant memories found. Try importing some data first with `gnosys import` or creating memories with `gnosys add`.",
+                sources: [],
+                deepQueryUsed: false,
+                searchMode: mode,
+                dearchivedIds: [],
+            };
+        }
+        // Step 2: Load full content for top results
+        results = await this.hybridSearch.loadContent(results);
+        // Step 3: Build prompt
+        const template = await this.loadPromptTemplate();
+        let context = this.formatContext(results);
+        // Prepend federated/cross-scope context if provided
+        if (options?.additionalContext) {
+            context = `## Cross-Scope Context (Federated Search)\n${options.additionalContext}\n\n## Local Context\n${context}`;
+        }
+        const systemPrompt = template
+            .replace("{{CONTEXT}}", context)
+            .replace("{{QUESTION}}", question);
+        // Step 4: LLM synthesis via abstraction layer
+        let answer;
+        if (options?.stream && callbacks?.onToken) {
+            answer = await this.provider.generate(question, { system: systemPrompt, stream: true }, { onToken: callbacks.onToken });
+        }
+        else {
+            answer = await this.provider.generate(question, { system: systemPrompt });
+        }
+        // Step 5: Check for deep query trigger
+        let deepQueryUsed = false;
+        const answerLower = answer.toLowerCase();
+        const needsMoreInfo = NEED_MORE_INFO_PHRASES.some((phrase) => answerLower.includes(phrase));
+        if (needsMoreInfo) {
+            const refinedQuery = this.extractRefinedQuery(question, answer);
+            callbacks?.onDeepQuery?.(refinedQuery);
+            // Run follow-up search
+            const moreResults = await this.hybridSearch.hybridSearch(refinedQuery, limit, mode);
+            if (moreResults.length > 0) {
+                // Merge with original results (dedup by path)
+                const existingPaths = new Set(results.map((r) => r.relativePath));
+                const newResults = moreResults.filter((r) => !existingPaths.has(r.relativePath));
+                if (newResults.length > 0) {
+                    const enrichedNew = await this.hybridSearch.loadContent(newResults);
+                    const allResults = [...results, ...enrichedNew];
+                    // Re-synthesize with expanded context
+                    const expandedContext = this.formatContext(allResults);
+                    const expandedPrompt = template
+                        .replace("{{CONTEXT}}", expandedContext)
+                        .replace("{{QUESTION}}", question);
+                    if (options?.stream && callbacks?.onToken) {
+                        answer = await this.provider.generate(question, { system: expandedPrompt, stream: true }, { onToken: callbacks.onToken });
+                    }
+                    else {
+                        answer = await this.provider.generate(question, {
+                            system: expandedPrompt,
+                        });
+                    }
+                    results = allResults;
+                    deepQueryUsed = true;
+                }
+            }
+        }
+        // Step 6: Extract sources from the answer (only cited files)
+        const sources = this.extractCitedSources(answer, results);
+        callbacks?.onSourcesReady?.(sources);
+        // Step 7: Auto-dearchive — move used archive memories back to active
+        const dearchivedIds = await this.dearchiveUsedMemories(results, sources);
+        // Audit log
+        auditLog({
+            operation: "ask",
+            query: question,
+            resultCount: sources.length,
+            details: {
+                deepQueryUsed,
+                dearchivedCount: dearchivedIds.length,
+                searchMode: mode,
+            },
+        });
+        return {
+            answer,
+            sources,
+            deepQueryUsed,
+            searchMode: mode,
+            dearchivedIds,
+        };
+    }
+    /**
+     * Dearchive memories that were used in the synthesis.
+     * Uses deterministic fallback: if cited paths don't match archive results,
+     * falls back to title-matching from the answer text to ensure anything
+     * the answer actually references gets dearchived.
+     */
+    async dearchiveUsedMemories(results, sources) {
+        if (!this.storePath || !this.resolver)
+            return [];
+        // Find archive results that were cited (or all archive results if they contributed to the answer)
+        const archiveResults = results.filter((r) => r.fromArchive && r.memoryId);
+        if (archiveResults.length === 0)
+            return [];
+        // Determine which archive results were actually used
+        const citedPaths = new Set(sources.map((s) => s.relativePath));
+        let usedArchiveIds = archiveResults
+            .filter((r) => citedPaths.has(r.relativePath))
+            .map((r) => r.memoryId)
+            .filter(Boolean);
+        // Deterministic fallback: if no archive results matched by path,
+        // check if any archive memory titles appear in the cited sources' titles
+        if (usedArchiveIds.length === 0) {
+            const citedTitles = new Set(sources.map((s) => s.title.toLowerCase()));
+            usedArchiveIds = archiveResults
+                .filter((r) => citedTitles.has(r.title.toLowerCase()))
+                .map((r) => r.memoryId)
+                .filter(Boolean);
+        }
+        // Final fallback: dearchive ALL archive results that were in the search context
+        // (they contributed to the LLM's answer even if not explicitly cited)
+        if (usedArchiveIds.length === 0 && archiveResults.length > 0) {
+            usedArchiveIds = archiveResults
+                .map((r) => r.memoryId)
+                .filter(Boolean);
+        }
+        if (usedArchiveIds.length === 0)
+            return [];
+        try {
+            const archive = new GnosysArchive(this.storePath);
+            if (!archive.isAvailable())
+                return [];
+            const writeTarget = this.resolver.getWriteTarget();
+            if (!writeTarget) {
+                archive.close();
+                return [];
+            }
+            const restored = await archive.dearchiveBatch(usedArchiveIds, writeTarget.store);
+            archive.close();
+            // Reinforce the restored memories
+            if (restored.length > 0) {
+                try {
+                    await GnosysMaintenanceEngine.reinforceBatch(writeTarget.store, restored);
+                }
+                catch {
+                    // Reinforcement is best-effort
+                }
+            }
+            return usedArchiveIds;
+        }
+        catch {
+            return [];
+        }
+    }
+    /**
+     * Extract sources that were actually cited in the answer.
+     */
+    extractCitedSources(answer, results) {
+        const cited = [];
+        const seen = new Set();
+        // Match [[filename.md]] patterns
+        const wikiLinkRegex = /\[\[([^\]]+)\]\]/g;
+        let match;
+        while ((match = wikiLinkRegex.exec(answer)) !== null) {
+            const cited_file = match[1];
+            // Find matching result
+            for (const r of results) {
+                const filename = r.relativePath.split("/").pop() || r.relativePath;
+                if ((r.relativePath === cited_file ||
+                    r.relativePath.endsWith(cited_file) ||
+                    filename === cited_file ||
+                    filename === cited_file + ".md") &&
+                    !seen.has(r.relativePath)) {
+                    seen.add(r.relativePath);
+                    cited.push({ relativePath: r.relativePath, title: r.title });
+                    break;
+                }
+            }
+        }
+        // If no wikilinks found in answer, include all search results as sources
+        if (cited.length === 0) {
+            for (const r of results) {
+                if (!seen.has(r.relativePath)) {
+                    seen.add(r.relativePath);
+                    cited.push({ relativePath: r.relativePath, title: r.title });
+                }
+            }
+        }
+        return cited;
+    }
+}
+//# sourceMappingURL=ask.js.map

package/dist/lib/ask.js.map

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

@@ -0,0 +1,47 @@
+/**
+ * Gnosys Audit — Structured JSON logging for every memory operation.
+ *
+ * Provides observability for enterprise agent systems. Every read, write,
+ * reinforce, dearchive, and recall operation is logged with timestamps
+ * and optional traceIds for correlation with the outer orchestrator.
+ *
+ * Logs are stored in .gnosys/.config/audit.jsonl (append-only).
+ */
+export interface AuditEntry {
+    timestamp: string;
+    operation: AuditOperation;
+    memoryId?: string;
+    memoryTitle?: string;
+    query?: string;
+    resultCount?: number;
+    durationMs?: number;
+    traceId?: string;
+    details?: Record<string, unknown>;
+}
+export type AuditOperation = "read" | "write" | "update" | "delete" | "reinforce" | "dearchive" | "archive" | "maintain" | "search" | "ask" | "recall" | "consolidate" | "decay";
+/**
+ * Initialize the audit log for a specific store path.
+ * Creates .gnosys/.config/audit.jsonl if it doesn't exist.
+ */
+export declare function initAudit(storePath: string): void;
+/**
+ * Log an audit entry. Fire-and-forget — never blocks the caller.
+ */
+export declare function auditLog(entry: Omit<AuditEntry, "timestamp">): void;
+/**
+ * Read audit entries, optionally filtered by days.
+ */
+export declare function readAuditLog(storePath: string, options?: {
+    days?: number;
+    operation?: AuditOperation;
+    limit?: number;
+}): AuditEntry[];
+/**
+ * Format audit entries as a human-readable timeline.
+ */
+export declare function formatAuditTimeline(entries: AuditEntry[]): string;
+/**
+ * Close the audit stream cleanly.
+ */
+export declare function closeAudit(): void;
+//# sourceMappingURL=audit.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/lib/audit.js

@@ -0,0 +1,136 @@
+/**
+ * Gnosys Audit — Structured JSON logging for every memory operation.
+ *
+ * Provides observability for enterprise agent systems. Every read, write,
+ * reinforce, dearchive, and recall operation is logged with timestamps
+ * and optional traceIds for correlation with the outer orchestrator.
+ *
+ * Logs are stored in .gnosys/.config/audit.jsonl (append-only).
+ */
+import fs from "fs";
+import path from "path";
+// ─── Module State ───────────────────────────────────────────────────────
+let auditFilePath = null;
+let auditStream = null;
+/**
+ * Initialize the audit log for a specific store path.
+ * Creates .gnosys/.config/audit.jsonl if it doesn't exist.
+ */
+export function initAudit(storePath) {
+    const configDir = path.join(storePath, ".config");
+    // Ensure .config dir exists (sync — called once at startup)
+    try {
+        fs.mkdirSync(configDir, { recursive: true });
+    }
+    catch {
+        // Already exists
+    }
+    auditFilePath = path.join(configDir, "audit.jsonl");
+    // Open append-only write stream
+    auditStream = fs.createWriteStream(auditFilePath, { flags: "a" });
+}
+/**
+ * Log an audit entry. Fire-and-forget — never blocks the caller.
+ */
+export function auditLog(entry) {
+    const full = {
+        timestamp: new Date().toISOString(),
+        ...entry,
+    };
+    if (auditStream && !auditStream.destroyed) {
+        auditStream.write(JSON.stringify(full) + "\n");
+    }
+}
+/**
+ * Read audit entries, optionally filtered by days.
+ */
+export function readAuditLog(storePath, options) {
+    const logPath = path.join(storePath, ".config", "audit.jsonl");
+    let raw;
+    try {
+        raw = fs.readFileSync(logPath, "utf-8");
+    }
+    catch {
+        return [];
+    }
+    const lines = raw.trim().split("\n").filter(Boolean);
+    let entries = [];
+    for (const line of lines) {
+        try {
+            entries.push(JSON.parse(line));
+        }
+        catch {
+            // Skip malformed lines
+        }
+    }
+    // Filter by days
+    if (options?.days) {
+        const cutoff = new Date();
+        cutoff.setDate(cutoff.getDate() - options.days);
+        const cutoffStr = cutoff.toISOString();
+        entries = entries.filter((e) => e.timestamp >= cutoffStr);
+    }
+    // Filter by operation
+    if (options?.operation) {
+        entries = entries.filter((e) => e.operation === options.operation);
+    }
+    // Limit (take most recent)
+    if (options?.limit) {
+        entries = entries.slice(-options.limit);
+    }
+    return entries;
+}
+/**
+ * Format audit entries as a human-readable timeline.
+ */
+export function formatAuditTimeline(entries) {
+    if (entries.length === 0) {
+        return "No audit entries found for the specified period.";
+    }
+    const lines = [
+        `Gnosys Audit Trail — ${entries.length} operations`,
+        "═".repeat(60),
+        "",
+    ];
+    // Group by date
+    const byDate = new Map();
+    for (const entry of entries) {
+        const date = entry.timestamp.split("T")[0];
+        if (!byDate.has(date))
+            byDate.set(date, []);
+        byDate.get(date).push(entry);
+    }
+    for (const [date, dayEntries] of byDate) {
+        lines.push(`── ${date} (${dayEntries.length} ops) ──`);
+        for (const e of dayEntries) {
+            const time = e.timestamp.split("T")[1]?.split(".")[0] || "";
+            const duration = e.durationMs ? ` (${e.durationMs.toFixed(1)}ms)` : "";
+            const trace = e.traceId ? ` [trace:${e.traceId.substring(0, 8)}]` : "";
+            const memory = e.memoryId ? ` → ${e.memoryId}` : "";
+            const query = e.query ? ` q="${e.query.substring(0, 30)}"` : "";
+            const count = e.resultCount !== undefined ? ` (${e.resultCount} results)` : "";
+            lines.push(`  ${time}  ${e.operation.toUpperCase().padEnd(12)}${memory}${query}${count}${duration}${trace}`);
+        }
+        lines.push("");
+    }
+    // Summary
+    const opCounts = new Map();
+    for (const e of entries) {
+        opCounts.set(e.operation, (opCounts.get(e.operation) || 0) + 1);
+    }
+    lines.push("Summary:");
+    for (const [op, count] of [...opCounts.entries()].sort((a, b) => b[1] - a[1])) {
+        lines.push(`  ${op}: ${count}`);
+    }
+    return lines.join("\n");
+}
+/**
+ * Close the audit stream cleanly.
+ */
+export function closeAudit() {
+    if (auditStream && !auditStream.destroyed) {
+        auditStream.end();
+        auditStream = null;
+    }
+}
+//# sourceMappingURL=audit.js.map

package/dist/lib/audit.js.map

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

@@ -0,0 +1,56 @@
+/**
+ * Gnosys Bootstrap — Batch-ingest existing documents into the memory store.
+ *
+ * Scans a directory for markdown/text files and creates memories from them.
+ * Supports both raw import (no LLM) and enriched import (LLM structures content).
+ */
+import { GnosysStore, MemoryFrontmatter } from "./store.js";
+export interface BootstrapOptions {
+    /** Source directory to scan */
+    sourceDir: string;
+    /** File glob patterns to include */
+    patterns?: string[];
+    /** Whether to skip files that already exist in the store */
+    skipExisting?: boolean;
+    /** Default category for ingested files */
+    defaultCategory?: string;
+    /** Default author */
+    defaultAuthor?: "human" | "ai" | "human+ai";
+    /** Default authority level */
+    defaultAuthority?: "declared" | "observed" | "imported" | "inferred";
+    /** Default confidence */
+    defaultConfidence?: number;
+    /** Whether to preserve existing frontmatter if present */
+    preserveFrontmatter?: boolean;
+    /** Dry run - report what would be imported without writing */
+    dryRun?: boolean;
+}
+export interface BootstrapResult {
+    /** Files that were successfully imported */
+    imported: string[];
+    /** Files that were skipped (already exist) */
+    skipped: string[];
+    /** Files that failed to import */
+    failed: Array<{
+        path: string;
+        error: string;
+    }>;
+    /** Total files scanned */
+    totalScanned: number;
+}
+/**
+ * Scan a directory and discover importable files.
+ */
+export declare function discoverFiles(sourceDir: string, patterns?: string[]): Promise<string[]>;
+/**
+ * Parse a single file and prepare it for import.
+ */
+export declare function parseFileForImport(content: string, relativePath: string, options: BootstrapOptions): {
+    frontmatter: Partial<MemoryFrontmatter>;
+    body: string;
+};
+/**
+ * Bootstrap: batch-import files from a directory into a Gnosys store.
+ */
+export declare function bootstrap(store: GnosysStore, options: BootstrapOptions): Promise<BootstrapResult>;
+//# sourceMappingURL=bootstrap.d.ts.map