refactor: restructure project layout and scheduler setup

AGENTS.md

@@ -170,7 +170,7 @@ Node.js-based AI harness application using LangGraph for state machines and Open
     └── schedules/              # Scheduled job output files
 ```
 
-Misc details: The `config.yaml` file is the single source of project configuration, loaded by `src/config/loader.js`. All subsystems wire into the entry point `index.js`.
+Misc details: The `config.yaml` file is the single source of project configuration, loaded by `src/config/loader.js`. All subsystems wire into the entry point `index.js` at the project root.
 
 ### 2.1 Quick Commands
 

CONTRIBUTING.md

@@ -105,7 +105,7 @@ chore: pin dependencies in package.json
 
 ### Architecture Notes
 
-- `config.yaml` + `src/config/loader.js` is the single source of truth for configuration
+- `config.yaml` at the project root + `src/config/loader.js` is the single source of truth for configuration
 - All subsystems wire into `index.js` via `src/` modules
 - Each public function or class needs test coverage
 - Test files mirror source: `src/memory/reader.js` → `tests/unit/memory.test.js`

Dockerfile

@@ -35,15 +35,15 @@ WORKDIR /app
 COPY --from=builder /app/node_modules ./node_modules
 COPY --from=builder /app/package*.json ./
 COPY LICENSE ./
+COPY index.js ./
 COPY src/ ./src/
+COPY config.yaml ./
 COPY prompts/ ./prompts/
 COPY system-skills/ ./system-skills/
 COPY docker-entrypoint.sh /docker-entrypoint.sh
 RUN chmod +x /docker-entrypoint.sh
 
-RUN mkdir -p /home/madz/.cache/madz/logs && \
-    touch /home/madz/.cache/madz/logs/madz_cron.log && \
-    chown -R madz:node /app /home/madz && \
+RUN chown -R madz:node /app /home/madz && \
     chmod -R g+rwX /app /home/madz
 
 ENTRYPOINT ["/docker-entrypoint.sh"]

src/index.js → index.js

@@ -18,26 +18,26 @@ const parsed = yargs(process.argv.slice(2))
 	}).argv;
 
 // Load config
-import { loadConfig } from "./config/loader.js";
+import { loadConfig } from "./src/config/loader.js";
 const config = loadConfig();
 import { fileURLToPath } from "node:url";
-import { loadSession } from "./session/loader.js";
+import { loadSession } from "./src/session/loader.js";
 
 import React from "react";
 
-const { setConfigValue } = await import("./config/loader.js");
-const { createDeepAgentsOrchestrator } = await import("./agent/deepAgents.js");
-const { logger } = await import("./logger.js");
+const { setConfigValue } = await import("./src/config/loader.js");
+const { createDeepAgentsOrchestrator } = await import("./src/agent/deepAgents.js");
+const { logger } = await import("./src/logger.js");
 
-const { default: pkg } = await import(new URL("../package.json", import.meta.url).href, {
+const { default: pkg } = await import(new URL("./package.json", import.meta.url).href, {
 	with: { type: "json" },
 });
 
 // Initialize subsystems
 // Sync crontab from persisted job definitions (runs before any subsystem)
 if (config.schedules.syncOnInit !== false) {
 	try {
-		const { Cron } = await import("./scheduler/cron.js");
+		const { Cron } = await import("./src/scheduler/cron.js");
 		if (config.schedules.logPath) {
 			Cron.setLogPath(config.schedules.logPath);
 		}
@@ -50,53 +50,22 @@ if (config.schedules.syncOnInit !== false) {
 				`[scheduler] Crontab sync complete: +${result.added} added, -${result.removed} removed, ~${result.updated} updated, =${result.skipped} skipped`,
 			);
 		}
-
-		// Ensure the daily reflection job exists in crontab and persisted (covers upgrading users
-		// who have no reflection-daily.json on disk). Cron.add() is idempotent.
-		const cwd = config.cwd;
-		const jobResult = Cron.add({
-			name: "reflection-daily",
-			cron: "0 2 * * *",
-			command: `cd ${cwd} && node index.js --message "Run the reflection skill"`,
-		});
-		if (jobResult.added || !jobResult.error) {
-			try {
-				const { existsSync, mkdirSync, writeFileSync } = await import("node:fs");
-				const { join } = await import("node:path");
-				const schedulesDir = config.memory?.schedulesDir || "memory/schedules/";
-				const filePath = join(schedulesDir, "reflection-daily.json");
-				if (!existsSync(filePath)) {
-					mkdirSync(schedulesDir, { recursive: true });
-					const jobData = {
-						name: "reflection-daily",
-						cron: "0 2 * * *",
-						command: `cd ${cwd} && node index.js --message "Run the reflection skill"`,
-						enabled: true,
-						createdAt: new Date().toISOString(),
-						updatedAt: new Date().toISOString(),
-					};
-					writeFileSync(filePath, JSON.stringify(jobData, null, 2));
-				}
-			} catch (err) {
-				logger.warn(`[scheduler] Failed to persist reflection-daily job file: ${err.message}`);
-			}
-		}
 	} catch (err) {
 		logger.warn(`[scheduler] Crontab sync error: ${err.message}`);
 	}
 }
 
 // Ensure sessions directory exists before any subsystem initialization
-const { ensureSessionsDir } = await import("./session/index.js");
+const { ensureSessionsDir } = await import("./src/session/index.js");
 await ensureSessionsDir(config.cwd + "/" + "memory/sessions/");
 
 // Initialize contextual onboarding if profile is missing (with graceful degradation)
 let onboardingInstance = null;
 try {
-	const { hasProfile, ATTRIBUTES } = await import("./memory/profile.js");
+	const { hasProfile, ATTRIBUTES } = await import("./src/memory/profile.js");
 	if (!hasProfile()) {
-		const { createOnboarding } = await import("./session/onboarding.js");
-		const { setupAutoSchedule } = await import("./scheduler/autoSchedule.js");
+		const { createOnboarding } = await import("./src/session/onboarding.js");
+		const { setupAutoSchedule } = await import("./src/scheduler/autoSchedule.js");
 		const autoSchedule = setupAutoSchedule();
 		onboardingInstance = createOnboarding(ATTRIBUTES, { onSave: autoSchedule });
 	}
@@ -108,27 +77,29 @@ try {
 let tracer = null;
 let shutdownFn = null;
 if (config.telemetry.enabled) {
-	const { initTelemetry, getTracer, shutdownTelemetry } = await import("./telemetry/provider.js");
+	const { initTelemetry, getTracer, shutdownTelemetry } =
+		await import("./src/telemetry/provider.js");
 	await initTelemetry(config.telemetry);
 	tracer = getTracer();
 	shutdownFn = shutdownTelemetry;
 }
 
 // Initialize skill registry
-const { SkillRegistry, resolvePermissions, ensureSkillsDir } = await import("./skills/index.js");
+const { SkillRegistry, resolvePermissions, ensureSkillsDir } =
+	await import("./src/skills/index.js");
 const registry = new SkillRegistry();
 await ensureSkillsDir(config.cwd + "/" + "skills/");
 registry.discover();
 
 // Initialize memory system
-const { writeMemoryFile, readMemoryFile, loadContext } = await import("./memory/index.js");
+const { writeMemoryFile, readMemoryFile, loadContext } = await import("./src/memory/index.js");
 
 // Initialize GC manager (if enabled)
 let gcManager = null;
 let gcTrace = null;
 let maxGcPerHour = 4;
 try {
-	const { initGC, gc: gcFn, isAvailable } = await import("./memory/gc.js");
+	const { initGC, gc: gcFn, isAvailable } = await import("./src/memory/gc.js");
 	const gcConfig = config.memory?.gc;
 	if (gcConfig?.enabled !== false) {
 		const idleTimeoutMs = gcConfig.idleTimeoutMs ?? 300000;
@@ -152,11 +123,11 @@ try {
 
 // Initialize session
 const { createSession, SessionStateManager, saveSession, handleShutdown, registerShutdownHandler } =
-	await import("./session/index.js");
-const { flush: flushLogger } = await import("./logger.js");
+	await import("./src/session/index.js");
+const { flush: flushLogger } = await import("./src/logger.js");
 
 // Initialize scheduler
-const { ScheduleManager } = await import("./scheduler/index.js");
+const { ScheduleManager } = await import("./src/scheduler/index.js");
 const scheduleManager = new ScheduleManager();
 
 // Create or restore session
@@ -168,7 +139,7 @@ const sessionState = new SessionStateManager(initialState);
 
 // Session-init: asynchronously clean up expired ephemeral memories (non-blocking)
 try {
-	const { expireEphemeralMemories } = await import("./memory/expireEphemeral.js");
+	const { expireEphemeralMemories } = await import("./src/memory/expireEphemeral.js");
 	queueMicrotask(() =>
 		expireEphemeralMemories(config.cwd + "/" + config.memory.contextDir).catch(() => {}),
 	);
@@ -177,7 +148,7 @@ try {
 }
 
 // Create checkpointer before tools so compactContext can access it
-const { createCheckpointer } = await import("./session/checkpointer.js");
+const { createCheckpointer } = await import("./src/session/checkpointer.js");
 const checkpointer = createCheckpointer(config.persistence);
 
 // Provider config for TUI
@@ -331,7 +302,7 @@ if (isMain) {
 		process.exit(0);
 	} else {
 		const { render } = await import("ink");
-		const App = (await import("./tui/app.js")).default;
+		const App = (await import("./src/tui/app.js")).default;
 		const appInfo = { name: config.tui.name, version: pkg.version };
 		render(
 			React.createElement(App, {
@@ -356,7 +327,7 @@ if (isMain) {
 			{
 				// Restore terminal with newline when app exits
 				onExit: async () => {
-					const shutdown = (await import("./session/index.js")).handleShutdown;
+					const shutdown = (await import("./src/session/index.js")).handleShutdown;
 					if (shutdown) await shutdown();
 					await flushLogger();
 					process.stdout.write("\n");

package.json

@@ -33,14 +33,14 @@
   ],
   "author": "Jason Mulligan <jason.mulligan@avoidwork.com>",
   "type": "module",
-  "main": "src/index.js",
-  "bin": "src/index.js",
+  "main": "index.js",
+  "bin": "index.js",
   "scripts": {
-    "start": "node src/index.js --mode interactive",
+    "start": "node index.js --mode interactive",
     "test": "node --test tests/**/*.test.js",
     "coverage": "node --test --experimental-test-coverage --test-coverage-exclude=dist/** --test-coverage-exclude=tests/** --test-reporter=spec tests/**/*.test.js 2>&1 | grep -A 1000 \"start of coverage report\" > coverage.txt",
-    "fix": "oxlint --fix *.js src tests/unit && oxfmt *.js src tests/unit --write",
-    "lint": "oxlint *.js src tests/unit && oxfmt *.js src/*.js tests/unit/*.js --check",
+    "fix": "oxlint --fix *.js src tests/unit tests/integration tests/tui && oxfmt *.js src tests/unit tests/integration tests/tui --write",
+    "lint": "oxlint *.js src tests/unit tests/integration tests/tui && oxfmt *.js src tests/unit tests/integration tests/tui --check",
     "docker:build": "docker build -t madz:latest .",
     "docker:tag": "docker tag madz:latest $DOCKER_USER/madz:$npm_package_version",
     "docker:push": "docker push $DOCKER_USER/madz:$npm_package_version",

src/config/loader.js

@@ -9,7 +9,7 @@ const _require = createRequire(import.meta.url);
 import { load, dump } from "js-yaml";
 
 const PROJECT_ROOT = dirname(fileURLToPath(import.meta.url));
-const CONFIG_PATH = join(PROJECT_ROOT, "../config.yaml");
+const CONFIG_PATH = join(PROJECT_ROOT, "../../config.yaml");
 
 /// -- Convert camelCase or kebab-case to SNAKE_CASE ---
 

src/scheduler/autoSchedule.js

@@ -1,4 +1,4 @@
-import { existsSync, mkdirSync, writeFileSync } from "node:fs";
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
 import { Cron } from "./cron.js";
 import { logger } from "../logger.js";
@@ -28,7 +28,7 @@ function createJobDefinition(cwd) {
 	return {
 		name: "reflection-daily",
 		cron: JOB_CRON,
-		command: `cd ${cwd} && timeout 300 node src/index.js --message "Run the reflection skill"`,
+		command: `cd ${cwd} && node index.js --message "Run the reflection skill"`,
 	};
 }
 
@@ -45,7 +45,14 @@ function persistJobFile(jobName, job, cwd) {
 	const filePath = join(schedulesDir, `${jobName}.json`);
 
 	if (existsSync(filePath)) {
-		return { written: true };
+		try {
+			const existing = JSON.parse(readFileSync(filePath, "utf8"));
+			if (existing.command === job.command) {
+				return { written: true };
+			}
+		} catch {
+			/* malformed JSON — fall through to overwrite */
+		}
 	}
 
 	try {
@@ -59,7 +66,7 @@ function persistJobFile(jobName, job, cwd) {
 		const jobData = Object.freeze({
 			name: job.name,
 			cron: job.cron,
-			command: `cd ${cwd} && timeout 300 node src/index.js --message "Run the reflection skill"`,
+			command: `cd ${cwd} && node index.js --message "Run the reflection skill"`,
 			enabled: true,
 			createdAt: new Date().toISOString(),
 			updatedAt: new Date().toISOString(),

tests/integration/full-flow.test.js

@@ -193,7 +193,7 @@ describe("integration - scheduler execution", () => {
 	it("enforces concurrent execution limits", async () => {
 		const maxConcurrent = 1;
 		let concurrent = 0;
-		const scheduleTasks = [
+		const _scheduleTasks = [
 			{ name: "A", cron: "0 9 * * *", skill: "x" },
 			{ name: "B", cron: "0 9 * * *", skill: "y" },
 		];

tests/unit/autoSchedule.test.js

@@ -65,7 +65,7 @@ describe("setupAutoSchedule", () => {
 		assert.strictEqual(capturedJob.cron, "0 2 * * *");
 		assert.ok(typeof capturedJob.command === "string");
 		assert.ok(
-			capturedJob.command.includes('node src/index.js --message "Run the reflection skill"'),
+			capturedJob.command.includes('node index.js --message "Run the reflection skill"'),
 			"Command should include the --message /reflection command",
 		);
 	});
@@ -99,7 +99,7 @@ describe("setupAutoSchedule", () => {
 		assert.strictEqual(content.cron, "0 2 * * *");
 		assert.ok(
 			content.command.startsWith("cd ") &&
-				content.command.includes('node src/index.js --message "Run the reflection skill"'),
+				content.command.includes('node index.js --message "Run the reflection skill"'),
 		);
 		assert.strictEqual(content.enabled, true);
 		assert.ok(content.createdAt);