amalfa 1.0.36 → 1.0.37

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "amalfa",
-	"version": "1.0.36",
+	"version": "1.0.37",
 	"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",
@@ -45,9 +45,9 @@
 	"devDependencies": {
 		"@biomejs/biome": "2.3.8",
 		"@types/bun": "1.3.4",
-		"only-allow": "^1.2.2",
-		"pino-pretty": "^13.1.3",
-		"typescript": "^5.9.3"
+		"only-allow": "1.2.2",
+		"pino-pretty": "13.1.3",
+		"typescript": "5.9.3"
 	},
 	"scripts": {
 		"precommit": "bun run scripts/maintenance/pre-commit.ts",
@@ -64,9 +64,12 @@
 	},
 	"dependencies": {
 		"@modelcontextprotocol/sdk": "1.25.2",
+		"drizzle-kit": "0.31.8",
+		"drizzle-orm": "0.45.1",
 		"fastembed": "2.0.0",
-		"graphology": "^0.26.0",
-		"graphology-library": "^0.8.0",
-		"pino": "^10.1.0"
+		"graphology": "0.26.0",
+		"graphology-library": "0.8.0",
+		"hono": "4.11.3",
+		"pino": "10.1.0"
 	}
 }

package/src/daemon/sonar-agent.ts

@@ -24,27 +24,14 @@ import { ServiceLifecycle } from "@src/utils/ServiceLifecycle";
 import { inferenceState } from "./sonar-inference";
 import {
 	handleBatchEnhancement,
-	handleChat,
-	handleContextExtraction,
 	handleGardenTask,
-	handleMetadataEnhancement,
 	handleResearchTask,
-	handleResultReranking,
-	handleSearchAnalysis,
 	handleSynthesisTask,
 	handleTimelineTask,
 	type SonarContext,
 } from "./sonar-logic";
 import { getTaskModel } from "./sonar-strategies";
-import type {
-	ChatRequest,
-	ChatSession,
-	MetadataEnhanceRequest,
-	SearchAnalyzeRequest,
-	SearchContextRequest,
-	SearchRerankRequest,
-	SonarTask,
-} from "./sonar-types";
+import type { ChatSession, SonarTask } from "./sonar-types";
 
 const args = process.argv.slice(2);
 const command = args[0] || "serve";
@@ -128,123 +115,18 @@ async function main() {
 	}
 }
 
+import { createSonarApp } from "./sonar-server";
+
 /**
- * Start Bun HTTP Server
+ * Start Bun HTTP Server via Hono
  */
 function startServer(port: number) {
-	const corsHeaders = {
-		"Access-Control-Allow-Origin": "*",
-		"Access-Control-Allow-Methods": "GET, POST, OPTIONS",
-		"Access-Control-Allow-Headers": "Content-Type",
-	};
-
 	const context: SonarContext = { db, graphEngine, gardener, chatSessions };
+	const app = createSonarApp(context);
 
 	Bun.serve({
 		port,
-		async fetch(req) {
-			if (req.method === "OPTIONS")
-				return new Response(null, { headers: corsHeaders });
-			const url = new URL(req.url);
-
-			// Health check
-			if (url.pathname === "/health") {
-				const cfg = await loadConfig();
-				const provider = cfg.sonar.cloud?.enabled ? "cloud" : "local";
-				const model = cfg.sonar.cloud?.enabled
-					? cfg.sonar.cloud.model
-					: inferenceState.ollamaModel || cfg.sonar.model;
-				return Response.json(
-					{
-						status: "ok",
-						ollama: inferenceState.ollamaAvailable,
-						provider,
-						model,
-					},
-					{ headers: corsHeaders },
-				);
-			}
-
-			// Chat endpoint
-			if (url.pathname === "/chat" && req.method === "POST") {
-				try {
-					const body = (await req.json()) as ChatRequest;
-					const { sessionId, message, model } = body;
-					const result = await handleChat(sessionId, message, context, model);
-					return Response.json(result, { headers: corsHeaders });
-				} catch (error) {
-					return Response.json(
-						{ error: String(error) },
-						{ status: 500, headers: corsHeaders },
-					);
-				}
-			}
-
-			// Metadata enhancement endpoint
-			if (url.pathname === "/metadata/enhance" && req.method === "POST") {
-				try {
-					const body = (await req.json()) as MetadataEnhanceRequest;
-					const { docId } = body;
-					await handleMetadataEnhancement(docId, context);
-					return Response.json({ status: "success" }, { headers: corsHeaders });
-				} catch (error) {
-					return Response.json(
-						{ error: String(error) },
-						{ status: 500, headers: corsHeaders },
-					);
-				}
-			}
-
-			// Graph Stats endpoint
-			if (url.pathname === "/graph/stats" && req.method === "GET") {
-				return Response.json(graphEngine.getStats(), { headers: corsHeaders });
-			}
-
-			// Search endpoints (analysis, rerank, context)
-			if (url.pathname === "/search/analyze" && req.method === "POST") {
-				try {
-					const body = (await req.json()) as SearchAnalyzeRequest;
-					const { query } = body;
-					const result = await handleSearchAnalysis(query, context);
-					return Response.json(result, { headers: corsHeaders });
-				} catch (error) {
-					return Response.json(
-						{ error: String(error) },
-						{ status: 500, headers: corsHeaders },
-					);
-				}
-			}
-
-			if (url.pathname === "/search/rerank" && req.method === "POST") {
-				try {
-					const body = (await req.json()) as SearchRerankRequest;
-					const { results, query, intent } = body;
-					const result = await handleResultReranking(results, query, intent);
-					return Response.json(result, { headers: corsHeaders });
-				} catch (error) {
-					return Response.json(
-						{ error: String(error) },
-						{ status: 500, headers: corsHeaders },
-					);
-				}
-			}
-
-			if (url.pathname === "/search/context" && req.method === "POST") {
-				try {
-					const body = (await req.json()) as SearchContextRequest;
-					const { result, query } = body;
-					const contextResult = await handleContextExtraction(result, query);
-					return Response.json(contextResult, { headers: corsHeaders });
-				} catch (error) {
-					return Response.json(
-						{ error: String(error) },
-						{ status: 500, headers: corsHeaders },
-					);
-				}
-			}
-
-			return new Response("Not Found", { status: 404, headers: corsHeaders });
-		},
+		fetch: app.fetch,
 	});
 
 	log.info(`Server started on port ${port}`);

package/src/daemon/sonar-server.ts

@@ -0,0 +1,133 @@
+import { loadConfig } from "@src/config/defaults";
+import { Hono } from "hono";
+import { cors } from "hono/cors";
+import { inferenceState } from "./sonar-inference";
+import {
+	handleChat,
+	handleContextExtraction,
+	handleMetadataEnhancement,
+	handleResultReranking,
+	handleSearchAnalysis,
+	type SonarContext,
+} from "./sonar-logic";
+import type {
+	ChatRequest,
+	MetadataEnhanceRequest,
+	SearchAnalyzeRequest,
+	SearchContextRequest,
+	SearchRerankRequest,
+} from "./sonar-types";
+
+/**
+ * Creates the Hono application for the Sonar Agent
+ */
+export function createSonarApp(context: SonarContext) {
+	const app = new Hono();
+
+	// Global Middleware
+	app.use(
+		"*",
+		cors({
+			origin: "*",
+			allowMethods: ["GET", "POST", "OPTIONS"],
+			allowHeaders: ["Content-Type"],
+		}),
+	);
+
+	/**
+	 * Health Check
+	 */
+	app.get("/health", async (c) => {
+		const cfg = await loadConfig();
+		const provider = cfg.sonar.cloud?.enabled ? "cloud" : "local";
+		const model = cfg.sonar.cloud?.enabled
+			? cfg.sonar.cloud.model
+			: inferenceState.ollamaModel || cfg.sonar.model;
+
+		return c.json({
+			status: "ok",
+			ollama: inferenceState.ollamaAvailable,
+			provider,
+			model,
+		});
+	});
+
+	/**
+	 * Chat Interface
+	 */
+	app.post("/chat", async (c) => {
+		try {
+			const body = await c.req.json<ChatRequest>();
+			const { sessionId, message, model } = body;
+			const result = await handleChat(sessionId, message, context, model);
+			return c.json(result);
+		} catch (error) {
+			return c.json({ error: String(error) }, 500);
+		}
+	});
+
+	/**
+	 * Metadata Enhancement
+	 */
+	app.post("/metadata/enhance", async (c) => {
+		try {
+			const body = await c.req.json<MetadataEnhanceRequest>();
+			const { docId } = body;
+			await handleMetadataEnhancement(docId, context);
+			return c.json({ status: "success" });
+		} catch (error) {
+			return c.json({ error: String(error) }, 500);
+		}
+	});
+
+	/**
+	 * Graph Stats
+	 */
+	app.get("/graph/stats", (c) => {
+		return c.json(context.graphEngine.getStats());
+	});
+
+	/**
+	 * Search: Query Analysis
+	 */
+	app.post("/search/analyze", async (c) => {
+		try {
+			const body = await c.req.json<SearchAnalyzeRequest>();
+			const { query } = body;
+			const result = await handleSearchAnalysis(query, context);
+			return c.json(result);
+		} catch (error) {
+			return c.json({ error: String(error) }, 500);
+		}
+	});
+
+	/**
+	 * Search: Reranking
+	 */
+	app.post("/search/rerank", async (c) => {
+		try {
+			const body = await c.req.json<SearchRerankRequest>();
+			const { results, query, intent } = body;
+			const result = await handleResultReranking(results, query, intent);
+			return c.json(result);
+		} catch (error) {
+			return c.json({ error: String(error) }, 500);
+		}
+	});
+
+	/**
+	 * Search: Context Extraction
+	 */
+	app.post("/search/context", async (c) => {
+		try {
+			const body = await c.req.json<SearchContextRequest>();
+			const { result, query } = body;
+			const contextResult = await handleContextExtraction(result, query);
+			return c.json(contextResult);
+		} catch (error) {
+			return c.json({ error: String(error) }, 500);
+		}
+	});
+
+	return app;
+}

package/src/resonance/DatabaseFactory.ts

@@ -13,7 +13,7 @@ import { Database } from "bun:sqlite";
 export const DatabaseFactory = {
 	/**
 	 * Connects specifically to the main Resonance Graph database.
-	 * @deprecated Use connect() with explicit path from config instead.
+	 * Kept for convenience and backward compatibility.
 	 */
 	connectToResonance(
 		dbPath: string = ".amalfa/resonance.db",

package/src/resonance/drizzle/README.md

@@ -0,0 +1,25 @@
+# Drizzle Schema Management
+
+## ⚠️ CRITICAL ARCHITECTURE RULE
+
+**Drizzle ORM is used HERE strictly for:**
+1.  **Schema Definition:** Single source of truth for table structures (`schema.ts`).
+2.  **Migrations:** Generating and running SQL migrations (`drizzle-kit`).
+
+**Drizzle ORM is NOT used for:**
+- **Runtime Queries:** Do NOT use Drizzle `db.select()` query builders in critical paths.
+- **Data Access:** All runtime data access uses `bun:sqlite` with raw parameterized SQL (`db.prepare()`).
+
+## Why?
+Our **FAFCAS** (Fast, Autonomous, Fractionally-Connected Agent System) architecture demands raw IO performance. We treat SQLite as a raw storage engine. The overhead of an ORM query builder—even a light one—is unnecessary.
+
+## ⛔ Agent Guardrail
+If you are an AI Agent reading this:
+- **DO NOT** refactor the existing `ResonanceDB` SQL queries to use Drizzle.
+- **DO NOT** introduce Drizzle usage into `GraphEngine` or `VectorEngine`.
+- **ONLY** modify this folder if the Database Schema (tables/columns) needs to change.
+
+## Workflow for Schema Changes
+1.  Edit `schema.ts`
+2.  Run `bunx drizzle-kit generate`
+3.  Run migrations (automated via scripts)

package/src/resonance/drizzle/migrations/0000_happy_thaddeus_ross.sql

@@ -0,0 +1,30 @@
+CREATE TABLE `edges` (
+	`source` text NOT NULL,
+	`target` text NOT NULL,
+	`type` text NOT NULL,
+	`confidence` real DEFAULT 1,
+	`veracity` real DEFAULT 1,
+	`context_source` text,
+	PRIMARY KEY(`source`, `target`, `type`)
+);
+--> statement-breakpoint
+CREATE INDEX `idx_edges_source` ON `edges` (`source`);--> statement-breakpoint
+CREATE INDEX `idx_edges_target` ON `edges` (`target`);--> statement-breakpoint
+CREATE TABLE `ember_state` (
+	`file_path` text PRIMARY KEY NOT NULL,
+	`last_analyzed` text,
+	`sidecar_created` integer,
+	`confidence` real
+);
+--> statement-breakpoint
+CREATE TABLE `nodes` (
+	`id` text PRIMARY KEY NOT NULL,
+	`type` text,
+	`title` text,
+	`domain` text,
+	`layer` text,
+	`embedding` blob,
+	`hash` text,
+	`meta` text,
+	`date` text
+);

package/src/resonance/drizzle/migrations/meta/0000_snapshot.json

@@ -0,0 +1,199 @@
+{
+	"version": "6",
+	"dialect": "sqlite",
+	"id": "577c9f07-f198-49d2-9fa3-f222a6ecee23",
+	"prevId": "00000000-0000-0000-0000-000000000000",
+	"tables": {
+		"edges": {
+			"name": "edges",
+			"columns": {
+				"source": {
+					"name": "source",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": true,
+					"autoincrement": false
+				},
+				"target": {
+					"name": "target",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": true,
+					"autoincrement": false
+				},
+				"type": {
+					"name": "type",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": true,
+					"autoincrement": false
+				},
+				"confidence": {
+					"name": "confidence",
+					"type": "real",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false,
+					"default": 1
+				},
+				"veracity": {
+					"name": "veracity",
+					"type": "real",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false,
+					"default": 1
+				},
+				"context_source": {
+					"name": "context_source",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				}
+			},
+			"indexes": {
+				"idx_edges_source": {
+					"name": "idx_edges_source",
+					"columns": ["source"],
+					"isUnique": false
+				},
+				"idx_edges_target": {
+					"name": "idx_edges_target",
+					"columns": ["target"],
+					"isUnique": false
+				}
+			},
+			"foreignKeys": {},
+			"compositePrimaryKeys": {
+				"edges_source_target_type_pk": {
+					"columns": ["source", "target", "type"],
+					"name": "edges_source_target_type_pk"
+				}
+			},
+			"uniqueConstraints": {},
+			"checkConstraints": {}
+		},
+		"ember_state": {
+			"name": "ember_state",
+			"columns": {
+				"file_path": {
+					"name": "file_path",
+					"type": "text",
+					"primaryKey": true,
+					"notNull": true,
+					"autoincrement": false
+				},
+				"last_analyzed": {
+					"name": "last_analyzed",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"sidecar_created": {
+					"name": "sidecar_created",
+					"type": "integer",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"confidence": {
+					"name": "confidence",
+					"type": "real",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				}
+			},
+			"indexes": {},
+			"foreignKeys": {},
+			"compositePrimaryKeys": {},
+			"uniqueConstraints": {},
+			"checkConstraints": {}
+		},
+		"nodes": {
+			"name": "nodes",
+			"columns": {
+				"id": {
+					"name": "id",
+					"type": "text",
+					"primaryKey": true,
+					"notNull": true,
+					"autoincrement": false
+				},
+				"type": {
+					"name": "type",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"title": {
+					"name": "title",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"domain": {
+					"name": "domain",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"layer": {
+					"name": "layer",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"embedding": {
+					"name": "embedding",
+					"type": "blob",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"hash": {
+					"name": "hash",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"meta": {
+					"name": "meta",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				},
+				"date": {
+					"name": "date",
+					"type": "text",
+					"primaryKey": false,
+					"notNull": false,
+					"autoincrement": false
+				}
+			},
+			"indexes": {},
+			"foreignKeys": {},
+			"compositePrimaryKeys": {},
+			"uniqueConstraints": {},
+			"checkConstraints": {}
+		}
+	},
+	"views": {},
+	"enums": {},
+	"_meta": {
+		"schemas": {},
+		"tables": {},
+		"columns": {}
+	},
+	"internal": {
+		"indexes": {}
+	}
+}

package/src/resonance/drizzle/migrations/meta/_journal.json

@@ -0,0 +1,13 @@
+{
+	"version": "7",
+	"dialect": "sqlite",
+	"entries": [
+		{
+			"idx": 0,
+			"version": "6",
+			"when": 1767981411501,
+			"tag": "0000_happy_thaddeus_ross",
+			"breakpoints": true
+		}
+	]
+}

package/src/resonance/drizzle/schema.ts

@@ -0,0 +1,60 @@
+import {
+	blob,
+	index,
+	integer,
+	primaryKey,
+	real,
+	sqliteTable,
+	text,
+} from "drizzle-orm/sqlite-core";
+
+/**
+ * NODES Table
+ * Core entity storage. Now "Hollow" (no content).
+ */
+export const nodes = sqliteTable("nodes", {
+	id: text("id").primaryKey(),
+	type: text("type"),
+	title: text("title"),
+	domain: text("domain"),
+	layer: text("layer"),
+	// Embeddings are stored as raw BLOBs (Float32Array bytes)
+	embedding: blob("embedding"),
+	hash: text("hash"),
+	meta: text("meta"), // JSON string
+	date: text("date"), // ISO string or YYYY-MM-DD
+});
+
+/**
+ * EDGES Table
+ * Defines relationships between nodes.
+ */
+export const edges = sqliteTable(
+	"edges",
+	{
+		source: text("source").notNull(),
+		target: text("target").notNull(),
+		type: text("type").notNull(),
+		confidence: real("confidence").default(1.0),
+		veracity: real("veracity").default(1.0),
+		contextSource: text("context_source"),
+	},
+	(table) => ({
+		// Composite Primary Key
+		pk: primaryKey({ columns: [table.source, table.target, table.type] }),
+		// Indices for traversal speed
+		sourceIdx: index("idx_edges_source").on(table.source),
+		targetIdx: index("idx_edges_target").on(table.target),
+	}),
+);
+
+/**
+ * EMBER STATE Table (Pilot)
+ * Tracks the state of the Ember Service (automated enrichment).
+ */
+export const emberState = sqliteTable("ember_state", {
+	filePath: text("file_path").primaryKey(),
+	lastAnalyzed: text("last_analyzed"),
+	sidecarCreated: integer("sidecar_created", { mode: "boolean" }),
+	confidence: real("confidence"),
+});