amalfa 1.0.31 → 1.0.34

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "amalfa",
-	"version": "1.0.31",
+	"version": "1.0.34",
 	"description": "Local-first knowledge graph engine for AI agents. Transforms markdown into searchable memory with MCP protocol.",
 	"license": "MIT",
 	"homepage": "https://github.com/pjsvis/amalfa#readme",
@@ -46,7 +46,8 @@
 		"@biomejs/biome": "2.3.8",
 		"@types/bun": "1.3.4",
 		"only-allow": "^1.2.2",
-		"pino-pretty": "^13.1.3"
+		"pino-pretty": "^13.1.3",
+		"typescript": "^5.9.3"
 	},
 	"scripts": {
 		"precommit": "bun run scripts/maintenance/pre-commit.ts",

package/src/cli/sonar-chat.ts

@@ -1,5 +1,5 @@
 // import { Command } from "commander";
-import { createInterface } from "readline";
+import { createInterface } from "node:readline";
 import { DaemonManager } from "../utils/DaemonManager";
 
 export async function chatLoop() {

package/src/cli.ts

@@ -1,7 +1,7 @@
 #!/usr/bin/env bun
-import { existsSync, statSync } from "fs";
-import { join } from "path";
-import { spawn } from "child_process";
+import { spawn } from "node:child_process";
+import { existsSync, statSync } from "node:fs";
+import { join } from "node:path";
 import pkg from "../package.json" with { type: "json" };
 
 const VERSION = pkg.version;
@@ -551,7 +551,7 @@ async function cmdSetupMcp() {
 		mcpServers: {
 			amalfa: {
 				command: "bun",
-				args: ["run", mcpScript],
+				args: ["run", "--cwd", cwd, mcpScript],
 				env: {
 					PATH: minimalPath,
 				},

package/src/config/defaults.ts

@@ -3,8 +3,8 @@
  * Default settings that can be overridden via amalfa.config.{ts,js,json}
  */
 
-import { mkdirSync, existsSync } from "fs";
-import { join } from "path";
+import { existsSync, mkdirSync } from "node:fs";
+import { join } from "node:path";
 
 /** AMALFA directory structure */
 export const AMALFA_DIRS = {
@@ -289,10 +289,7 @@ export async function loadConfig(): Promise<AmalfaConfig> {
 
 				return merged;
 			}
-		} catch (e) {
-			// Silently continue to next config file
-			continue;
-		}
+		} catch (_e) {}
 	}
 
 	// Return defaults if no config found

package/src/core/EdgeWeaver.ts

@@ -134,7 +134,7 @@ export class EdgeWeaver {
 
 		for (const match of matches) {
 			if (!match[2]) continue;
-			let linkPath = match[2].trim();
+			const linkPath = match[2].trim();
 
 			// Skip external links (http/https)
 			if (linkPath.startsWith("http://") || linkPath.startsWith("https://")) {

package/src/core/GraphEngine.ts

@@ -1,11 +1,11 @@
 import type { Database } from "bun:sqlite";
+import { getLogger } from "@src/utils/Logger";
 import { MultiDirectedGraph } from "graphology";
-import { bidirectional as shortestPath } from "graphology-shortest-path/unweighted";
 import communitiesLouvain from "graphology-communities-louvain";
-import pagerank from "graphology-metrics/centrality/pagerank";
-import betweenness from "graphology-metrics/centrality/betweenness";
 import { connectedComponents } from "graphology-components";
-import { getLogger } from "@src/utils/Logger";
+import betweenness from "graphology-metrics/centrality/betweenness";
+import pagerank from "graphology-metrics/centrality/pagerank";
+import { bidirectional as shortestPath } from "graphology-shortest-path/unweighted";
 
 const log = getLogger("GraphEngine");
 

package/src/core/MarkdownMasker.ts

@@ -1,4 +1,4 @@
-import { randomUUID } from "crypto";
+import { randomUUID } from "node:crypto";
 
 export class MarkdownMasker {
 	private stash: Map<string, string> = new Map();

package/src/daemon/index.ts

@@ -1,22 +1,22 @@
 #!/usr/bin/env bun
+
 /**
  * AMALFA Daemon
  * File watcher for incremental database updates
  */
 
-import { existsSync } from "fs";
-import { watch } from "fs";
-import { join } from "path";
+import { existsSync, watch } from "node:fs";
+import { join } from "node:path";
 import {
-	loadConfig,
 	AMALFA_DIRS,
 	type AmalfaConfig,
+	loadConfig,
 } from "@src/config/defaults";
 import { AmalfaIngestor } from "@src/pipeline/AmalfaIngestor";
 import { ResonanceDB } from "@src/resonance/db";
 import { getLogger } from "@src/utils/Logger";
-import { ServiceLifecycle } from "@src/utils/ServiceLifecycle";
 import { sendNotification } from "@src/utils/Notifications";
+import { ServiceLifecycle } from "@src/utils/ServiceLifecycle";
 
 const args = process.argv.slice(2);
 const command = args[0] || "serve";
@@ -101,7 +101,7 @@ function startWatcher(sourceDir: string, debounceMs: number) {
 	try {
 		watch(watchPath, { recursive: true }, (event, filename) => {
 			// Only process markdown files
-			if (filename && filename.endsWith(".md")) {
+			if (filename?.endsWith(".md")) {
 				const fullPath = join(watchPath, filename);
 
 				log.debug(

package/src/daemon/sonar-agent.ts

@@ -21,6 +21,7 @@ import {
 	discoverOllamaCapabilities,
 } from "@src/utils/ollama-discovery";
 import { ServiceLifecycle } from "@src/utils/ServiceLifecycle";
+import { inferenceState } from "./sonar-inference";
 import {
 	handleBatchEnhancement,
 	handleChat,
@@ -44,7 +45,6 @@ import type {
 	SearchRerankRequest,
 	SonarTask,
 } from "./sonar-types";
-import { inferenceState } from "./sonar-inference";
 
 const args = process.argv.slice(2);
 const command = args[0] || "serve";

package/src/daemon/sonar-inference.ts

@@ -1,4 +1,4 @@
-import { AMALFA_DIRS, loadConfig } from "@src/config/defaults";
+import { loadConfig } from "@src/config/defaults";
 import { getLogger } from "@src/utils/Logger";
 import type { Message, RequestOptions } from "./sonar-types";
 

package/src/daemon/sonar-logic.ts

@@ -197,14 +197,22 @@ export async function handleSearchAnalysis(
 				{
 					role: "system",
 					content:
-						'Analyze search queries and extract intent, entities and suggested filters. Return JSON: { "intent": "", "entities": [], "filters": {} }',
+						'Analyze the user query. Extract the search intent, key entities, and any implicit filters. You MUST return valid JSON. Example: { "intent": "informational", "entities": ["vector"], "filters": {} }. Do not include any text outside the JSON object.',
 				},
 				{ role: "user", content: query },
 			],
 			{ temperature: 0.1, format: "json" },
 		);
 
-		return JSON.parse(response.message.content);
+		const parsed = safeJsonParse(response.message.content);
+		if (!parsed) {
+			log.warn(
+				{ content: response.message.content },
+				"Failed to parse JSON response, using fallback",
+			);
+			return { intent: "search", entities: [query], filters: {} };
+		}
+		return parsed;
 	} catch (error) {
 		log.error({ error, query }, "Query analysis failed");
 		throw error;
@@ -250,7 +258,10 @@ export async function handleResultReranking(
 
 		const content = response.message.content;
 		try {
-			const rankings = JSON.parse(content);
+			const rankings = safeJsonParse(content);
+			if (!rankings || !Array.isArray(rankings))
+				throw new Error("Invalid JSON");
+
 			return results.map((result, idx) => {
 				const ranking = rankings.find(
 					(r: { index: number }) => r.index === idx + 1,
@@ -283,19 +294,25 @@ export async function handleContextExtraction(
 				{
 					role: "system",
 					content:
-						"Extract the most relevant 200-300 character snippet from the document for the given query.",
+						"You are a helpful assistant. Extract the exact text snippet from the document that answers the query. Return ONLY the snippet text. If the answer is not found, return the most relevant paragraph.",
 				},
 				{
 					role: "user",
-					content: `Query: ${query}\nDocument [${result.id}]:\n${result.content.slice(0, 4000)}`,
+					content: `Query: ${query}\n\nDocument Text:\n${result.content.slice(0, 4000)}`,
 				},
 			],
-			{ temperature: 0 },
+			{ temperature: 0.1 },
 		);
 
+		const snippet = response.message.content.trim();
+
+		// Fallback if model refuses to extract or returns empty
+		const finalSnippet =
+			snippet.length > 5 ? snippet : result.content.slice(0, 300).trim();
+
 		return {
 			id: result.id,
-			snippet: response.message.content.trim(),
+			snippet: finalSnippet,
 		};
 	} catch (error) {
 		log.error({ error, docId: result.id }, "Context extraction failed");
@@ -520,17 +537,11 @@ Return JSON: { "action": "SEARCH"|"READ"|"EXPLORE"|"FINISH", "query": "...", "no
 				nodeId?: string;
 				reasoning: string;
 				answer?: string;
-			};
-			try {
-				decision = JSON.parse(content);
-			} catch {
-				// Try to extract JSON from markdown blocks
-				const match = content.match(/\{[\s\S]*\}/);
-				if (match) {
-					decision = JSON.parse(match[0]);
-				} else {
-					throw new Error("Could not parse JSON from response");
-				}
+			} | null = null;
+
+			decision = safeJsonParse(content);
+			if (!decision) {
+				throw new Error("Could not parse JSON from response");
 			}
 			output += `> **Reasoning:** ${decision.reasoning}\n\n`;
 
@@ -635,13 +646,7 @@ Return JSON: { "answered": true|false, "missing_info": "...", "final_answer": ".
 			missing_info: string;
 			final_answer: string;
 		};
-		let audit: AuditResult | null = null;
-		try {
-			audit = JSON.parse(resultSnippet);
-		} catch {
-			const match = resultSnippet.match(/\{[\s\S]*\}/);
-			audit = match ? JSON.parse(match[0]) : null;
-		}
+		const audit = safeJsonParse(resultSnippet) as AuditResult | null;
 
 		if (audit) {
 			if (!audit.answered) {
@@ -660,3 +665,23 @@ Return JSON: { "answered": true|false, "missing_info": "...", "final_answer": ".
 
 	return output;
 }
+
+/**
+ * Helper to safely parse JSON from LLM responses, handling markdown blocks
+ */
+function safeJsonParse(content: string): any {
+	try {
+		return JSON.parse(content);
+	} catch {
+		// Try to extract JSON from markdown blocks
+		const match = content.match(/\{[\s\S]*\}/);
+		if (match) {
+			try {
+				return JSON.parse(match[0]);
+			} catch {
+				return null;
+			}
+		}
+		return null;
+	}
+}

package/src/daemon/sonar-strategies.ts

@@ -1,7 +1,6 @@
 import { loadConfig } from "@src/config/defaults";
 import { getLogger } from "@src/utils/Logger";
 import { callOllama, inferenceState } from "./sonar-inference";
-import type { SonarTask } from "./sonar-types";
 
 const log = getLogger("SonarStrategies");
 

package/src/mcp/index.ts

@@ -1,5 +1,5 @@
-import { appendFileSync } from "fs";
-import { join } from "path";
+import { appendFileSync } from "node:fs";
+import { join } from "node:path";
 import { Server } from "@modelcontextprotocol/sdk/server/index.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import {
@@ -200,7 +200,7 @@ async function runServer() {
 					let queryAnalysis: Awaited<
 						ReturnType<typeof sonarClient.analyzeQuery>
 					> | null = null;
-					let queryIntent: string | undefined = undefined;
+					let queryIntent: string | undefined;
 
 					if (sonarAvailable) {
 						log.info({ query }, "🔍 Analyzing query with Sonar");

package/src/pipeline/AmalfaIngestor.ts

@@ -4,7 +4,7 @@
  * No Persona/CDA complexity - just pure markdown → knowledge graph
  */
 
-import { join } from "path";
+import { join } from "node:path";
 import type { AmalfaConfig } from "@src/config/defaults";
 import { EdgeWeaver } from "@src/core/EdgeWeaver";
 import type { Node, ResonanceDB } from "@src/resonance/db";

package/src/pipeline/PreFlightAnalyzer.ts

@@ -1,20 +1,27 @@
 /**
  * PreFlightAnalyzer
- * 
+ *
  * Validates source directories before ingestion to detect issues:
  * - Large files that need splitting
  * - Symlinks and circular references
  * - Empty or invalid files
  * - Estimated resource usage
- * 
+ *
  * Generates .amalfa/logs/pre-flight.log with recommendations.
  */
 
-import { existsSync, lstatSync, readdirSync, realpathSync, statSync, writeFileSync } from "fs";
-import { join, relative } from "path";
-import { getLogger } from "@src/utils/Logger";
+import {
+	existsSync,
+	lstatSync,
+	readdirSync,
+	realpathSync,
+	statSync,
+	writeFileSync,
+} from "node:fs";
+import { join } from "node:path";
 import type { AmalfaConfig } from "@src/config/defaults";
-import { AMALFA_DIRS, initAmalfaDirs } from "@src/config/defaults";
+import { initAmalfaDirs } from "@src/config/defaults";
+import { getLogger } from "@src/utils/Logger";
 
 const log = getLogger("PreFlightAnalyzer");
 
@@ -27,7 +34,13 @@ const WARN_TOTAL_SIZE_MB = 100;
 
 export interface FileIssue {
 	path: string;
-	issue: "too_large" | "too_small" | "symlink" | "circular_ref" | "empty" | "non_markdown";
+	issue:
+		| "too_large"
+		| "too_small"
+		| "symlink"
+		| "circular_ref"
+		| "empty"
+		| "non_markdown";
 	severity: "error" | "warning" | "info";
 	details: string;
 	recommendation?: string;
@@ -49,7 +62,6 @@ export class PreFlightAnalyzer {
 	private config: AmalfaConfig;
 	private visitedPaths = new Set<string>();
 	private issues: FileIssue[] = [];
-	private logPath = join(AMALFA_DIRS.logs, "pre-flight.log");
 
 	constructor(config: AmalfaConfig) {
 		this.config = config;
@@ -181,13 +193,14 @@ export class PreFlightAnalyzer {
 							issue: "circular_ref",
 							severity: "error",
 							details: "Circular symlink reference detected",
-							recommendation: "Remove circular symlink to prevent infinite loops",
+							recommendation:
+								"Remove circular symlink to prevent infinite loops",
 						});
 						return { valid: false, size: 0 };
 					}
 
 					this.visitedPaths.add(realPath);
-				} catch (err) {
+				} catch (_err) {
 					this.issues.push({
 						path: filePath,
 						issue: "circular_ref",
@@ -416,7 +429,9 @@ export class PreFlightAnalyzer {
 		lines.push("");
 		lines.push("Why this limit exists:");
 		lines.push("- Prevents excessive memory usage during embedding generation");
-		lines.push("- Ensures good search quality (large files = poor granularity)");
+		lines.push(
+			"- Ensures good search quality (large files = poor granularity)",
+		);
 		lines.push("- Maintains reasonable graph structure");
 		lines.push("");
 		lines.push("How to handle large files:");

package/src/pipeline/SemanticHarvester.ts

@@ -10,8 +10,8 @@
  * await harvester.loadIntoResonance(graph);
  */
 
-import { existsSync } from "fs";
-import { join } from "path";
+import { existsSync } from "node:fs";
+import { join } from "node:path";
 import { getLogger } from "@src/utils/Logger";
 import { $ } from "bun";
 

package/src/resonance/DatabaseFactory.ts

@@ -15,7 +15,10 @@ export const DatabaseFactory = {
 	 * Connects specifically to the main Resonance Graph database.
 	 * @deprecated Use connect() with explicit path from config instead.
 	 */
-	connectToResonance(dbPath: string = ".amalfa/resonance.db", options: { readonly?: boolean } = {}): Database {
+	connectToResonance(
+		dbPath: string = ".amalfa/resonance.db",
+		options: { readonly?: boolean } = {},
+	): Database {
 		return DatabaseFactory.connect(dbPath, options);
 	},
 	/**

package/src/resonance/services/embedder.ts

@@ -1,4 +1,4 @@
-import { join } from "path";
+import { join } from "node:path";
 import { toFafcas } from "@src/resonance/db";
 import { EmbeddingModel, FlagEmbedding } from "fastembed";
 

package/src/resonance/services/simpleTokenizer.ts

@@ -59,18 +59,18 @@ export class SimpleTokenizerService {
 					const realTerm = match ? match[0] : term;
 
 					if (tag === "Protocol") {
-						if (!result.protocols!.includes(realTerm))
-							result.protocols!.push(realTerm);
+						if (!result.protocols?.includes(realTerm))
+							result.protocols?.push(realTerm);
 					} else if (tag === "Concept") {
-						if (!result.concepts!.includes(realTerm))
-							result.concepts!.push(realTerm);
+						if (!result.concepts?.includes(realTerm))
+							result.concepts?.push(realTerm);
 					} else if (tag === "Organization") {
 						if (!result.organizations.includes(realTerm))
 							result.organizations.push(realTerm);
 					} else {
 						// Default to concepts
-						if (!result.concepts!.includes(realTerm))
-							result.concepts!.push(realTerm);
+						if (!result.concepts?.includes(realTerm))
+							result.concepts?.push(realTerm);
 					}
 				}
 			}

package/src/resonance/services/vector-daemon.ts

@@ -1,16 +1,17 @@
 #!/usr/bin/env bun
+
 /**
  * Vector Daemon - HTTP server for fast embedding generation
  * Keeps FastEmbed model loaded in memory for <100ms embedding lookups
  */
 
-import { serve } from "bun";
-import { join } from "path";
-import { EmbeddingModel, FlagEmbedding } from "fastembed";
+import { join } from "node:path";
+import { AMALFA_DIRS } from "@src/config/defaults";
 import { toFafcas } from "@src/resonance/db";
 import { getLogger } from "@src/utils/Logger";
 import { ServiceLifecycle } from "@src/utils/ServiceLifecycle";
-import { AMALFA_DIRS } from "@src/config/defaults";
+import { serve } from "bun";
+import { EmbeddingModel, FlagEmbedding } from "fastembed";
 
 const log = getLogger("VectorDaemon");
 const PORT = Number(process.env.VECTOR_PORT || 3010);
@@ -33,16 +34,16 @@ const currentModel = EmbeddingModel.BGESmallENV15;
 async function initEmbedder() {
 	if (!embedder) {
 		log.info({ model: currentModel }, "🔄 Initializing embedding model...");
-		
+
 		// Ensure cache directory exists
 		const cacheDir = ".amalfa/cache";
 		const { mkdir } = await import("node:fs/promises");
 		try {
 			await mkdir(cacheDir, { recursive: true });
-		} catch (e) {
+		} catch (_e) {
 			// Directory might already exist, that's fine
 		}
-		
+
 		embedder = await FlagEmbedding.init({
 			model: currentModel,
 			cacheDir,
@@ -60,7 +61,7 @@ async function runServer() {
 	await initEmbedder();
 
 	// Start HTTP server
-	const server = serve({
+	const _server = serve({
 		port: PORT,
 		async fetch(req) {
 			const url = new URL(req.url);

package/src/utils/DaemonManager.ts

@@ -1,7 +1,7 @@
-import { existsSync } from "fs";
-import { join } from "path";
-import { ServiceLifecycle } from "./ServiceLifecycle";
+import { existsSync } from "node:fs";
+import { join } from "node:path";
 import { AMALFA_DIRS } from "@src/config/defaults";
+import { ServiceLifecycle } from "./ServiceLifecycle";
 
 export interface DaemonStatus {
 	running: boolean;

package/src/utils/Notifications.ts

@@ -1,5 +1,5 @@
-import { spawn } from "child_process";
-import { platform } from "os";
+import { spawn } from "node:child_process";
+import { platform } from "node:os";
 
 /**
  * Send a native desktop notification

package/src/utils/ServiceLifecycle.ts

@@ -1,7 +1,6 @@
-import { existsSync } from "fs";
-import { unlink } from "fs/promises";
-import { join } from "path";
-import { AMALFA_DIRS, initAmalfaDirs } from "@src/config/defaults";
+import { existsSync } from "node:fs";
+import { unlink } from "node:fs/promises";
+import { initAmalfaDirs } from "@src/config/defaults";
 
 export interface ServiceConfig {
 	name: string; // e.g. "Daemon"

package/src/utils/StatsTracker.ts

@@ -1,5 +1,5 @@
-import { existsSync, mkdirSync } from "fs";
-import { join } from "path";
+import { existsSync, mkdirSync } from "node:fs";
+import { join } from "node:path";
 import { AMALFA_DIRS } from "@src/config/defaults";
 
 export interface DatabaseSnapshot {

package/src/utils/TagInjector.ts

@@ -1,4 +1,4 @@
-import { readFileSync, writeFileSync, existsSync } from "node:fs";
+import { existsSync, readFileSync, writeFileSync } from "node:fs";
 import { getLogger } from "@src/utils/Logger";
 
 const log = getLogger("TagInjector");
@@ -79,7 +79,7 @@ export class TagInjector {
 
 			if (content.includes(link)) return true;
 
-			content = content.trimEnd() + `\n\nSee also: ${link}\n`;
+			content = `${content.trimEnd()}\n\nSee also: ${link}\n`;
 			writeFileSync(filePath, content, "utf-8");
 			return true;
 		} catch (error) {

package/src/utils/ollama-discovery.ts

@@ -128,7 +128,7 @@ export async function discoverOllamaCapabilities(): Promise<OllamaCapabilities>
 		}
 
 		// Get model details for the selected model
-		const phi3 = models.find((m) => m.name === "phi3:latest");
+		const _phi3 = models.find((m) => m.name === "phi3:latest");
 
 		let modelInfo: unknown = null;
 		try {
@@ -136,7 +136,7 @@ export async function discoverOllamaCapabilities(): Promise<OllamaCapabilities>
 			if (showResult.exitCode === 0) {
 				modelInfo = parseModelInfo(showResult.stdout?.toString() ?? "");
 			}
-		} catch (e) {
+		} catch (_e) {
 			log.warn(`⚠️  Could not get details for ${searchModel}`);
 		}
 

package/src/utils/sonar-client.ts

@@ -35,7 +35,7 @@ export interface SonarClient {
 		result: { id: string; content: string },
 		query: string,
 	): Promise<{ snippet: string; context: string; confidence: number } | null>;
-	getGaps(limit?: number): Promise<any[]>;
+	getGaps(limit?: number): Promise<unknown[]>;
 }
 
 /**
@@ -56,7 +56,6 @@ export async function createSonarClient(): Promise<SonarClient> {
 
 	// Check if Sonar is enabled
 	// Checking both for backward compatibility or migration
-	// @ts-ignore
 	const isEnabled = config.sonar?.enabled ?? config.phi3?.enabled;
 
 	if (!isEnabled) {
@@ -64,9 +63,8 @@ export async function createSonarClient(): Promise<SonarClient> {
 		return createDisabledClient();
 	}
 
-	// @ts-ignore
 	const hostArgs = config.sonar || config.phi3 || {};
-	const host = hostArgs.host || "localhost:11434";
+	const _host = hostArgs.host || "localhost:11434";
 	const port = hostArgs.port || 3012;
 	const baseUrl = `http://localhost:${port}`;
 	const timeout = hostArgs.tasks?.search?.timeout || 5000;
@@ -257,12 +255,12 @@ export async function createSonarClient(): Promise<SonarClient> {
 			}
 		},
 
-		async getGaps(limit?: number): Promise<any[]> {
+		async getGaps(_limit?: number): Promise<unknown[]> {
 			if (!(await isAvailable())) return [];
 			try {
 				const response = await fetch(`${baseUrl}/graph/explore`);
 				if (!response.ok) return [];
-				const data = (await response.json()) as { gaps?: any[] };
+				const data = (await response.json()) as { gaps?: unknown[] };
 				return data.gaps || [];
 			} catch (error) {
 				log.error({ error }, "Failed to fetch gaps");
@@ -304,7 +302,7 @@ function createDisabledClient(): SonarClient {
 		} | null> {
 			return null;
 		},
-		async getGaps(): Promise<any[]> {
+		async getGaps(): Promise<unknown[]> {
 			return [];
 		},
 	};