fix(evolution): pipeline bugs - JUDGE_API_KEY, dedup, routing, procedures, backup, observability

config/phantom.yaml

@@ -1,7 +1,7 @@
 name: phantom
 port: 3100
 role: swe
-model: claude-sonnet-4-6
+model: claude-opus-4-6
 effort: max
 max_budget_usd: 0
 timeout_minutes: 240

src/agent/__tests__/prompt-assembler.test.ts

@@ -7,6 +7,7 @@ const baseConfig: PhantomConfig = {
 	port: 3100,
 	role: "swe",
 	model: "claude-opus-4-6",
+	model_source: "config",
 	effort: "max",
 	max_budget_usd: 0,
 	timeout_minutes: 240,

src/cli/__tests__/init.test.ts

@@ -62,7 +62,7 @@ describe("phantom init", () => {
 		expect(config.name).toBe("phantom");
 		expect(config.role).toBe("swe");
 		expect(config.port).toBe(3100);
-		expect(config.model).toBe("claude-sonnet-4-6");
+		expect(config.model).toBe("claude-opus-4-6");
 	});
 
 	test("accepts custom name and role", async () => {
@@ -313,7 +313,7 @@ describe("phantom init --yes (environment-aware)", () => {
 
 		const raw = readFileSync("config/phantom.yaml", "utf-8");
 		const config = YAML.parse(raw);
-		expect(config.model).toBe("claude-sonnet-4-6");
+		expect(config.model).toBe("claude-opus-4-6");
 	});
 
 	test("reads PHANTOM_DOMAIN from environment", async () => {

src/cli/doctor.ts

@@ -1,4 +1,4 @@
-import { existsSync, readFileSync } from "node:fs";
+import { constants, accessSync, existsSync, readFileSync } from "node:fs";
 import { parseArgs } from "node:util";
 
 type CheckResult = {
@@ -148,6 +148,52 @@ async function checkEvolvedConfig(): Promise<CheckResult> {
 	return { name: "Evolved Config", status: "ok", message: "All config files present" };
 }
 
+async function checkEvolutionPipeline(): Promise<CheckResult> {
+	const sessionLog = "phantom-config/memory/session-log.jsonl";
+	const metricsFile = "phantom-config/meta/metrics.json";
+
+	if (!existsSync("phantom-config")) {
+		return { name: "Evolution Pipeline", status: "warn", message: "phantom-config/ not found", fix: "phantom init" };
+	}
+
+	// Check session-log.jsonl is writable
+	if (!existsSync(sessionLog)) {
+		return {
+			name: "Evolution Pipeline",
+			status: "warn",
+			message: "session-log.jsonl not found",
+			fix: "Run a session to generate it, or run phantom init",
+		};
+	}
+
+	try {
+		accessSync(sessionLog, constants.R_OK | constants.W_OK);
+	} catch {
+		return { name: "Evolution Pipeline", status: "fail", message: "session-log.jsonl not writable" };
+	}
+
+	// Check metrics.json shows pipeline activity
+	if (!existsSync(metricsFile)) {
+		return { name: "Evolution Pipeline", status: "warn", message: "metrics.json not found", fix: "phantom init" };
+	}
+
+	try {
+		const raw = readFileSync(metricsFile, "utf-8");
+		const metrics = JSON.parse(raw) as { session_count?: number };
+		const count = metrics.session_count ?? 0;
+		if (count === 0) {
+			return {
+				name: "Evolution Pipeline",
+				status: "warn",
+				message: "No sessions recorded yet (pipeline not yet active)",
+			};
+		}
+		return { name: "Evolution Pipeline", status: "ok", message: `${count} sessions processed` };
+	} catch {
+		return { name: "Evolution Pipeline", status: "fail", message: "metrics.json not parseable" };
+	}
+}
+
 async function checkPhantomHealth(port: number): Promise<CheckResult> {
 	try {
 		const resp = await fetch(`http://localhost:${port}/health`, { signal: AbortSignal.timeout(3000) });
@@ -194,6 +240,7 @@ export async function runDoctor(args: string[]): Promise<void> {
 		checkMcpConfig(),
 		checkDatabase(),
 		checkEvolvedConfig(),
+		checkEvolutionPipeline(),
 		checkPhantomHealth(port),
 	]);
 

src/cli/init.ts

@@ -198,7 +198,7 @@ export async function runInit(args: string[]): Promise<void> {
 			name: values.name ?? envName ?? "phantom",
 			role: values.role ?? envRole ?? "swe",
 			port: values.port ? Number.parseInt(values.port, 10) : envPort ? Number.parseInt(envPort, 10) : 3100,
-			model: envModel ?? "claude-sonnet-4-6",
+			model: envModel ?? "claude-opus-4-6",
 			domain: envDomain,
 			public_url: envPublicUrl,
 			effort: envEffort,
@@ -224,7 +224,7 @@ export async function runInit(args: string[]): Promise<void> {
 				port: values.port
 					? Number.parseInt(values.port, 10)
 					: Number.parseInt(await prompt(rl, "HTTP port", "3100"), 10),
-				model: await prompt(rl, "Model (claude-sonnet-4-6, claude-opus-4-6)", "claude-sonnet-4-6"),
+				model: await prompt(rl, "Model (claude-opus-4-6, claude-sonnet-4-6)", "claude-opus-4-6"),
 			};
 
 			console.log("\nSlack setup (optional, press Enter to skip):");

src/cli/status.ts

@@ -6,9 +6,16 @@ type HealthResponse = {
 	version: string;
 	agent: string;
 	role: { id: string; name: string };
+	model?: string;
+	model_source?: "config" | "env";
 	channels: Record<string, boolean>;
 	memory: { qdrant: boolean; ollama: boolean };
-	evolution: { generation: number };
+	evolution: {
+		generation: number;
+		session_count?: number;
+		sessions_since_consolidation?: number;
+		session_log_depth?: number;
+	};
 	onboarding?: string;
 	peers?: Record<string, { healthy: boolean; latencyMs: number; error?: string }>;
 };
@@ -74,9 +81,18 @@ export async function runStatus(args: string[]): Promise<void> {
 	const memoryStr =
 		data.memory.qdrant && data.memory.ollama ? "ok" : data.memory.qdrant || data.memory.ollama ? "degraded" : "offline";
 
+	const modelStr = data.model ? `${data.model}${data.model_source === "env" ? " (env override)" : ""}` : "unknown";
+
+	const evo = data.evolution;
+	const evoDetail =
+		evo.session_count != null
+			? `gen ${evo.generation} (${evo.session_count} sessions, ${evo.sessions_since_consolidation ?? 0} since consolidation, ${evo.session_log_depth ?? 0} queued)`
+			: `gen ${evo.generation}`;
+
 	console.log(
 		`${data.agent} | ${data.role.name} | v${data.version} | ` +
-			`gen ${data.evolution.generation} | ` +
+			`${evoDetail} | ` +
+			`model: ${modelStr} | ` +
 			`up ${formatUptime(data.uptime)} | ` +
 			`channels: ${channelStr} | ` +
 			`memory: ${memoryStr}`,

src/config/__tests__/loader.test.ts

@@ -106,6 +106,7 @@ model: claude-opus-4-6
 			process.env.PHANTOM_MODEL = "claude-sonnet-4-6";
 			const config = loadConfig(path);
 			expect(config.model).toBe("claude-sonnet-4-6");
+			expect(config.model_source).toBe("env");
 		} finally {
 			if (saved !== undefined) {
 				process.env.PHANTOM_MODEL = saved;
@@ -116,6 +117,27 @@ model: claude-opus-4-6
 		}
 	});
 
+	test("model_source defaults to config when no env override", () => {
+		const path = writeYaml(
+			"model-source-default.yaml",
+			`
+name: test-phantom
+model: claude-opus-4-6
+`,
+		);
+		const saved = process.env.PHANTOM_MODEL;
+		try {
+			process.env.PHANTOM_MODEL = undefined;
+			const config = loadConfig(path);
+			expect(config.model_source).toBe("config");
+		} finally {
+			if (saved !== undefined) {
+				process.env.PHANTOM_MODEL = saved;
+			}
+			cleanup();
+		}
+	});
+
 	test("env var overrides YAML domain", () => {
 		const path = writeYaml(
 			"env-domain.yaml",

src/config/loader.ts

@@ -29,7 +29,12 @@ export function loadConfig(path?: string): PhantomConfig {
 	// Environment variable overrides for runtime flexibility.
 	// These let operators change settings via env without editing YAML.
 	if (process.env.PHANTOM_MODEL) {
-		config.model = process.env.PHANTOM_MODEL;
+		const envModel = process.env.PHANTOM_MODEL;
+		if (envModel !== config.model) {
+			console.warn(`[config] Model override: ${config.model} (yaml) -> ${envModel} (env)`);
+		}
+		config.model = envModel;
+		config.model_source = "env";
 	}
 	if (process.env.PHANTOM_DOMAIN) {
 		config.domain = process.env.PHANTOM_DOMAIN;

src/config/schemas.ts

@@ -13,7 +13,8 @@ export const PhantomConfigSchema = z.object({
 	public_url: z.string().url().optional(),
 	port: z.number().int().min(1).max(65535).default(3100),
 	role: z.string().min(1).default("swe"),
-	model: z.string().min(1).default("claude-sonnet-4-6"),
+	model: z.string().min(1).default("claude-opus-4-6"),
+	model_source: z.enum(["config", "env"]).default("config"),
 	effort: z.enum(["low", "medium", "high", "max"]).default("max"),
 	max_budget_usd: z.number().min(0).default(0),
 	timeout_minutes: z.number().min(1).default(240),

src/core/server.ts

@@ -10,12 +10,20 @@ import { handleUiRequest } from "../ui/serve.ts";
 const VERSION = "0.18.2";
 
 type MemoryHealthProvider = () => Promise<MemoryHealth>;
+type EvolutionInfo = {
+	generation: number;
+	session_count: number;
+	sessions_since_consolidation: number;
+	session_log_depth: number;
+};
 type EvolutionVersionProvider = () => number;
+type EvolutionInfoProvider = () => EvolutionInfo;
 type McpServerProvider = () => PhantomMcpServer | null;
 type ChannelHealthProvider = () => Record<string, boolean>;
 type RoleInfoProvider = () => { id: string; name: string } | null;
 type OnboardingStatusProvider = () => string;
 type WebhookHandler = (req: Request) => Promise<Response>;
+type ModelInfoProvider = () => { model: string; model_source: "config" | "env" };
 type PeerHealthProvider = () => Record<string, { healthy: boolean; latencyMs: number; error?: string }>;
 type TriggerDeps = {
 	runtime: AgentRuntime;
@@ -25,11 +33,13 @@ type TriggerDeps = {
 
 let memoryHealthProvider: MemoryHealthProvider | null = null;
 let evolutionVersionProvider: EvolutionVersionProvider | null = null;
+let evolutionInfoProvider: EvolutionInfoProvider | null = null;
 let mcpServerProvider: McpServerProvider | null = null;
 let channelHealthProvider: ChannelHealthProvider | null = null;
 let roleInfoProvider: RoleInfoProvider | null = null;
 let onboardingStatusProvider: OnboardingStatusProvider | null = null;
 let webhookHandler: WebhookHandler | null = null;
+let modelInfoProvider: ModelInfoProvider | null = null;
 let peerHealthProvider: PeerHealthProvider | null = null;
 let triggerDeps: TriggerDeps | null = null;
 
@@ -41,6 +51,10 @@ export function setEvolutionVersionProvider(provider: EvolutionVersionProvider):
 	evolutionVersionProvider = provider;
 }
 
+export function setEvolutionInfoProvider(provider: EvolutionInfoProvider): void {
+	evolutionInfoProvider = provider;
+}
+
 export function setMcpServerProvider(provider: McpServerProvider): void {
 	mcpServerProvider = provider;
 }
@@ -61,6 +75,10 @@ export function setWebhookHandler(handler: WebhookHandler): void {
 	webhookHandler = handler;
 }
 
+export function setModelInfoProvider(provider: ModelInfoProvider): void {
+	modelInfoProvider = provider;
+}
+
 export function setPeerHealthProvider(provider: PeerHealthProvider): void {
 	peerHealthProvider = provider;
 }
@@ -92,11 +110,13 @@ export function startServer(config: PhantomConfig, startedAt: number): ReturnTyp
 				// Both up -> ok. One up -> degraded. Both down + configured -> down. Not configured -> ok.
 				const status = allHealthy ? "ok" : someHealthy ? "degraded" : memory.configured ? "down" : "ok";
 				const evolutionGeneration = evolutionVersionProvider ? evolutionVersionProvider() : 0;
+				const evolutionInfo = evolutionInfoProvider ? evolutionInfoProvider() : null;
 
 				const roleInfo = roleInfoProvider ? roleInfoProvider() : null;
 
 				const onboardingStatus = onboardingStatusProvider ? onboardingStatusProvider() : null;
 				const peers = peerHealthProvider ? peerHealthProvider() : null;
+				const modelInfo = modelInfoProvider ? modelInfoProvider() : null;
 
 				return Response.json({
 					status,
@@ -105,9 +125,10 @@ export function startServer(config: PhantomConfig, startedAt: number): ReturnTyp
 					agent: config.name,
 					...(config.public_url ? { public_url: config.public_url } : {}),
 					role: roleInfo ?? { id: config.role, name: config.role },
+					...(modelInfo ? { model: modelInfo.model, model_source: modelInfo.model_source } : {}),
 					channels,
 					memory,
-					evolution: {
+					evolution: evolutionInfo ?? {
 						generation: evolutionGeneration,
 					},
 					...(onboardingStatus ? { onboarding: onboardingStatus } : {}),

src/evolution/__tests__/application.test.ts

@@ -62,8 +62,11 @@ describe("Application", () => {
 
 			const content = readFileSync(`${TEST_DIR}/user-profile.md`, "utf-8");
 			expect(content).toContain("Prefers TypeScript");
-			expect(change.file).toBe("user-profile.md");
-			expect(change.content).toBe("- Prefers TypeScript");
+			expect(change).not.toBeNull();
+			if (change) {
+				expect(change.file).toBe("user-profile.md");
+				expect(change.content).toBe("- Prefers TypeScript");
+			}
 		});
 
 		test("replaces content in file", () => {
@@ -99,6 +102,73 @@ describe("Application", () => {
 			expect(content).not.toContain("Preferences go here.");
 		});
 
+		test("skips append when all content lines already exist", () => {
+			writeFileSync(`${TEST_DIR}/user-profile.md`, "# User Profile\n\n- Prefers TypeScript\n", "utf-8");
+			const delta: ConfigDelta = {
+				file: "user-profile.md",
+				type: "append",
+				content: "- Prefers TypeScript",
+				rationale: "User said so",
+				session_ids: ["s1"],
+				tier: "free",
+			};
+			applyDelta(delta, testConfig());
+
+			const content = readFileSync(`${TEST_DIR}/user-profile.md`, "utf-8");
+			// Should not have duplicated the line
+			const matches = content.match(/Prefers TypeScript/g);
+			expect(matches).toHaveLength(1);
+		});
+
+		test("appends only new lines from partial overlap", () => {
+			writeFileSync(`${TEST_DIR}/user-profile.md`, "# User Profile\n\n- Prefers TypeScript\n", "utf-8");
+			const delta: ConfigDelta = {
+				file: "user-profile.md",
+				type: "append",
+				content: "- Prefers TypeScript\n- Uses Bun runtime",
+				rationale: "Mixed new and existing",
+				session_ids: ["s1"],
+				tier: "free",
+			};
+			applyDelta(delta, testConfig());
+
+			const content = readFileSync(`${TEST_DIR}/user-profile.md`, "utf-8");
+			const tsMatches = content.match(/Prefers TypeScript/g);
+			expect(tsMatches).toHaveLength(1);
+			expect(content).toContain("Uses Bun runtime");
+		});
+
+		test("returns null for no-op append", () => {
+			writeFileSync(`${TEST_DIR}/user-profile.md`, "# User Profile\n\n- Prefers TypeScript\n", "utf-8");
+			const delta: ConfigDelta = {
+				file: "user-profile.md",
+				type: "append",
+				content: "- Prefers TypeScript",
+				rationale: "Duplicate",
+				session_ids: ["s1"],
+				tier: "free",
+			};
+			const result = applyDelta(delta, testConfig());
+			expect(result).toBeNull();
+		});
+
+		test("appends when content is genuinely new", () => {
+			writeFileSync(`${TEST_DIR}/user-profile.md`, "# User Profile\n\n- Prefers TypeScript\n", "utf-8");
+			const delta: ConfigDelta = {
+				file: "user-profile.md",
+				type: "append",
+				content: "- Uses Bun runtime",
+				rationale: "New preference",
+				session_ids: ["s1"],
+				tier: "free",
+			};
+			applyDelta(delta, testConfig());
+
+			const content = readFileSync(`${TEST_DIR}/user-profile.md`, "utf-8");
+			expect(content).toContain("Prefers TypeScript");
+			expect(content).toContain("Uses Bun runtime");
+		});
+
 		test("creates new file if it does not exist", () => {
 			const delta: ConfigDelta = {
 				file: "new-file.md",