diff --git a/README.md b/README.md
index df32c47..4676063 100644
--- a/README.md
+++ b/README.md
@@ -14,10 +14,10 @@ TypeScript runtime for deterministic multi-agent execution with:
 ## Architecture Summary
 
 - `SchemaDrivenExecutionEngine.runSession(...)` is the single execution entrypoint.
-- `PipelineExecutor` owns runtime control flow and topology dispatch.
+- `PipelineExecutor` owns runtime control flow and topology dispatch while delegating failure classification and persistence/event side-effects to dedicated policies.
 - `AgentManager` is an internal utility used by the pipeline when fan-out/retry-unrolled behavior is required.
 - Session state is persisted under `AGENT_STATE_ROOT`.
-- Project state is persisted under `AGENT_PROJECT_CONTEXT_PATH` with domains:
+- Project state is persisted under `AGENT_PROJECT_CONTEXT_PATH` with schema-versioned JSON (`schemaVersion`) and domains:
   - `globalFlags`
   - `artifactPointers`
   - `taskQueue`
@@ -26,7 +26,9 @@ TypeScript runtime for deterministic multi-agent execution with:
 
 - `src/agents`
   - `orchestration.ts`: engine facade and runtime wiring
-  - `pipeline.ts`: DAG runner, retry matrix, abort propagation, domain-event routing
+  - `pipeline.ts`: DAG runner, retry matrix, aggregate session status, abort propagation, domain-event routing
+  - `failure-policy.ts`: hard/soft failure classification policy
+  - `lifecycle-observer.ts`: persistence/event lifecycle hooks for node attempts
   - `manifest.ts`: schema parsing/validation for personas/topologies/edges
   - `manager.ts`: recursive fan-out utility used by pipeline
   - `state-context.ts`: persisted node handoffs + session state
@@ -36,6 +38,7 @@ TypeScript runtime for deterministic multi-agent execution with:
   - `provisioning.ts`: resource provisioning and child suballocation helpers
 - `src/mcp`: MCP config types/conversion/handlers
 - `src/examples`: provider entrypoints (`codex.ts`, `claude.ts`)
+- `src/config.ts`: centralized env parsing/validation/defaulting
 - `tests`: manager, manifest, pipeline/orchestration, state, provisioning, MCP
 
 ## Setup
@@ -93,6 +96,7 @@ Actors can emit events in `ActorExecutionResult.events`. Pipeline status also em
 - hard failures: timeout/network/403-like failures tracked sequentially; at 2 consecutive hard failures the pipeline aborts fast
 - `AbortSignal` is passed into every actor execution input
 - session closure aborts child recursive work
+- run summaries expose aggregate `status`: success requires successful terminal executed DAG nodes and no critical-path failure
 
 ## Environment Variables
 
diff --git a/docs/pipeline-policies.md b/docs/pipeline-policies.md
new file mode 100644
index 0000000..f443cc1
--- /dev/null
+++ b/docs/pipeline-policies.md
@@ -0,0 +1,30 @@
+# Pipeline Policies and Lifecycle Hooks
+
+## Why this exists
+
+`PipelineExecutor` previously handled DAG traversal, failure heuristics, state persistence, and domain-event emission in one execution loop. This made behavior harder to isolate and test.
+
+## Current structure
+
+- `FailurePolicy` (`src/agents/failure-policy.ts`)
+  - Owns hard vs soft failure classification.
+  - Determines whether a sequence of hard failures should abort execution.
+- `PersistenceLifecycleObserver` (`src/agents/lifecycle-observer.ts`)
+  - Handles state patching, project-context updates, and domain-event publishing for each node attempt.
+- `PipelineExecutor` (`src/agents/pipeline.ts`)
+  - Coordinates DAG traversal and retry behavior.
+  - Computes aggregate run status from executed terminal nodes plus critical-path failures.
+
+## Aggregate status semantics
+
+Run status is `success` only when both are true:
+
+1. All executed terminal nodes (leaves in the executed subgraph) have final status `success`.
+2. No executed node in the critical path has final status `failure`.
+
+Otherwise status is `failure`.
+
+## Persistence guarantees
+
+State and project-context writes are now atomic via temp-file + rename.
+Project-context patch/write operations are serialized both in-process (promise queue) and cross-process (lock file).
diff --git a/src/agents/failure-policy.ts b/src/agents/failure-policy.ts
new file mode 100644
index 0000000..66dd739
--- /dev/null
+++ b/src/agents/failure-policy.ts
@@ -0,0 +1,66 @@
+import type { ActorExecutionResult, ActorFailureKind } from "./pipeline.js";
+
+function toErrorMessage(error: unknown): string {
+  if (error instanceof Error) {
+    return error.message;
+  }
+  return String(error);
+}
+
+function containsHardFailureSignal(value: string): boolean {
+  return /(timeout|timed out|network|econnreset|econnrefused|enotfound|403|forbidden)/i.test(value);
+}
+
+function toFailureCodeFromError(error: unknown): string | undefined {
+  if (!(error instanceof Error)) {
+    return undefined;
+  }
+
+  const maybeCode = (error as NodeJS.ErrnoException).code;
+  return typeof maybeCode === "string" ? maybeCode : undefined;
+}
+
+export class FailurePolicy {
+  isHardFailure(result: ActorExecutionResult): boolean {
+    if (result.failureKind === "hard") {
+      return true;
+    }
+
+    if (result.status !== "failure") {
+      return false;
+    }
+
+    const payloadText = (() => {
+      const message = result.payload?.error;
+      return typeof message === "string" ? message : "";
+    })();
+
+    const codeText = result.failureCode ?? "";
+    return containsHardFailureSignal(`${codeText} ${payloadText}`);
+  }
+
+  classifyFailureFromError(error: unknown): {
+    payloadErrorMessage: string;
+    failureCode?: string;
+    failureKind: ActorFailureKind;
+  } {
+    const message = toErrorMessage(error);
+    const failureCode = toFailureCodeFromError(error);
+    const failureKind = containsHardFailureSignal(`${failureCode ?? ""} ${message}`)
+      ? "hard"
+      : "soft";
+
+    return {
+      payloadErrorMessage: message,
+      ...(failureCode ? { failureCode } : {}),
+      failureKind,
+    };
+  }
+
+  shouldAbortAfterSequentialHardFailures(
+    sequentialHardFailureCount: number,
+    threshold: number,
+  ): boolean {
+    return sequentialHardFailureCount >= threshold;
+  }
+}
diff --git a/src/agents/file-persistence.ts b/src/agents/file-persistence.ts
new file mode 100644
index 0000000..59b251d
--- /dev/null
+++ b/src/agents/file-persistence.ts
@@ -0,0 +1,105 @@
+import { randomUUID } from "node:crypto";
+import { mkdir, open, rename, stat, unlink, writeFile } from "node:fs/promises";
+import { basename, dirname, resolve } from "node:path";
+
+function sleep(ms: number): Promise<void> {
+  return new Promise((resolveSleep) => {
+    setTimeout(resolveSleep, ms);
+  });
+}
+
+async function cleanupFile(path: string): Promise<void> {
+  try {
+    await unlink(path);
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code !== "ENOENT") {
+      throw error;
+    }
+  }
+}
+
+export async function writeUtf8FileAtomic(path: string, content: string): Promise<void> {
+  const directory = dirname(path);
+  await mkdir(directory, { recursive: true });
+
+  const tempFileName = `.${basename(path)}.${String(process.pid)}.${randomUUID()}.tmp`;
+  const tempPath = resolve(directory, tempFileName);
+
+  try {
+    await writeFile(tempPath, content, "utf8");
+    await rename(tempPath, path);
+  } catch (error) {
+    await cleanupFile(tempPath);
+    throw error;
+  }
+}
+
+async function tryAcquireFileLock(
+  lockPath: string,
+): Promise<Awaited<ReturnType<typeof open>> | undefined> {
+  try {
+    const handle = await open(lockPath, "wx");
+    await handle.writeFile(`${JSON.stringify({ pid: process.pid, acquiredAt: new Date().toISOString() })}\n`);
+    return handle;
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code === "EEXIST") {
+      return undefined;
+    }
+    throw error;
+  }
+}
+
+async function clearStaleLock(lockPath: string, staleAfterMs: number): Promise<void> {
+  try {
+    const stats = await stat(lockPath);
+    const ageMs = Date.now() - stats.mtimeMs;
+    if (ageMs <= staleAfterMs) {
+      return;
+    }
+
+    await cleanupFile(lockPath);
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code !== "ENOENT") {
+      throw error;
+    }
+  }
+}
+
+export async function withFileLock<T>(
+  lockPath: string,
+  operation: () => Promise<T>,
+  options?: {
+    maxWaitMs?: number;
+    retryDelayMs?: number;
+    staleAfterMs?: number;
+  },
+): Promise<T> {
+  const maxWaitMs = options?.maxWaitMs ?? 5000;
+  const retryDelayMs = options?.retryDelayMs ?? 25;
+  const staleAfterMs = options?.staleAfterMs ?? 30_000;
+
+  await mkdir(dirname(lockPath), { recursive: true });
+
+  const startedAt = Date.now();
+
+  // Busy-wait with bounded retries to coordinate concurrent writers across processes.
+  while (true) {
+    const handle = await tryAcquireFileLock(lockPath);
+    if (handle) {
+      try {
+        return await operation();
+      } finally {
+        await handle.close();
+        await cleanupFile(lockPath);
+      }
+    }
+
+    await clearStaleLock(lockPath, staleAfterMs);
+
+    if (Date.now() - startedAt >= maxWaitMs) {
+      throw new Error(`Timed out waiting for file lock: ${lockPath}`);
+    }
+
+    await sleep(retryDelayMs);
+  }
+}
diff --git a/src/agents/lifecycle-observer.ts b/src/agents/lifecycle-observer.ts
new file mode 100644
index 0000000..079d62e
--- /dev/null
+++ b/src/agents/lifecycle-observer.ts
@@ -0,0 +1,126 @@
+import {
+  DomainEventBus,
+  type DomainEvent,
+  type DomainEventType,
+} from "./domain-events.js";
+import type { PipelineNode } from "./manifest.js";
+import { type ProjectContextPatch, type FileSystemProjectContextStore } from "./project-context.js";
+import { PersonaRegistry } from "./persona-registry.js";
+import {
+  FileSystemStateContextManager,
+  type SessionHistoryEntry,
+} from "./state-context.js";
+import type { ActorExecutionResult, ActorResultStatus } from "./pipeline.js";
+
+export type PipelineNodeAttemptObservedEvent = {
+  sessionId: string;
+  node: PipelineNode;
+  attempt: number;
+  result: ActorExecutionResult;
+  domainEvents: DomainEvent[];
+};
+
+function toBehaviorEvent(status: ActorResultStatus): "onTaskComplete" | "onValidationFail" | undefined {
+  if (status === "success") {
+    return "onTaskComplete";
+  }
+  if (status === "validation_fail") {
+    return "onValidationFail";
+  }
+  return undefined;
+}
+
+export interface PipelineLifecycleObserver {
+  onNodeAttempt(event: PipelineNodeAttemptObservedEvent): Promise<void>;
+}
+
+export class PersistenceLifecycleObserver implements PipelineLifecycleObserver {
+  constructor(
+    private readonly input: {
+      personaRegistry: PersonaRegistry;
+      stateManager: FileSystemStateContextManager;
+      projectContextStore: FileSystemProjectContextStore;
+      domainEventBus?: DomainEventBus;
+    },
+  ) {}
+
+  async onNodeAttempt(event: PipelineNodeAttemptObservedEvent): Promise<void> {
+    const behaviorEvent = toBehaviorEvent(event.result.status);
+    const behaviorPatch = behaviorEvent
+      ? await this.input.personaRegistry.emitBehaviorEvent({
+          personaId: event.node.personaId,
+          event: behaviorEvent,
+          sessionId: event.sessionId,
+          nodeId: event.node.id,
+          payload: event.result.payload ?? {},
+        })
+      : {};
+
+    const legacyHistoryEvent: SessionHistoryEntry = {
+      nodeId: event.node.id,
+      event: event.result.status,
+      timestamp: new Date().toISOString(),
+      ...(event.result.payload ? { data: event.result.payload } : {}),
+    };
+
+    const domainHistoryEvents: SessionHistoryEntry[] = event.domainEvents.map((domainEvent) => ({
+      nodeId: event.node.id,
+      event: domainEvent.type,
+      timestamp: domainEvent.timestamp,
+      data: {
+        source: domainEvent.source,
+        attempt: domainEvent.attempt,
+        ...(domainEvent.payload.summary ? { summary: domainEvent.payload.summary } : {}),
+        ...(domainEvent.payload.errorCode ? { errorCode: domainEvent.payload.errorCode } : {}),
+        ...(domainEvent.payload.artifactPointer
+          ? { artifactPointer: domainEvent.payload.artifactPointer }
+          : {}),
+        ...(domainEvent.payload.details ? { details: domainEvent.payload.details } : {}),
+      },
+    }));
+
+    await this.input.stateManager.patchState(event.sessionId, {
+      ...(event.result.stateFlags ? { flags: event.result.stateFlags } : {}),
+      metadata: {
+        ...(event.result.stateMetadata ?? {}),
+        ...behaviorPatch,
+      },
+      historyEvent: legacyHistoryEvent,
+      historyEvents: domainHistoryEvents,
+    });
+
+    const domainEventBus = this.input.domainEventBus;
+    if (domainEventBus) {
+      for (const domainEvent of event.domainEvents) {
+        await domainEventBus.publish(domainEvent);
+      }
+    }
+
+    const patch: ProjectContextPatch = {
+      ...(event.result.projectContextPatch ?? {}),
+      artifactPointers: {
+        [`sessions/${event.sessionId}/last_completed_node`]: event.node.id,
+        [`sessions/${event.sessionId}/last_attempt`]: String(event.attempt),
+        ...(event.result.projectContextPatch?.artifactPointers ?? {}),
+      },
+    };
+
+    await this.input.projectContextStore.patchState(patch);
+  }
+}
+
+export class DomainEventCollector {
+  private readonly events: DomainEvent[] = [];
+
+  record(events: DomainEvent[]): void {
+    this.events.push(...events);
+  }
+
+  toEventTypes(events: DomainEvent[]): DomainEventType[] {
+    return events.map((event) => event.type);
+  }
+
+  getAll(): DomainEvent[] {
+    return [...this.events];
+  }
+}
diff --git a/src/agents/orchestration.ts b/src/agents/orchestration.ts
index 2657f80..1fb549f 100644
--- a/src/agents/orchestration.ts
+++ b/src/agents/orchestration.ts
@@ -1,4 +1,6 @@
 import { resolve } from "node:path";
+import { getConfig, loadConfig, type AppConfig } from "../config.js";
+import { createDefaultMcpRegistry, McpRegistry } from "../mcp.js";
 import { parseAgentManifest, type AgentManifest } from "./manifest.js";
 import { AgentManager } from "./manager.js";
 import {
@@ -8,7 +10,6 @@ import {
 } from "./persona-registry.js";
 import { PipelineExecutor, type ActorExecutor, type PipelineRunSummary } from "./pipeline.js";
 import { FileSystemProjectContextStore } from "./project-context.js";
-import { loadAgentManagerLimitsFromEnv } from "./runtime.js";
 import { FileSystemStateContextManager, type StoredSessionState } from "./state-context.js";
 import type { JsonObject } from "./types.js";
 
@@ -26,59 +27,16 @@ export type BehaviorHandlerRegistry = Partial<
   Record<string, Partial<Record<PersonaBehaviorEvent, PersonaBehaviorHandler>>>
 >;
 
-function readOptionalIntegerEnv(
-  key:
-    | "AGENT_TOPOLOGY_MAX_DEPTH"
-    | "AGENT_TOPOLOGY_MAX_RETRIES"
-    | "AGENT_RELATIONSHIP_MAX_CHILDREN",
-  fallback: number,
-  min: number,
-): number {
-  const raw = process.env[key]?.trim();
-  if (!raw) {
-    return fallback;
-  }
-
-  const parsed = Number(raw);
-  if (!Number.isInteger(parsed) || parsed < min) {
-    throw new Error(`Environment variable ${key} must be an integer >= ${String(min)}.`);
-  }
-
-  return parsed;
-}
-
-function readOptionalStringEnv(key: "AGENT_STATE_ROOT", fallback: string): string {
-  const raw = process.env[key]?.trim();
-  if (!raw) {
-    return fallback;
-  }
-  return raw;
-}
-
-function readOptionalProjectContextPathEnv(
-  key: "AGENT_PROJECT_CONTEXT_PATH",
-  fallback: string,
-): string {
-  const raw = process.env[key]?.trim();
-  if (!raw) {
-    return fallback;
-  }
-  return raw;
-}
-
-export function loadOrchestrationSettingsFromEnv(): Omit<
-  OrchestrationSettings,
-  "workspaceRoot" | "runtimeContext"
-> {
+export function loadOrchestrationSettingsFromEnv(
+  env: NodeJS.ProcessEnv = process.env,
+): Omit<OrchestrationSettings, "workspaceRoot" | "runtimeContext"> {
+  const config = loadConfig(env);
   return {
-    stateRoot: readOptionalStringEnv("AGENT_STATE_ROOT", ".ai_ops/state"),
-    projectContextPath: readOptionalProjectContextPathEnv(
-      "AGENT_PROJECT_CONTEXT_PATH",
-      ".ai_ops/project-context.json",
-    ),
-    maxDepth: readOptionalIntegerEnv("AGENT_TOPOLOGY_MAX_DEPTH", 4, 1),
-    maxRetries: readOptionalIntegerEnv("AGENT_TOPOLOGY_MAX_RETRIES", 2, 0),
-    maxChildren: readOptionalIntegerEnv("AGENT_RELATIONSHIP_MAX_CHILDREN", 4, 1),
+    stateRoot: config.orchestration.stateRoot,
+    projectContextPath: config.orchestration.projectContextPath,
+    maxDepth: config.orchestration.maxDepth,
+    maxRetries: config.orchestration.maxRetries,
+    maxChildren: config.orchestration.maxChildren,
   };
 }
 
@@ -115,6 +73,7 @@ export class SchemaDrivenExecutionEngine {
   private readonly settings: OrchestrationSettings;
   private readonly childrenByParent: Map<string, AgentManifest["relationships"]>;
   private readonly manager: AgentManager;
+  private readonly mcpRegistry: McpRegistry;
 
   constructor(input: {
     manifest: AgentManifest | unknown;
@@ -125,17 +84,21 @@ export class SchemaDrivenExecutionEngine {
       runtimeContext?: Record<string, string | number | boolean>;
     };
     manager?: AgentManager;
+    mcpRegistry?: McpRegistry;
+    config?: Readonly<AppConfig>;
   }) {
     this.manifest = parseAgentManifest(input.manifest);
 
-    const defaults = loadOrchestrationSettingsFromEnv();
+    const config = input.config ?? getConfig();
     this.settings = {
       workspaceRoot: resolve(input.settings?.workspaceRoot ?? process.cwd()),
-      stateRoot: resolve(input.settings?.stateRoot ?? defaults.stateRoot),
-      projectContextPath: resolve(input.settings?.projectContextPath ?? defaults.projectContextPath),
-      maxDepth: input.settings?.maxDepth ?? defaults.maxDepth,
-      maxRetries: input.settings?.maxRetries ?? defaults.maxRetries,
-      maxChildren: input.settings?.maxChildren ?? defaults.maxChildren,
+      stateRoot: resolve(input.settings?.stateRoot ?? config.orchestration.stateRoot),
+      projectContextPath: resolve(
+        input.settings?.projectContextPath ?? config.orchestration.projectContextPath,
+      ),
+      maxDepth: input.settings?.maxDepth ?? config.orchestration.maxDepth,
+      maxRetries: input.settings?.maxRetries ?? config.orchestration.maxRetries,
+      maxChildren: input.settings?.maxChildren ?? config.orchestration.maxChildren,
       runtimeContext: {
         ...(input.settings?.runtimeContext ?? {}),
       },
@@ -149,7 +112,14 @@ export class SchemaDrivenExecutionEngine {
     });
 
     this.actorExecutors = toExecutorMap(input.actorExecutors);
-    this.manager = input.manager ?? new AgentManager(loadAgentManagerLimitsFromEnv());
+    this.manager =
+      input.manager ??
+      new AgentManager({
+        maxConcurrentAgents: config.agentManager.maxConcurrentAgents,
+        maxSessionAgents: config.agentManager.maxSessionAgents,
+        maxRecursiveDepth: config.agentManager.maxRecursiveDepth,
+      });
+    this.mcpRegistry = input.mcpRegistry ?? createDefaultMcpRegistry();
 
     for (const persona of this.manifest.personas) {
       this.personaRegistry.register({
@@ -227,6 +197,7 @@ export class SchemaDrivenExecutionEngine {
         manager: this.manager,
         managerSessionId,
         projectContextStore: this.projectContextStore,
+        mcpRegistry: this.mcpRegistry,
       },
     );
     try {
diff --git a/src/agents/pipeline.ts b/src/agents/pipeline.ts
index f78b792..2144dc8 100644
--- a/src/agents/pipeline.ts
+++ b/src/agents/pipeline.ts
@@ -9,14 +9,19 @@ import {
   type DomainEventPayload,
   type DomainEventType,
 } from "./domain-events.js";
+import { FailurePolicy } from "./failure-policy.js";
+import {
+  PersistenceLifecycleObserver,
+  type PipelineLifecycleObserver,
+} from "./lifecycle-observer.js";
 import type { AgentManifest, PipelineEdge, PipelineNode, RouteCondition } from "./manifest.js";
 import type { AgentManager, RecursiveChildIntent } from "./manager.js";
+import type { McpRegistry } from "../mcp/handlers.js";
 import { PersonaRegistry } from "./persona-registry.js";
 import { type ProjectContextPatch, type FileSystemProjectContextStore } from "./project-context.js";
 import {
   FileSystemStateContextManager,
   type NodeExecutionContext,
-  type SessionHistoryEntry,
   type StoredSessionState,
 } from "./state-context.js";
 import type { JsonObject } from "./types.js";
@@ -59,11 +64,14 @@ export type PipelineExecutionRecord = {
 
 export type PipelineRunSummary = {
   sessionId: string;
+  status: PipelineAggregateStatus;
   records: PipelineExecutionRecord[];
   events: DomainEvent[];
   finalState: StoredSessionState;
 };
 
+export type PipelineAggregateStatus = "success" | "failure";
+
 export type PipelineExecutorOptions = {
   workspaceRoot: string;
   runtimeContext: Record<string, string | number | boolean>;
@@ -72,6 +80,10 @@ export type PipelineExecutorOptions = {
   manager: AgentManager;
   managerSessionId: string;
   projectContextStore: FileSystemProjectContextStore;
+  mcpRegistry: McpRegistry;
+  failurePolicy?: FailurePolicy;
+  lifecycleObserver?: PipelineLifecycleObserver;
+  hardFailureThreshold?: number;
 };
 
 type QueueItem = {
@@ -110,16 +122,6 @@ type NodeExecutionOutcome = {
   hardFailureAttempts: boolean[];
 };
 
-function toBehaviorEvent(status: ActorResultStatus): "onTaskComplete" | "onValidationFail" | undefined {
-  if (status === "success") {
-    return "onTaskComplete";
-  }
-  if (status === "validation_fail") {
-    return "onValidationFail";
-  }
-  return undefined;
-}
-
 function shouldEdgeRun(
   edge: PipelineEdge,
   status: ActorResultStatus,
@@ -228,51 +230,6 @@ function toAbortError(signal: AbortSignal): Error {
   return error;
 }
 
-function toErrorMessage(error: unknown): string {
-  if (error instanceof Error) {
-    return error.message;
-  }
-  return String(error);
-}
-
-function toErrorPayload(error: unknown): JsonObject {
-  const errorMessage = toErrorMessage(error);
-  return {
-    error: errorMessage,
-  };
-}
-
-function toFailureCodeFromError(error: unknown): string | undefined {
-  if (!(error instanceof Error)) {
-    return undefined;
-  }
-
-  const maybeCode = (error as NodeJS.ErrnoException).code;
-  return typeof maybeCode === "string" ? maybeCode : undefined;
-}
-
-function containsHardFailureSignal(value: string): boolean {
-  return /(timeout|timed out|network|econnreset|econnrefused|enotfound|403|forbidden)/i.test(value);
-}
-
-function inferHardFailure(result: ActorExecutionResult): boolean {
-  if (result.failureKind === "hard") {
-    return true;
-  }
-
-  if (result.status !== "failure") {
-    return false;
-  }
-
-  const payloadText = (() => {
-    const message = result.payload?.error;
-    return typeof message === "string" ? message : "";
-  })();
-
-  const codeText = result.failureCode ?? "";
-  return containsHardFailureSignal(`${codeText} ${payloadText}`);
-}
-
 function defaultEventPayloadForStatus(status: ActorResultStatus): DomainEventPayload {
   if (status === "success") {
     return {
@@ -323,6 +280,9 @@ export class PipelineExecutor {
   private readonly nodeById = new Map<string, PipelineNode>();
   private readonly edgesBySource = new Map<string, PipelineEdge[]>();
   private readonly domainEventBus = new DomainEventBus();
+  private readonly failurePolicy: FailurePolicy;
+  private readonly lifecycleObserver: PipelineLifecycleObserver;
+  private readonly hardFailureThreshold: number;
   private managerRunCounter = 0;
 
   constructor(
@@ -332,6 +292,17 @@ export class PipelineExecutor {
     private readonly actorExecutors: ReadonlyMap<string, ActorExecutor>,
     private readonly options: PipelineExecutorOptions,
   ) {
+    this.failurePolicy = options.failurePolicy ?? new FailurePolicy();
+    this.hardFailureThreshold = options.hardFailureThreshold ?? 2;
+    this.lifecycleObserver =
+      options.lifecycleObserver ??
+      new PersistenceLifecycleObserver({
+        personaRegistry: this.personaRegistry,
+        stateManager: this.stateManager,
+        projectContextStore: this.options.projectContextStore,
+        domainEventBus: this.domainEventBus,
+      });
+
     for (const node of manifest.pipeline.nodes) {
       this.nodeById.set(node.id, node);
     }
@@ -418,9 +389,14 @@ export class PipelineExecutor {
               sequentialHardFailures = 0;
             }
 
-            if (sequentialHardFailures >= 2) {
+            if (
+              this.failurePolicy.shouldAbortAfterSequentialHardFailures(
+                sequentialHardFailures,
+                this.hardFailureThreshold,
+              )
+            ) {
               throw new Error(
-                "Hard failure threshold reached (>=2 sequential API/network/403 failures). Pipeline aborted.",
+                `Hard failure threshold reached (>=${String(this.hardFailureThreshold)} sequential API/network/403 failures). Pipeline aborted.`,
               );
             }
           }
@@ -461,7 +437,8 @@ export class PipelineExecutor {
     }
 
     const finalState = await this.stateManager.readState(input.sessionId);
-    if (records.length > 0 && records[records.length - 1]?.status === "success") {
+    const status = this.computeAggregateStatus(records);
+    if (status === "success") {
       await this.options.projectContextStore.patchState({
         artifactPointers: {
           [`sessions/${input.sessionId}/final_state`]: this.stateManager.getSessionStatePath(input.sessionId),
@@ -471,12 +448,39 @@ export class PipelineExecutor {
 
     return {
       sessionId: input.sessionId,
+      status,
       records,
       events,
       finalState,
     };
   }
 
+  private computeAggregateStatus(records: PipelineExecutionRecord[]): PipelineAggregateStatus {
+    if (records.length === 0) {
+      return "failure";
+    }
+
+    const finalStatusByNode = new Map<string, ActorResultStatus>();
+    for (const record of records) {
+      finalStatusByNode.set(record.nodeId, record.status);
+    }
+
+    const executedNodeIds = new Set(finalStatusByNode.keys());
+    const terminalNodeIds = [...executedNodeIds].filter((nodeId) => {
+      const outgoingEdges = this.edgesBySource.get(nodeId) ?? [];
+      return !outgoingEdges.some((edge) => executedNodeIds.has(edge.to));
+    });
+
+    const allTerminalNodesSucceeded =
+      terminalNodeIds.length > 0 &&
+      terminalNodeIds.every((nodeId) => finalStatusByNode.get(nodeId) === "success");
+    const hasCriticalPathFailure = [...finalStatusByNode.values()].some(
+      (status) => status === "failure",
+    );
+
+    return allTerminalNodesSucceeded && !hasCriticalPathFailure ? "success" : "failure";
+  }
+
   private buildExecutionGroups(frontier: QueueItem[]): ExecutionGroup[] {
     const groupsByKey = new Map<string, ExecutionGroup>();
 
@@ -611,7 +615,7 @@ export class PipelineExecutor {
             customEvents: result.events,
           });
 
-          await this.persistNodeAttempt({
+          await this.lifecycleObserver.onNodeAttempt({
             sessionId,
             node,
             attempt,
@@ -629,7 +633,7 @@ export class PipelineExecutor {
           });
           nodeEvents.push(...domainEvents);
 
-          const hardFailure = inferHardFailure(result);
+          const hardFailure = this.failurePolicy.isHardFailure(result);
           hardFailureAttempts.push(hardFailure);
 
           const payloadForNext = result.payload ?? context.handoff.payload;
@@ -721,16 +725,15 @@ export class PipelineExecutor {
         throw toAbortError(input.signal);
       }
 
-      const failureCode = toFailureCodeFromError(error);
-      const failureKind = containsHardFailureSignal(`${failureCode ?? ""} ${toErrorMessage(error)}`)
-        ? "hard"
-        : "soft";
+      const classified = this.failurePolicy.classifyFailureFromError(error);
 
       return {
         status: "failure",
-        payload: toErrorPayload(error),
-        failureCode,
-        failureKind,
+        payload: {
+          error: classified.payloadErrorMessage,
+        },
+        failureCode: classified.failureCode,
+        failureKind: classified.failureKind,
       };
     }
   }
@@ -763,68 +766,4 @@ export class PipelineExecutor {
       }),
     );
   }
-
-  private async persistNodeAttempt(input: {
-    sessionId: string;
-    node: PipelineNode;
-    attempt: number;
-    result: ActorExecutionResult;
-    domainEvents: DomainEvent[];
-  }): Promise<void> {
-    const behaviorEvent = toBehaviorEvent(input.result.status);
-    const behaviorPatch = behaviorEvent
-      ? await this.personaRegistry.emitBehaviorEvent({
-          personaId: input.node.personaId,
-          event: behaviorEvent,
-          sessionId: input.sessionId,
-          nodeId: input.node.id,
-          payload: input.result.payload ?? {},
-        })
-      : {};
-
-    const legacyHistoryEvent: SessionHistoryEntry = {
-      nodeId: input.node.id,
-      event: input.result.status,
-      timestamp: new Date().toISOString(),
-      ...(input.result.payload ? { data: input.result.payload } : {}),
-    };
-
-    const domainHistoryEvents: SessionHistoryEntry[] = input.domainEvents.map((event) => ({
-      nodeId: input.node.id,
-      event: event.type,
-      timestamp: event.timestamp,
-      data: {
-        source: event.source,
-        attempt: event.attempt,
-        ...(event.payload.summary ? { summary: event.payload.summary } : {}),
-        ...(event.payload.errorCode ? { errorCode: event.payload.errorCode } : {}),
-        ...(event.payload.artifactPointer ? { artifactPointer: event.payload.artifactPointer } : {}),
-        ...(event.payload.details ? { details: event.payload.details } : {}),
-      },
-    }));
-
-    await this.stateManager.patchState(input.sessionId, {
-      ...(input.result.stateFlags ? { flags: input.result.stateFlags } : {}),
-      metadata: {
-        ...(input.result.stateMetadata ?? {}),
-        ...behaviorPatch,
-      },
-      historyEvent: legacyHistoryEvent,
-      historyEvents: domainHistoryEvents,
-    });
-
-    for (const event of input.domainEvents) {
-      await this.domainEventBus.publish(event);
-    }
-
-    const patch: ProjectContextPatch = {
-      ...(input.result.projectContextPatch ?? {}),
-      artifactPointers: {
-        [`sessions/${input.sessionId}/last_completed_node`]: input.node.id,
-        [`sessions/${input.sessionId}/last_attempt`]: String(input.attempt),
-        ...(input.result.projectContextPatch?.artifactPointers ?? {}),
-      },
-    };
-    await this.options.projectContextStore.patchState(patch);
-  }
 }
diff --git a/src/agents/project-context.ts b/src/agents/project-context.ts
index e96e07c..45d575a 100644
--- a/src/agents/project-context.ts
+++ b/src/agents/project-context.ts
@@ -1,7 +1,10 @@
-import { mkdir, readFile, writeFile } from "node:fs/promises";
-import { dirname, resolve } from "node:path";
+import { readFile } from "node:fs/promises";
+import { resolve } from "node:path";
+import { withFileLock, writeUtf8FileAtomic } from "./file-persistence.js";
 import { deepCloneJson, isRecord, type JsonObject, type JsonValue } from "./types.js";
 
+export const PROJECT_CONTEXT_SCHEMA_VERSION = 1;
+
 export type ProjectTaskStatus = "pending" | "in_progress" | "blocked" | "done";
 
 export type ProjectTask = {
@@ -13,6 +16,7 @@ export type ProjectTask = {
 };
 
 export type ProjectContextState = {
+  schemaVersion: number;
   globalFlags: Record<string, boolean>;
   artifactPointers: Record<string, string>;
   taskQueue: ProjectTask[];
@@ -27,6 +31,7 @@ export type ProjectContextPatch = {
 };
 
 const DEFAULT_PROJECT_CONTEXT: ProjectContextState = {
+  schemaVersion: PROJECT_CONTEXT_SCHEMA_VERSION,
   globalFlags: {},
   artifactPointers: {},
   taskQueue: [],
@@ -103,20 +108,41 @@ function toStringRecord(value: unknown, label: string): Record<string, string> {
   return out;
 }
 
+function toSchemaVersion(value: unknown): number {
+  if (value === undefined) {
+    return PROJECT_CONTEXT_SCHEMA_VERSION;
+  }
+
+  if (typeof value !== "number" || !Number.isInteger(value) || value < 1) {
+    throw new Error("Project context schemaVersion must be an integer >= 1.");
+  }
+
+  return value;
+}
+
 function toProjectContextState(value: unknown): ProjectContextState {
   if (!isRecord(value)) {
     throw new Error("Project context store is malformed.");
   }
 
   const tasksRaw = value.taskQueue;
-  if (!Array.isArray(tasksRaw)) {
+  if (tasksRaw !== undefined && !Array.isArray(tasksRaw)) {
     throw new Error("Project context taskQueue is malformed.");
   }
 
   return {
-    globalFlags: toBooleanRecord(value.globalFlags, "Project context globalFlags"),
-    artifactPointers: toStringRecord(value.artifactPointers, "Project context artifactPointers"),
-    taskQueue: tasksRaw.map((task, index) => toProjectTask(task, `Project context taskQueue[${String(index)}]`)),
+    schemaVersion: toSchemaVersion(value.schemaVersion),
+    globalFlags:
+      value.globalFlags === undefined
+        ? { ...DEFAULT_PROJECT_CONTEXT.globalFlags }
+        : toBooleanRecord(value.globalFlags, "Project context globalFlags"),
+    artifactPointers:
+      value.artifactPointers === undefined
+        ? { ...DEFAULT_PROJECT_CONTEXT.artifactPointers }
+        : toStringRecord(value.artifactPointers, "Project context artifactPointers"),
+    taskQueue: (tasksRaw ?? []).map((task, index) =>
+      toProjectTask(task, `Project context taskQueue[${String(index)}]`),
+    ),
   };
 }
 
@@ -142,10 +168,12 @@ function mergeUpsertTasks(current: ProjectTask[], upserts: ProjectTask[]): Proje
 
 export class FileSystemProjectContextStore {
   private readonly filePath: string;
+  private readonly lockPath: string;
   private queue: Promise<void> = Promise.resolve();
 
   constructor(input: { filePath: string }) {
     this.filePath = resolve(input.filePath);
+    this.lockPath = `${this.filePath}.lock`;
   }
 
   getFilePath(): string {
@@ -153,6 +181,57 @@ export class FileSystemProjectContextStore {
   }
 
   async readState(): Promise<ProjectContextState> {
+    return this.readStateFromDisk();
+  }
+
+  async writeState(state: ProjectContextState): Promise<void> {
+    await this.runSerialized(async () => {
+      await withFileLock(this.lockPath, async () => {
+        const normalizedState = toProjectContextState(state);
+        await writeUtf8FileAtomic(this.filePath, `${JSON.stringify(normalizedState, null, 2)}\n`);
+      });
+    });
+  }
+
+  async patchState(patch: ProjectContextPatch): Promise<ProjectContextState> {
+    return this.runSerialized(async () =>
+      withFileLock(this.lockPath, async () => {
+        const current = await this.readStateFromDisk();
+
+        if (patch.globalFlags) {
+          Object.assign(current.globalFlags, patch.globalFlags);
+        }
+        if (patch.artifactPointers) {
+          Object.assign(current.artifactPointers, patch.artifactPointers);
+        }
+        if (patch.taskQueue) {
+          current.taskQueue = patch.taskQueue.map((task, index) =>
+            toProjectTask(task, `Project context patch taskQueue[${String(index)}]`),
+          );
+        }
+        if (patch.enqueueTasks && patch.enqueueTasks.length > 0) {
+          current.taskQueue.push(
+            ...patch.enqueueTasks.map((task, index) =>
+              toProjectTask(task, `Project context patch enqueueTasks[${String(index)}]`),
+            ),
+          );
+        }
+        if (patch.upsertTasks && patch.upsertTasks.length > 0) {
+          const upsertTasks = patch.upsertTasks.map((task, index) =>
+            toProjectTask(task, `Project context patch upsertTasks[${String(index)}]`),
+          );
+          current.taskQueue = mergeUpsertTasks(current.taskQueue, upsertTasks);
+        }
+
+        current.schemaVersion = Math.max(current.schemaVersion, PROJECT_CONTEXT_SCHEMA_VERSION);
+
+        await writeUtf8FileAtomic(this.filePath, `${JSON.stringify(current, null, 2)}\n`);
+        return current;
+      }),
+    );
+  }
+
+  private async readStateFromDisk(): Promise<ProjectContextState> {
     try {
       const content = await readFile(this.filePath, "utf8");
       const parsed = JSON.parse(content) as unknown;
@@ -165,48 +244,6 @@ export class FileSystemProjectContextStore {
     }
   }
 
-  async writeState(state: ProjectContextState): Promise<void> {
-    await this.runSerialized(async () => {
-      await mkdir(dirname(this.filePath), { recursive: true });
-      await writeFile(this.filePath, `${JSON.stringify(state, null, 2)}\n`, "utf8");
-    });
-  }
-
-  async patchState(patch: ProjectContextPatch): Promise<ProjectContextState> {
-    return this.runSerialized(async () => {
-      const current = await this.readState();
-
-      if (patch.globalFlags) {
-        Object.assign(current.globalFlags, patch.globalFlags);
-      }
-      if (patch.artifactPointers) {
-        Object.assign(current.artifactPointers, patch.artifactPointers);
-      }
-      if (patch.taskQueue) {
-        current.taskQueue = patch.taskQueue.map((task, index) =>
-          toProjectTask(task, `Project context patch taskQueue[${String(index)}]`),
-        );
-      }
-      if (patch.enqueueTasks && patch.enqueueTasks.length > 0) {
-        current.taskQueue.push(
-          ...patch.enqueueTasks.map((task, index) =>
-            toProjectTask(task, `Project context patch enqueueTasks[${String(index)}]`),
-          ),
-        );
-      }
-      if (patch.upsertTasks && patch.upsertTasks.length > 0) {
-        const upsertTasks = patch.upsertTasks.map((task, index) =>
-          toProjectTask(task, `Project context patch upsertTasks[${String(index)}]`),
-        );
-        current.taskQueue = mergeUpsertTasks(current.taskQueue, upsertTasks);
-      }
-
-      await mkdir(dirname(this.filePath), { recursive: true });
-      await writeFile(this.filePath, `${JSON.stringify(current, null, 2)}\n`, "utf8");
-      return current;
-    });
-  }
-
   private runSerialized<T>(operation: () => Promise<T>): Promise<T> {
     const run = this.queue.then(operation, operation);
     this.queue = run.then(
diff --git a/src/agents/runtime.ts b/src/agents/runtime.ts
index 4f4712d..31a0318 100644
--- a/src/agents/runtime.ts
+++ b/src/agents/runtime.ts
@@ -1,3 +1,4 @@
+import { getConfig, loadConfig, type AppConfig } from "../config.js";
 import { AgentManager, type AgentManagerLimits } from "./manager.js";
 import {
   createDefaultResourceProvisioningOrchestrator,
@@ -5,143 +6,58 @@ import {
   type ResourceProvisioningOrchestrator,
 } from "./provisioning.js";
 
-const DEFAULT_LIMITS: AgentManagerLimits = {
-  maxConcurrentAgents: 4,
-  maxSessionAgents: 2,
-  maxRecursiveDepth: 3,
-};
-
-const DEFAULT_PROVISIONING_CONFIG: BuiltInProvisioningConfigInput = {
-  gitWorktree: {
-    rootDirectory: ".ai_ops/worktrees",
-    baseRef: "HEAD",
-  },
-  portRange: {
-    basePort: 36000,
-    blockSize: 32,
-    blockCount: 512,
-    primaryPortOffset: 0,
-    lockDirectory: ".ai_ops/locks/ports",
-  },
-};
-
-function readPositiveIntegerEnv(
-  key: "AGENT_MAX_CONCURRENT" | "AGENT_MAX_SESSION" | "AGENT_MAX_RECURSIVE_DEPTH",
-  fallback: number,
-): number {
-  const rawValue = process.env[key]?.trim();
-  if (!rawValue) {
-    return fallback;
-  }
-
-  const parsed = Number(rawValue);
-  if (!Number.isInteger(parsed) || parsed < 1) {
-    throw new Error(`Environment variable ${key} must be a positive integer.`);
-  }
-
-  return parsed;
-}
-
-function readOptionalStringEnv(key: string, fallback: string): string {
-  const rawValue = process.env[key]?.trim();
-  if (!rawValue) {
-    return fallback;
-  }
-  return rawValue;
-}
-
-function readIntegerEnv(
-  key: string,
-  fallback: number,
-  bounds: {
-    min: number;
-  },
-): number {
-  const rawValue = process.env[key]?.trim();
-  if (!rawValue) {
-    return fallback;
-  }
-
-  const parsed = Number(rawValue);
-  if (!Number.isInteger(parsed) || parsed < bounds.min) {
-    throw new Error(`Environment variable ${key} must be an integer >= ${String(bounds.min)}.`);
-  }
-  return parsed;
-}
-
-export function loadAgentManagerLimitsFromEnv(): AgentManagerLimits {
+function toProvisioningConfig(input: Readonly<AppConfig>): BuiltInProvisioningConfigInput {
   return {
-    maxConcurrentAgents: readPositiveIntegerEnv(
-      "AGENT_MAX_CONCURRENT",
-      DEFAULT_LIMITS.maxConcurrentAgents,
-    ),
-    maxSessionAgents: readPositiveIntegerEnv(
-      "AGENT_MAX_SESSION",
-      DEFAULT_LIMITS.maxSessionAgents,
-    ),
-    maxRecursiveDepth: readPositiveIntegerEnv(
-      "AGENT_MAX_RECURSIVE_DEPTH",
-      DEFAULT_LIMITS.maxRecursiveDepth,
-    ),
+    gitWorktree: {
+      rootDirectory: input.provisioning.gitWorktree.rootDirectory,
+      baseRef: input.provisioning.gitWorktree.baseRef,
+    },
+    portRange: {
+      basePort: input.provisioning.portRange.basePort,
+      blockSize: input.provisioning.portRange.blockSize,
+      blockCount: input.provisioning.portRange.blockCount,
+      primaryPortOffset: input.provisioning.portRange.primaryPortOffset,
+      lockDirectory: input.provisioning.portRange.lockDirectory,
+    },
+  };
+}
+
+export function loadAgentManagerLimitsFromEnv(env: NodeJS.ProcessEnv = process.env): AgentManagerLimits {
+  const config = loadConfig(env);
+  return {
+    maxConcurrentAgents: config.agentManager.maxConcurrentAgents,
+    maxSessionAgents: config.agentManager.maxSessionAgents,
+    maxRecursiveDepth: config.agentManager.maxRecursiveDepth,
   };
 }
 
 let managerSingleton: AgentManager | undefined;
 let provisioningSingleton: ResourceProvisioningOrchestrator | undefined;
 
-export function getAgentManager(): AgentManager {
+export function getAgentManager(config: Readonly<AppConfig> = getConfig()): AgentManager {
   if (!managerSingleton) {
-    managerSingleton = new AgentManager(loadAgentManagerLimitsFromEnv());
+    managerSingleton = new AgentManager({
+      maxConcurrentAgents: config.agentManager.maxConcurrentAgents,
+      maxSessionAgents: config.agentManager.maxSessionAgents,
+      maxRecursiveDepth: config.agentManager.maxRecursiveDepth,
+    });
   }
 
   return managerSingleton;
 }
 
-export function loadProvisioningConfigFromEnv(): BuiltInProvisioningConfigInput {
-  return {
-    gitWorktree: {
-      rootDirectory: readOptionalStringEnv(
-        "AGENT_WORKTREE_ROOT",
-        DEFAULT_PROVISIONING_CONFIG.gitWorktree?.rootDirectory ?? ".ai_ops/worktrees",
-      ),
-      baseRef: readOptionalStringEnv(
-        "AGENT_WORKTREE_BASE_REF",
-        DEFAULT_PROVISIONING_CONFIG.gitWorktree?.baseRef ?? "HEAD",
-      ),
-    },
-    portRange: {
-      basePort: readIntegerEnv(
-        "AGENT_PORT_BASE",
-        DEFAULT_PROVISIONING_CONFIG.portRange?.basePort ?? 36000,
-        { min: 1 },
-      ),
-      blockSize: readIntegerEnv(
-        "AGENT_PORT_BLOCK_SIZE",
-        DEFAULT_PROVISIONING_CONFIG.portRange?.blockSize ?? 32,
-        { min: 1 },
-      ),
-      blockCount: readIntegerEnv(
-        "AGENT_PORT_BLOCK_COUNT",
-        DEFAULT_PROVISIONING_CONFIG.portRange?.blockCount ?? 512,
-        { min: 1 },
-      ),
-      primaryPortOffset: readIntegerEnv(
-        "AGENT_PORT_PRIMARY_OFFSET",
-        DEFAULT_PROVISIONING_CONFIG.portRange?.primaryPortOffset ?? 0,
-        { min: 0 },
-      ),
-      lockDirectory: readOptionalStringEnv(
-        "AGENT_PORT_LOCK_DIR",
-        DEFAULT_PROVISIONING_CONFIG.portRange?.lockDirectory ?? ".ai_ops/locks/ports",
-      ),
-    },
-  };
+export function loadProvisioningConfigFromEnv(
+  env: NodeJS.ProcessEnv = process.env,
+): BuiltInProvisioningConfigInput {
+  return toProvisioningConfig(loadConfig(env));
 }
 
-export function getResourceProvisioningOrchestrator(): ResourceProvisioningOrchestrator {
+export function getResourceProvisioningOrchestrator(
+  config: Readonly<AppConfig> = getConfig(),
+): ResourceProvisioningOrchestrator {
   if (!provisioningSingleton) {
     provisioningSingleton = createDefaultResourceProvisioningOrchestrator(
-      loadProvisioningConfigFromEnv(),
+      toProvisioningConfig(config),
     );
   }
   return provisioningSingleton;
diff --git a/src/agents/state-context.ts b/src/agents/state-context.ts
index 6a8ae97..df3a80d 100644
--- a/src/agents/state-context.ts
+++ b/src/agents/state-context.ts
@@ -1,5 +1,6 @@
-import { mkdir, readFile, writeFile } from "node:fs/promises";
+import { mkdir, readFile } from "node:fs/promises";
 import { dirname, resolve } from "node:path";
+import { writeUtf8FileAtomic } from "./file-persistence.js";
 import { deepCloneJson, isRecord, type JsonObject, type JsonValue } from "./types.js";
 
 export type SessionHistoryEntry = {
@@ -200,7 +201,7 @@ export class FileSystemStateContextManager {
   async writeState(sessionId: string, state: StoredSessionState): Promise<void> {
     const path = toStatePath(this.rootDirectory, sessionId);
     await mkdir(dirname(path), { recursive: true });
-    await writeFile(path, `${JSON.stringify(state, null, 2)}\n`, "utf8");
+    await writeUtf8FileAtomic(path, `${JSON.stringify(state, null, 2)}\n`);
   }
 
   async patchState(
@@ -248,7 +249,7 @@ export class FileSystemStateContextManager {
 
     const path = toHandoffPath(this.rootDirectory, sessionId, handoff.nodeId);
     await mkdir(dirname(path), { recursive: true });
-    await writeFile(path, `${JSON.stringify(nodeHandoff, null, 2)}\n`, "utf8");
+    await writeUtf8FileAtomic(path, `${JSON.stringify(nodeHandoff, null, 2)}\n`);
     return nodeHandoff;
   }
 
diff --git a/src/config.ts b/src/config.ts
new file mode 100644
index 0000000..8f6f14c
--- /dev/null
+++ b/src/config.ts
@@ -0,0 +1,277 @@
+import type { AgentManagerLimits } from "./agents/manager.js";
+import type { BuiltInProvisioningConfig } from "./agents/provisioning.js";
+
+export type ProviderRuntimeConfig = {
+  codexApiKey?: string;
+  openAiApiKey?: string;
+  openAiBaseUrl?: string;
+  codexSkipGitCheck: boolean;
+  anthropicApiKey?: string;
+  claudeModel?: string;
+  claudeCodePath?: string;
+};
+
+export type McpRuntimeConfig = {
+  configPath: string;
+};
+
+export type OrchestrationRuntimeConfig = {
+  stateRoot: string;
+  projectContextPath: string;
+  maxDepth: number;
+  maxRetries: number;
+  maxChildren: number;
+};
+
+export type DiscoveryRuntimeConfig = {
+  fileRelativePath: string;
+};
+
+export type AppConfig = {
+  provider: ProviderRuntimeConfig;
+  mcp: McpRuntimeConfig;
+  agentManager: AgentManagerLimits;
+  orchestration: OrchestrationRuntimeConfig;
+  provisioning: BuiltInProvisioningConfig;
+  discovery: DiscoveryRuntimeConfig;
+};
+
+const DEFAULT_AGENT_MANAGER: AgentManagerLimits = {
+  maxConcurrentAgents: 4,
+  maxSessionAgents: 2,
+  maxRecursiveDepth: 3,
+};
+
+const DEFAULT_ORCHESTRATION: OrchestrationRuntimeConfig = {
+  stateRoot: ".ai_ops/state",
+  projectContextPath: ".ai_ops/project-context.json",
+  maxDepth: 4,
+  maxRetries: 2,
+  maxChildren: 4,
+};
+
+const DEFAULT_PROVISIONING: BuiltInProvisioningConfig = {
+  gitWorktree: {
+    rootDirectory: ".ai_ops/worktrees",
+    baseRef: "HEAD",
+  },
+  portRange: {
+    basePort: 36000,
+    blockSize: 32,
+    blockCount: 512,
+    primaryPortOffset: 0,
+    lockDirectory: ".ai_ops/locks/ports",
+  },
+};
+
+const DEFAULT_DISCOVERY: DiscoveryRuntimeConfig = {
+  fileRelativePath: ".agent-context/resources.json",
+};
+
+function readOptionalString(
+  env: NodeJS.ProcessEnv,
+  key: string,
+): string | undefined {
+  const value = env[key]?.trim();
+  if (!value) {
+    return undefined;
+  }
+  return value;
+}
+
+function readStringWithFallback(
+  env: NodeJS.ProcessEnv,
+  key: string,
+  fallback: string,
+): string {
+  return readOptionalString(env, key) ?? fallback;
+}
+
+function readIntegerWithBounds(
+  env: NodeJS.ProcessEnv,
+  key: string,
+  fallback: number,
+  bounds: {
+    min: number;
+  },
+): number {
+  const raw = env[key]?.trim();
+  if (!raw) {
+    return fallback;
+  }
+
+  const parsed = Number(raw);
+  if (!Number.isInteger(parsed) || parsed < bounds.min) {
+    throw new Error(`Environment variable ${key} must be an integer >= ${String(bounds.min)}.`);
+  }
+
+  return parsed;
+}
+
+function readBooleanWithFallback(
+  env: NodeJS.ProcessEnv,
+  key: string,
+  fallback: boolean,
+): boolean {
+  const raw = env[key]?.trim();
+  if (!raw) {
+    return fallback;
+  }
+
+  if (raw === "true") {
+    return true;
+  }
+  if (raw === "false") {
+    return false;
+  }
+
+  throw new Error(`Environment variable ${key} must be "true" or "false".`);
+}
+
+function deepFreeze<T>(value: T): Readonly<T> {
+  if (value === null || typeof value !== "object") {
+    return value;
+  }
+
+  const record = value as Record<string, unknown>;
+  for (const nested of Object.values(record)) {
+    deepFreeze(nested);
+  }
+
+  return Object.freeze(value);
+}
+
+export function loadConfig(env: NodeJS.ProcessEnv = process.env): Readonly<AppConfig> {
+  const config: AppConfig = {
+    provider: {
+      codexApiKey: readOptionalString(env, "CODEX_API_KEY"),
+      openAiApiKey: readOptionalString(env, "OPENAI_API_KEY"),
+      openAiBaseUrl: readOptionalString(env, "OPENAI_BASE_URL"),
+      codexSkipGitCheck: readBooleanWithFallback(env, "CODEX_SKIP_GIT_CHECK", true),
+      anthropicApiKey: readOptionalString(env, "ANTHROPIC_API_KEY"),
+      claudeModel: readOptionalString(env, "CLAUDE_MODEL"),
+      claudeCodePath: readOptionalString(env, "CLAUDE_CODE_PATH"),
+    },
+    mcp: {
+      configPath: readStringWithFallback(env, "MCP_CONFIG_PATH", "./mcp.config.json"),
+    },
+    agentManager: {
+      maxConcurrentAgents: readIntegerWithBounds(
+        env,
+        "AGENT_MAX_CONCURRENT",
+        DEFAULT_AGENT_MANAGER.maxConcurrentAgents,
+        { min: 1 },
+      ),
+      maxSessionAgents: readIntegerWithBounds(
+        env,
+        "AGENT_MAX_SESSION",
+        DEFAULT_AGENT_MANAGER.maxSessionAgents,
+        { min: 1 },
+      ),
+      maxRecursiveDepth: readIntegerWithBounds(
+        env,
+        "AGENT_MAX_RECURSIVE_DEPTH",
+        DEFAULT_AGENT_MANAGER.maxRecursiveDepth,
+        { min: 1 },
+      ),
+    },
+    orchestration: {
+      stateRoot: readStringWithFallback(
+        env,
+        "AGENT_STATE_ROOT",
+        DEFAULT_ORCHESTRATION.stateRoot,
+      ),
+      projectContextPath: readStringWithFallback(
+        env,
+        "AGENT_PROJECT_CONTEXT_PATH",
+        DEFAULT_ORCHESTRATION.projectContextPath,
+      ),
+      maxDepth: readIntegerWithBounds(
+        env,
+        "AGENT_TOPOLOGY_MAX_DEPTH",
+        DEFAULT_ORCHESTRATION.maxDepth,
+        { min: 1 },
+      ),
+      maxRetries: readIntegerWithBounds(
+        env,
+        "AGENT_TOPOLOGY_MAX_RETRIES",
+        DEFAULT_ORCHESTRATION.maxRetries,
+        { min: 0 },
+      ),
+      maxChildren: readIntegerWithBounds(
+        env,
+        "AGENT_RELATIONSHIP_MAX_CHILDREN",
+        DEFAULT_ORCHESTRATION.maxChildren,
+        { min: 1 },
+      ),
+    },
+    provisioning: {
+      gitWorktree: {
+        rootDirectory: readStringWithFallback(
+          env,
+          "AGENT_WORKTREE_ROOT",
+          DEFAULT_PROVISIONING.gitWorktree.rootDirectory,
+        ),
+        baseRef: readStringWithFallback(
+          env,
+          "AGENT_WORKTREE_BASE_REF",
+          DEFAULT_PROVISIONING.gitWorktree.baseRef,
+        ),
+      },
+      portRange: {
+        basePort: readIntegerWithBounds(
+          env,
+          "AGENT_PORT_BASE",
+          DEFAULT_PROVISIONING.portRange.basePort,
+          { min: 1 },
+        ),
+        blockSize: readIntegerWithBounds(
+          env,
+          "AGENT_PORT_BLOCK_SIZE",
+          DEFAULT_PROVISIONING.portRange.blockSize,
+          { min: 1 },
+        ),
+        blockCount: readIntegerWithBounds(
+          env,
+          "AGENT_PORT_BLOCK_COUNT",
+          DEFAULT_PROVISIONING.portRange.blockCount,
+          { min: 1 },
+        ),
+        primaryPortOffset: readIntegerWithBounds(
+          env,
+          "AGENT_PORT_PRIMARY_OFFSET",
+          DEFAULT_PROVISIONING.portRange.primaryPortOffset,
+          { min: 0 },
+        ),
+        lockDirectory: readStringWithFallback(
+          env,
+          "AGENT_PORT_LOCK_DIR",
+          DEFAULT_PROVISIONING.portRange.lockDirectory,
+        ),
+      },
+    },
+    discovery: {
+      fileRelativePath: readStringWithFallback(
+        env,
+        "AGENT_DISCOVERY_FILE_RELATIVE_PATH",
+        DEFAULT_DISCOVERY.fileRelativePath,
+      ),
+    },
+  };
+
+  return deepFreeze(config);
+}
+
+let configSingleton: Readonly<AppConfig> | undefined;
+
+export function getConfig(): Readonly<AppConfig> {
+  if (!configSingleton) {
+    configSingleton = loadConfig(process.env);
+  }
+
+  return configSingleton;
+}
+
+export function clearConfigCacheForTests(): void {
+  configSingleton = undefined;
+}
diff --git a/src/examples/claude.ts b/src/examples/claude.ts
index fc3f68b..7db2f2d 100644
--- a/src/examples/claude.ts
+++ b/src/examples/claude.ts
@@ -1,99 +1,75 @@
 import "dotenv/config";
 import { query, type Options } from "@anthropic-ai/claude-agent-sdk";
 import { pathToFileURL } from "node:url";
-import { getAgentManager, getResourceProvisioningOrchestrator } from "../agents/runtime.js";
-import { loadMcpConfigFromEnv } from "../mcp.js";
+import { getConfig } from "../config.js";
+import { createSessionContext } from "./session-context.js";
 
 function requiredPrompt(argv: string[]): string {
   const prompt = argv.slice(2).join(" ").trim();
   if (!prompt) {
-    throw new Error("Usage: npm run claude -- \"your prompt\"");
+    throw new Error('Usage: npm run claude -- "your prompt"');
   }
   return prompt;
 }
 
-function buildOptions(): Options {
+function buildOptions(config = getConfig()): Options {
   return {
     maxTurns: 1,
-    ...(process.env.CLAUDE_MODEL ? { model: process.env.CLAUDE_MODEL } : {}),
-    ...(process.env.CLAUDE_CODE_PATH
-      ? { pathToClaudeCodeExecutable: process.env.CLAUDE_CODE_PATH }
+    ...(config.provider.claudeModel ? { model: config.provider.claudeModel } : {}),
+    ...(config.provider.claudeCodePath
+      ? { pathToClaudeCodeExecutable: config.provider.claudeCodePath }
       : {}),
   };
 }
 
 export async function runClaudePrompt(prompt: string): Promise<void> {
-  const agentManager = getAgentManager();
-  const agentSession = agentManager.createSession();
-  const resourceProvisioning = getResourceProvisioningOrchestrator();
-  const mcp = loadMcpConfigFromEnv({
-    providerHint: "claude",
+  const config = getConfig();
+  const sessionContext = await createSessionContext("claude", {
     prompt,
+    config,
   });
-  let provisionedResources:
-    | Awaited<ReturnType<typeof resourceProvisioning.provisionSession>>
-    | undefined;
 
   try {
-    provisionedResources = await resourceProvisioning.provisionSession({
-      sessionId: agentSession.id,
-      resources: [{ kind: "git-worktree" }, { kind: "port-range" }],
-    });
-    const runtimeInjection = await provisionedResources.buildRuntimeInjection({
-      discoveryFileRelativePath: process.env.AGENT_DISCOVERY_FILE_RELATIVE_PATH,
-      baseEnv: process.env,
-    });
-    const promptWithContext = provisionedResources.composePrompt(prompt, [
-      `Discovery file: ${runtimeInjection.discoveryFilePath}`,
-      "Resource env vars are pre-injected (AGENT_WORKTREE_PATH, AGENT_PORT_RANGE_START, AGENT_PORT_RANGE_END, AGENT_PORT_PRIMARY).",
-    ]);
+    const finalResponse = await sessionContext.runInSession(async () => {
+      const session = query({
+        prompt: sessionContext.promptWithContext,
+        options: {
+          ...buildOptions(config),
+          ...(sessionContext.mcp.claudeMcpServers ? { mcpServers: sessionContext.mcp.claudeMcpServers } : {}),
+          cwd: sessionContext.runtimeInjection.workingDirectory,
+          env: sessionContext.runtimeInjection.env,
+        },
+      });
 
-    const finalResponse = await agentSession.runAgent({
-      depth: 0,
-      run: async () => {
-        const session = query({
-          prompt: promptWithContext,
-          options: {
-            ...buildOptions(),
-            ...(mcp.claudeMcpServers ? { mcpServers: mcp.claudeMcpServers } : {}),
-            cwd: runtimeInjection.workingDirectory,
-            env: runtimeInjection.env,
-          },
-        });
+      let result = "";
 
-        let result = "";
-
-        try {
-          for await (const message of session) {
-            if (message.type === "result" && message.subtype === "success") {
-              result = message.result.trim();
-            }
-
-            if (message.type === "result" && message.subtype !== "success") {
-              const detail = message.errors.join("; ");
-              throw new Error(
-                `Claude query failed (${message.subtype})${detail ? `: ${detail}` : ""}`,
-              );
-            }
+      try {
+        for await (const message of session) {
+          if (message.type === "result" && message.subtype === "success") {
+            result = message.result.trim();
           }
-        } finally {
-          session.close();
-        }
 
-        if (!result) {
-          throw new Error("Claude run completed without a final result.");
+          if (message.type === "result" && message.subtype !== "success") {
+            const detail = message.errors.join("; ");
+            throw new Error(
+              `Claude query failed (${message.subtype})${detail ? `: ${detail}` : ""}`,
+            );
+          }
         }
+      } finally {
+        session.close();
+      }
 
-        return result;
-      },
+      if (!result) {
+        throw new Error("Claude run completed without a final result.");
+      }
+
+      return result;
     });
 
     console.log(finalResponse);
   } finally {
-    if (provisionedResources) {
-      await provisionedResources.release();
-    }
-    agentSession.close();
+    await sessionContext.close();
   }
 }
 
diff --git a/src/examples/codex.ts b/src/examples/codex.ts
index 97ecb12..d12d4d9 100644
--- a/src/examples/codex.ts
+++ b/src/examples/codex.ts
@@ -1,67 +1,43 @@
 import "dotenv/config";
 import { Codex } from "@openai/codex-sdk";
 import { pathToFileURL } from "node:url";
-import { getAgentManager, getResourceProvisioningOrchestrator } from "../agents/runtime.js";
-import { loadMcpConfigFromEnv } from "../mcp.js";
+import { getConfig } from "../config.js";
+import { createSessionContext } from "./session-context.js";
 
 function requiredPrompt(argv: string[]): string {
   const prompt = argv.slice(2).join(" ").trim();
   if (!prompt) {
-    throw new Error("Usage: npm run codex -- \"your prompt\"");
+    throw new Error('Usage: npm run codex -- "your prompt"');
   }
   return prompt;
 }
 
 export async function runCodexPrompt(prompt: string): Promise<void> {
-  const agentManager = getAgentManager();
-  const agentSession = agentManager.createSession();
-  const resourceProvisioning = getResourceProvisioningOrchestrator();
-  const apiKey = process.env.CODEX_API_KEY ?? process.env.OPENAI_API_KEY;
-  const mcp = loadMcpConfigFromEnv({
-    providerHint: "codex",
+  const config = getConfig();
+  const sessionContext = await createSessionContext("codex", {
     prompt,
+    config,
   });
-  let provisionedResources:
-    | Awaited<ReturnType<typeof resourceProvisioning.provisionSession>>
-    | undefined;
 
   try {
-    provisionedResources = await resourceProvisioning.provisionSession({
-      sessionId: agentSession.id,
-      resources: [{ kind: "git-worktree" }, { kind: "port-range" }],
-    });
-    const runtimeInjection = await provisionedResources.buildRuntimeInjection({
-      discoveryFileRelativePath: process.env.AGENT_DISCOVERY_FILE_RELATIVE_PATH,
-      baseEnv: process.env,
-    });
+    const apiKey = config.provider.codexApiKey ?? config.provider.openAiApiKey;
 
     const codex = new Codex({
       ...(apiKey ? { apiKey } : {}),
-      ...(process.env.OPENAI_BASE_URL ? { baseUrl: process.env.OPENAI_BASE_URL } : {}),
-      ...(mcp.codexConfig ? { config: mcp.codexConfig } : {}),
-      env: runtimeInjection.env,
+      ...(config.provider.openAiBaseUrl ? { baseUrl: config.provider.openAiBaseUrl } : {}),
+      ...(sessionContext.mcp.codexConfig ? { config: sessionContext.mcp.codexConfig } : {}),
+      env: sessionContext.runtimeInjection.env,
     });
 
     const thread = codex.startThread({
-      workingDirectory: runtimeInjection.workingDirectory,
-      skipGitRepoCheck: process.env.CODEX_SKIP_GIT_CHECK !== "false",
+      workingDirectory: sessionContext.runtimeInjection.workingDirectory,
+      skipGitRepoCheck: config.provider.codexSkipGitCheck,
     });
 
-    const promptWithContext = provisionedResources.composePrompt(prompt, [
-      `Discovery file: ${runtimeInjection.discoveryFilePath}`,
-      "Resource env vars are pre-injected (AGENT_WORKTREE_PATH, AGENT_PORT_RANGE_START, AGENT_PORT_RANGE_END, AGENT_PORT_PRIMARY).",
-    ]);
-
-    const turn = await agentSession.runAgent({
-      depth: 0,
-      run: () => thread.run(promptWithContext),
-    });
+    const turn = await sessionContext.runInSession(() => thread.run(sessionContext.promptWithContext));
     console.log(turn.finalResponse.trim() || "(No response text returned)");
   } finally {
-    if (provisionedResources) {
-      await provisionedResources.release();
-    }
-    agentSession.close();
+    await sessionContext.close();
   }
 }
 
diff --git a/src/examples/session-context.ts b/src/examples/session-context.ts
new file mode 100644
index 0000000..32c9db6
--- /dev/null
+++ b/src/examples/session-context.ts
@@ -0,0 +1,105 @@
+import { getConfig, type AppConfig } from "../config.js";
+import type { AgentSession } from "../agents/manager.js";
+import type { ProvisionedResources } from "../agents/provisioning.js";
+import {
+  getAgentManager,
+  getResourceProvisioningOrchestrator,
+} from "../agents/runtime.js";
+import {
+  getDefaultMcpRegistry,
+  loadMcpConfigFromEnv,
+  type LoadedMcpConfig,
+  type McpRegistry,
+} from "../mcp.js";
+
+export type SessionProvider = "codex" | "claude";
+
+export type SessionContext = {
+  provider: SessionProvider;
+  sessionId: string;
+  mcp: LoadedMcpConfig;
+  promptWithContext: string;
+  runtimeInjection: Awaited<ReturnType<ProvisionedResources["buildRuntimeInjection"]>>;
+  runInSession: <T>(run: () => Promise<T>) => Promise<T>;
+  close: () => Promise<void>;
+};
+
+export async function createSessionContext(
+  provider: SessionProvider,
+  input: {
+    prompt: string;
+    config?: Readonly<AppConfig>;
+    mcpRegistry?: McpRegistry;
+  },
+): Promise<SessionContext> {
+  const config = input.config ?? getConfig();
+  const mcpRegistry = input.mcpRegistry ?? getDefaultMcpRegistry();
+  const agentManager = getAgentManager(config);
+  const agentSession = agentManager.createSession();
+  const resourceProvisioning = getResourceProvisioningOrchestrator(config);
+
+  let provisionedResources: ProvisionedResources | undefined;
+  let closed = false;
+
+  const close = async (): Promise<void> => {
+    if (closed) {
+      return;
+    }
+    closed = true;
+
+    if (provisionedResources) {
+      await provisionedResources.release();
+    }
+
+    agentSession.close();
+  };
+
+  try {
+    provisionedResources = await resourceProvisioning.provisionSession({
+      sessionId: agentSession.id,
+      resources: [{ kind: "git-worktree" }, { kind: "port-range" }],
+    });
+
+    const runtimeInjection = await provisionedResources.buildRuntimeInjection({
+      discoveryFileRelativePath: config.discovery.fileRelativePath,
+      baseEnv: process.env,
+    });
+
+    const promptWithContext = provisionedResources.composePrompt(input.prompt, [
+      `Discovery file: ${runtimeInjection.discoveryFilePath}`,
+      "Resource env vars are pre-injected (AGENT_WORKTREE_PATH, AGENT_PORT_RANGE_START, AGENT_PORT_RANGE_END, AGENT_PORT_PRIMARY).",
+    ]);
+
+    const mcp = loadMcpConfigFromEnv(
+      {
+        providerHint: provider,
+        prompt: input.prompt,
+      },
+      {
+        config,
+        registry: mcpRegistry,
+      },
+    );
+
+    return {
+      provider,
+      sessionId: agentSession.id,
+      mcp,
+      promptWithContext,
+      runtimeInjection,
+      runInSession: <T>(run: () => Promise<T>) =>
+        runWithAgentSession(agentSession, run),
+      close,
+    };
+  } catch (error) {
+    await close();
+    throw error;
+  }
+}
+
+async function runWithAgentSession<T>(agentSession: AgentSession, run: () => Promise<T>): Promise<T> {
+  return agentSession.runAgent({
+    depth: 0,
+    run,
+  });
+}
diff --git a/src/mcp.ts b/src/mcp.ts
index 2e8bb3a..47cd4a6 100644
--- a/src/mcp.ts
+++ b/src/mcp.ts
@@ -1,17 +1,18 @@
 import { existsSync, readFileSync } from "node:fs";
 import { resolve } from "node:path";
 import type { CodexOptions } from "@openai/codex-sdk";
+import { getConfig, type AppConfig } from "./config.js";
+import { normalizeSharedMcpConfigFile } from "./mcp/converters.js";
 import {
+  createDefaultMcpRegistry,
   createMcpHandlerShell,
-  listMcpHandlers,
-  registerMcpHandler,
-  resolveServerWithHandler,
   type McpHandlerBusinessLogic,
   type McpHandlerBusinessLogicInput,
   type McpHandlerInput,
   type McpHandlerResult,
   type McpHandlerShellOptions,
   type McpHandlerUtils,
+  McpRegistry,
   type McpServerHandler,
 } from "./mcp/handlers.js";
 import type {
@@ -24,16 +25,15 @@ function isRecord(value: unknown): value is Record<string, unknown> {
   return typeof value === "object" && value !== null && !Array.isArray(value);
 }
 
-function readConfigFile(pathFromEnv: string | undefined): {
+function readConfigFile(configPath: string): {
   config?: SharedMcpConfigFile;
   sourcePath?: string;
 } {
-  const explicitPath = pathFromEnv?.trim();
-  const candidatePath = explicitPath || "./mcp.config.json";
+  const candidatePath = configPath.trim() || "./mcp.config.json";
   const resolvedPath = resolve(process.cwd(), candidatePath);
 
   if (!existsSync(resolvedPath)) {
-    if (explicitPath) {
+    if (candidatePath !== "./mcp.config.json") {
       throw new Error(`MCP config file not found: ${resolvedPath}`);
     }
     return {};
@@ -45,11 +45,29 @@ function readConfigFile(pathFromEnv: string | undefined): {
     throw new Error(`MCP config file must contain a JSON object: ${resolvedPath}`);
   }
 
-  return { config: parsed as SharedMcpConfigFile, sourcePath: resolvedPath };
+  return {
+    config: normalizeSharedMcpConfigFile(parsed as SharedMcpConfigFile),
+    sourcePath: resolvedPath,
+  };
 }
 
-export function loadMcpConfigFromEnv(context: McpLoadContext = {}): LoadedMcpConfig {
-  const { config, sourcePath } = readConfigFile(process.env.MCP_CONFIG_PATH);
+const defaultMcpRegistry = createDefaultMcpRegistry();
+
+export function getDefaultMcpRegistry(): McpRegistry {
+  return defaultMcpRegistry;
+}
+
+export function loadMcpConfigFromEnv(
+  context: McpLoadContext = {},
+  options?: {
+    config?: Readonly<AppConfig>;
+    registry?: McpRegistry;
+  },
+): LoadedMcpConfig {
+  const runtimeConfig = options?.config ?? getConfig();
+  const registry = options?.registry ?? defaultMcpRegistry;
+
+  const { config, sourcePath } = readConfigFile(runtimeConfig.mcp.configPath);
   if (!config) {
     return {};
   }
@@ -59,7 +77,7 @@ export function loadMcpConfigFromEnv(context: McpLoadContext = {}): LoadedMcpCon
   const resolvedHandlers: Record<string, string> = {};
 
   for (const [serverName, server] of Object.entries(config.servers ?? {})) {
-    const resolved = resolveServerWithHandler({
+    const resolved = registry.resolveServerWithHandler({
       serverName,
       server,
       context,
@@ -102,7 +120,15 @@ export function loadMcpConfigFromEnv(context: McpLoadContext = {}): LoadedMcpCon
   };
 }
 
-export { createMcpHandlerShell, listMcpHandlers, registerMcpHandler };
+export function registerMcpHandler(handler: McpServerHandler): void {
+  defaultMcpRegistry.register(handler);
+}
+
+export function listMcpHandlers(): McpServerHandler[] {
+  return defaultMcpRegistry.listHandlers();
+}
+
+export { createDefaultMcpRegistry, createMcpHandlerShell, McpRegistry };
 export type {
   LoadedMcpConfig,
   McpHandlerBusinessLogic,
diff --git a/src/mcp/converters.ts b/src/mcp/converters.ts
index 01e5a06..bf98594 100644
--- a/src/mcp/converters.ts
+++ b/src/mcp/converters.ts
@@ -1,5 +1,42 @@
 import type { McpServerConfig } from "@anthropic-ai/claude-agent-sdk";
-import type { CodexConfigObject, SharedMcpServer, Transport } from "./types.js";
+import type {
+  CodexConfigObject,
+  SharedMcpConfigFile,
+  SharedMcpServer,
+  Transport,
+} from "./types.js";
+
+function mergeHeaders(server: SharedMcpServer): Record<string, string> | undefined {
+  const merged = {
+    ...(server.http_headers ?? {}),
+    ...(server.headers ?? {}),
+  };
+
+  return Object.keys(merged).length > 0 ? merged : undefined;
+}
+
+export function normalizeSharedMcpServer(server: SharedMcpServer): SharedMcpServer {
+  const { headers: _headers, http_headers: _httpHeaders, ...rest } = server;
+  const normalizedHeaders = mergeHeaders(server);
+
+  return {
+    ...rest,
+    ...(normalizedHeaders ? { headers: normalizedHeaders } : {}),
+  };
+}
+
+export function normalizeSharedMcpConfigFile(config: SharedMcpConfigFile): SharedMcpConfigFile {
+  const normalizedServers: Record<string, SharedMcpServer> = {};
+
+  for (const [serverName, server] of Object.entries(config.servers ?? {})) {
+    normalizedServers[serverName] = normalizeSharedMcpServer(server);
+  }
+
+  return {
+    ...config,
+    ...(Object.keys(normalizedServers).length > 0 ? { servers: normalizedServers } : {}),
+  };
+}
 
 export function inferTransport(server: SharedMcpServer): Transport {
   if (server.type) {
@@ -10,6 +47,7 @@ export function inferTransport(server: SharedMcpServer): Transport {
 
 export function toCodexServerConfig(serverName: string, server: SharedMcpServer): CodexConfigObject {
   const type = inferTransport(server);
+  const headers = mergeHeaders(server);
 
   if (type === "stdio" && !server.command) {
     throw new Error(`Shared MCP server "${serverName}" requires "command" for stdio transport.`);
@@ -38,9 +76,8 @@ export function toCodexServerConfig(serverName: string, server: SharedMcpServer)
   if (server.bearer_token_env_var) {
     config.bearer_token_env_var = server.bearer_token_env_var;
   }
-  const httpHeaders = server.http_headers ?? server.headers;
-  if (httpHeaders) {
-    config.http_headers = httpHeaders;
+  if (headers) {
+    config.http_headers = headers;
   }
   if (server.env_http_headers) config.env_http_headers = server.env_http_headers;
   if (server.env_vars) config.env_vars = server.env_vars;
@@ -50,6 +87,7 @@ export function toCodexServerConfig(serverName: string, server: SharedMcpServer)
 
 export function toClaudeServerConfig(serverName: string, server: SharedMcpServer): McpServerConfig {
   const type = inferTransport(server);
+  const headers = mergeHeaders(server);
 
   if (type === "stdio") {
     if (!server.command) {
@@ -70,7 +108,6 @@ export function toClaudeServerConfig(serverName: string, server: SharedMcpServer
   return {
     type,
     url: server.url,
-    ...(server.headers ? { headers: server.headers } : {}),
+    ...(headers ? { headers } : {}),
   };
 }
-
diff --git a/src/mcp/handlers.ts b/src/mcp/handlers.ts
index 8668c57..40e941c 100644
--- a/src/mcp/handlers.ts
+++ b/src/mcp/handlers.ts
@@ -127,107 +127,121 @@ function applyEnabledByDefault(input: McpHandlerBusinessLogicInput): McpHandlerR
     : input.baseResult;
 }
 
-const context7Handler = createMcpHandlerShell({
-  id: "context7",
-  description:
-    "Dedicated extension point for Context7 policy/behavior. Business logic belongs in applyBusinessLogic.",
-  matches: (input) => isNamedLike(input, ["context7"]),
-  applyBusinessLogic: applyEnabledByDefault,
-});
-
-const claudeTaskMasterHandler = createMcpHandlerShell({
-  id: "claude-task-master",
-  description:
-    "Dedicated extension point for Claude Task Master policy/behavior. Business logic belongs in applyBusinessLogic.",
-  matches: (input) =>
-    isNamedLike(input, ["claude-task-master", "task-master", "taskmaster"]),
-  applyBusinessLogic: applyEnabledByDefault,
-});
-
-const genericHandler: McpServerHandler = {
-  id: "generic",
-  description: "Default passthrough mapping for project-specific MCP servers.",
-  matches: () => true,
-  resolve: ({ serverName, server, utils: localUtils }) =>
-    createDefaultResult({ serverName, server, localUtils }),
-};
-
-const handlerRegistry = new Map<string, McpServerHandler>();
-const handlerOrder: string[] = [];
-
-function installBuiltinHandlers(): void {
-  registerMcpHandler(context7Handler);
-  registerMcpHandler(claudeTaskMasterHandler);
-  registerMcpHandler(genericHandler);
-}
-
-export function registerMcpHandler(handler: McpServerHandler): void {
-  if (handlerRegistry.has(handler.id)) {
-    handlerRegistry.set(handler.id, handler);
-    return;
-  }
-  handlerRegistry.set(handler.id, handler);
-  handlerOrder.push(handler.id);
-}
-
-export function listMcpHandlers(): McpServerHandler[] {
-  return handlerOrder
-    .map((id) => handlerRegistry.get(id))
-    .filter((handler): handler is McpServerHandler => Boolean(handler));
-}
-
-function resolveHandler(serverName: string, server: SharedMcpServer): McpServerHandler {
-  if (server.handler) {
-    const explicit = handlerRegistry.get(server.handler);
-    if (!explicit) {
-      throw new Error(
-        `Unknown MCP handler "${server.handler}" configured for server "${serverName}".`,
-      );
-    }
-    return explicit;
-  }
-
-  for (const id of handlerOrder) {
-    const handler = handlerRegistry.get(id);
-    if (!handler || id === "generic") {
-      continue;
-    }
-    if (handler.matches({ serverName, server })) {
-      return handler;
-    }
-  }
-
-  const fallback = handlerRegistry.get("generic");
-  if (!fallback) {
-    throw new Error('No MCP fallback handler registered. Expected handler id "generic".');
-  }
-  return fallback;
-}
-
-export function resolveServerWithHandler(input: {
-  serverName: string;
-  server: SharedMcpServer;
-  context: McpLoadContext;
-  fullConfig: SharedMcpConfigFile;
-}): McpHandlerResult & { handlerId: string } {
-  const { serverName, server, context, fullConfig } = input;
-  const handler = resolveHandler(serverName, server);
-  const handlerConfig = {
-    ...(fullConfig.handlerSettings?.[handler.id] ?? {}),
-    ...(server.handlerOptions ?? {}),
-  };
-  const result = handler.resolve({
-    serverName,
-    server,
-    context,
-    handlerConfig,
-    fullConfig,
-    utils,
+function createBuiltinHandlers(): McpServerHandler[] {
+  const context7Handler = createMcpHandlerShell({
+    id: "context7",
+    description:
+      "Dedicated extension point for Context7 policy/behavior. Business logic belongs in applyBusinessLogic.",
+    matches: (input) => isNamedLike(input, ["context7"]),
+    applyBusinessLogic: applyEnabledByDefault,
   });
-  return {
-    ...result,
-    handlerId: handler.id,
+
+  const claudeTaskMasterHandler = createMcpHandlerShell({
+    id: "claude-task-master",
+    description:
+      "Dedicated extension point for Claude Task Master policy/behavior. Business logic belongs in applyBusinessLogic.",
+    matches: (input) =>
+      isNamedLike(input, ["claude-task-master", "task-master", "taskmaster"]),
+    applyBusinessLogic: applyEnabledByDefault,
+  });
+
+  const genericHandler: McpServerHandler = {
+    id: "generic",
+    description: "Default passthrough mapping for project-specific MCP servers.",
+    matches: () => true,
+    resolve: ({ serverName, server, utils: localUtils }) =>
+      createDefaultResult({ serverName, server, localUtils }),
   };
+
+  return [context7Handler, claudeTaskMasterHandler, genericHandler];
 }
 
-installBuiltinHandlers();
+export class McpRegistry {
+  private readonly handlerRegistry = new Map<string, McpServerHandler>();
+  private readonly handlerOrder: string[] = [];
+
+  constructor(input?: { handlers?: McpServerHandler[] }) {
+    for (const handler of input?.handlers ?? []) {
+      this.register(handler);
+    }
+  }
+
+  register(handler: McpServerHandler): void {
+    if (this.handlerRegistry.has(handler.id)) {
+      this.handlerRegistry.set(handler.id, handler);
+      return;
+    }
+
+    this.handlerRegistry.set(handler.id, handler);
+    this.handlerOrder.push(handler.id);
+  }
+
+  listHandlers(): McpServerHandler[] {
+    return this.handlerOrder
+      .map((id) => this.handlerRegistry.get(id))
+      .filter((handler): handler is McpServerHandler => Boolean(handler));
+  }
+
+  resolveServerWithHandler(input: {
+    serverName: string;
+    server: SharedMcpServer;
+    context: McpLoadContext;
+    fullConfig: SharedMcpConfigFile;
+  }): McpHandlerResult & { handlerId: string } {
+    const { serverName, server, context, fullConfig } = input;
+    const handler = this.resolveHandler(serverName, server);
+    const handlerConfig = {
+      ...(fullConfig.handlerSettings?.[handler.id] ?? {}),
+      ...(server.handlerOptions ?? {}),
+    };
+
+    const result = handler.resolve({
+      serverName,
+      server,
+      context,
+      handlerConfig,
+      fullConfig,
+      utils,
+    });
+
+    return {
+      ...result,
+      handlerId: handler.id,
+    };
+  }
+
+  private resolveHandler(serverName: string, server: SharedMcpServer): McpServerHandler {
+    if (server.handler) {
+      const explicit = this.handlerRegistry.get(server.handler);
+      if (!explicit) {
+        throw new Error(
+          `Unknown MCP handler "${server.handler}" configured for server "${serverName}".`,
+        );
+      }
+      return explicit;
+    }
+
+    for (const id of this.handlerOrder) {
+      const handler = this.handlerRegistry.get(id);
+      if (!handler || id === "generic") {
+        continue;
+      }
+      if (handler.matches({ serverName, server })) {
+        return handler;
+      }
+    }
+
+    const fallback = this.handlerRegistry.get("generic");
+    if (!fallback) {
+      throw new Error('No MCP fallback handler registered. Expected handler id "generic".');
+    }
+
+    return fallback;
+  }
+}
+
+export function createDefaultMcpRegistry(): McpRegistry {
+  return new McpRegistry({
+    handlers: createBuiltinHandlers(),
+  });
+}
diff --git a/tests/config.test.ts b/tests/config.test.ts
new file mode 100644
index 0000000..bea5122
--- /dev/null
+++ b/tests/config.test.ts
@@ -0,0 +1,22 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+import { loadConfig } from "../src/config.js";
+
+test("loads defaults and freezes config", () => {
+  const config = loadConfig({});
+
+  assert.equal(config.agentManager.maxConcurrentAgents, 4);
+  assert.equal(config.orchestration.maxDepth, 4);
+  assert.equal(config.provisioning.portRange.basePort, 36000);
+  assert.equal(config.discovery.fileRelativePath, ".agent-context/resources.json");
+  assert.equal(Object.isFrozen(config), true);
+  assert.equal(Object.isFrozen(config.orchestration), true);
+});
+
+test("validates boolean env values", () => {
+  assert.throws(
+    () => loadConfig({ CODEX_SKIP_GIT_CHECK: "maybe" }),
+    /must be "true" or "false"/,
+  );
+});
+
diff --git a/tests/mcp-converters.test.ts b/tests/mcp-converters.test.ts
index 8d2c191..2070967 100644
--- a/tests/mcp-converters.test.ts
+++ b/tests/mcp-converters.test.ts
@@ -2,6 +2,7 @@ import test from "node:test";
 import assert from "node:assert/strict";
 import {
   inferTransport,
+  normalizeSharedMcpServer,
   toClaudeServerConfig,
   toCodexServerConfig,
 } from "../src/mcp/converters.js";
@@ -41,6 +42,42 @@ test("maps shared headers to codex http_headers", () => {
   });
 });
 
+test("normalizes header aliases into a single headers object", () => {
+  const normalized = normalizeSharedMcpServer({
+    url: "http://localhost:3000/mcp",
+    http_headers: {
+      "X-Source": "legacy",
+    },
+    headers: {
+      Authorization: "Bearer token",
+    },
+  });
+
+  assert.deepEqual(normalized.headers, {
+    "X-Source": "legacy",
+    Authorization: "Bearer token",
+  });
+  assert.equal("http_headers" in normalized, false);
+});
+
+test("maps legacy http_headers alias for claude conversion", () => {
+  const claudeConfig = toClaudeServerConfig("legacy-http-headers", {
+    type: "http",
+    url: "http://localhost:3000/mcp",
+    http_headers: {
+      Authorization: "Bearer token",
+    },
+  });
+
+  assert.deepEqual(claudeConfig, {
+    type: "http",
+    url: "http://localhost:3000/mcp",
+    headers: {
+      Authorization: "Bearer token",
+    },
+  });
+});
+
 test("throws for claude http server without url", () => {
   assert.throws(
     () => toClaudeServerConfig("bad-http", { type: "http" }),
diff --git a/tests/mcp-registry.test.ts b/tests/mcp-registry.test.ts
new file mode 100644
index 0000000..83ee9ff
--- /dev/null
+++ b/tests/mcp-registry.test.ts
@@ -0,0 +1,65 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+import {
+  McpRegistry,
+  createDefaultMcpRegistry,
+  createMcpHandlerShell,
+} from "../src/mcp/handlers.js";
+
+test("mcp registries are isolated instances", () => {
+  const registryA = createDefaultMcpRegistry();
+  const registryB = createDefaultMcpRegistry();
+
+  registryA.register(
+    createMcpHandlerShell({
+      id: "custom-a",
+      description: "custom handler",
+      matches: () => false,
+    }),
+  );
+
+  assert.equal(registryA.listHandlers().some((handler) => handler.id === "custom-a"), true);
+  assert.equal(registryB.listHandlers().some((handler) => handler.id === "custom-a"), false);
+});
+
+test("mcp registry resolves generic fallback by default", () => {
+  const registry = createDefaultMcpRegistry();
+
+  const resolved = registry.resolveServerWithHandler({
+    serverName: "local-files",
+    server: {
+      type: "stdio",
+      command: "npx",
+      args: ["-y", "@modelcontextprotocol/server-filesystem", "."],
+    },
+    context: {},
+    fullConfig: {
+      servers: {},
+    },
+  });
+
+  assert.equal(resolved.handlerId, "generic");
+  assert.ok(resolved.codex);
+  assert.ok(resolved.claude);
+});
+
+test("mcp registry rejects unknown explicit handlers", () => {
+  const registry = new McpRegistry();
+
+  assert.throws(
+    () =>
+      registry.resolveServerWithHandler({
+        serverName: "broken",
+        server: {
+          type: "http",
+          url: "http://localhost:3000/mcp",
+          handler: "missing-handler",
+        },
+        context: {},
+        fullConfig: {
+          servers: {},
+        },
+      }),
+    /Unknown MCP handler/,
+  );
+});
diff --git a/tests/orchestration-engine.test.ts b/tests/orchestration-engine.test.ts
index 0768199..3d3cf7b 100644
--- a/tests/orchestration-engine.test.ts
+++ b/tests/orchestration-engine.test.ts
@@ -230,6 +230,7 @@ test("runs DAG pipeline with state-dependent routing and retry behavior", async
       task: "Implement pipeline",
     },
   });
+  assert.equal(result.status, "success");
 
   assert.deepEqual(
     result.records.map((record) => `${record.nodeId}:${record.status}:${String(record.attempt)}`),
@@ -471,6 +472,7 @@ test("runs parallel topology blocks concurrently and routes via domain-event edg
   const result = await runPromise;
 
   assert.equal(maxConcurrentCoders, 2);
+  assert.equal(result.status, "success");
   assert.deepEqual(
     result.records.map((record) => `${record.nodeId}:${record.status}`),
     ["plan:success", "code-a:success", "code-b:success", "integrate:success"],
@@ -577,6 +579,96 @@ test("fails fast after two sequential hard failures", async () => {
   );
 });
 
+test("marks aggregate status as failure when a terminal node fails", async () => {
+  const workspaceRoot = await mkdtemp(resolve(tmpdir(), "ai-ops-workspace-"));
+  const stateRoot = await mkdtemp(resolve(tmpdir(), "ai-ops-session-state-"));
+  const projectContextPath = resolve(stateRoot, "project-context.json");
+
+  const manifest = {
+    schemaVersion: "1",
+    topologies: ["sequential"],
+    personas: [
+      {
+        id: "coder",
+        displayName: "Coder",
+        systemPromptTemplate: "Coder",
+        toolClearance: {
+          allowlist: [],
+          banlist: [],
+        },
+      },
+    ],
+    relationships: [],
+    topologyConstraints: {
+      maxDepth: 3,
+      maxRetries: 0,
+    },
+    pipeline: {
+      entryNodeId: "build",
+      nodes: [
+        {
+          id: "build",
+          actorId: "build_actor",
+          personaId: "coder",
+        },
+        {
+          id: "verify",
+          actorId: "verify_actor",
+          personaId: "coder",
+        },
+      ],
+      edges: [
+        {
+          from: "build",
+          to: "verify",
+          on: "success",
+        },
+      ],
+    },
+  } as const;
+
+  const engine = new SchemaDrivenExecutionEngine({
+    manifest,
+    settings: {
+      workspaceRoot,
+      stateRoot,
+      projectContextPath,
+      maxDepth: 3,
+      maxRetries: 0,
+      maxChildren: 2,
+      runtimeContext: {},
+    },
+    actorExecutors: {
+      build_actor: async () => ({
+        status: "success",
+        payload: {
+          step: "build",
+        },
+      }),
+      verify_actor: async () => ({
+        status: "failure",
+        payload: {
+          error: "verification failed",
+        },
+        failureKind: "soft",
+      }),
+    },
+  });
+
+  const result = await engine.runSession({
+    sessionId: "session-terminal-failure",
+    initialPayload: {
+      task: "Aggregate failure status",
+    },
+  });
+
+  assert.equal(result.status, "failure");
+  assert.deepEqual(
+    result.records.map((record) => `${record.nodeId}:${record.status}`),
+    ["build:success", "verify:failure"],
+  );
+});
+
 test("propagates abort signal into actor execution and stops the run", async () => {
   const workspaceRoot = await mkdtemp(resolve(tmpdir(), "ai-ops-workspace-"));
   const stateRoot = await mkdtemp(resolve(tmpdir(), "ai-ops-session-state-"));
diff --git a/tests/project-context.test.ts b/tests/project-context.test.ts
index d7de7b8..7c7ec5b 100644
--- a/tests/project-context.test.ts
+++ b/tests/project-context.test.ts
@@ -1,6 +1,6 @@
 import test from "node:test";
 import assert from "node:assert/strict";
-import { mkdtemp } from "node:fs/promises";
+import { mkdtemp, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { resolve } from "node:path";
 import { FileSystemProjectContextStore } from "../src/agents/project-context.js";
@@ -13,6 +13,7 @@ test("project context store reads defaults and applies domain patches", async ()
 
   const initial = await store.readState();
   assert.deepEqual(initial, {
+    schemaVersion: 1,
     globalFlags: {},
     artifactPointers: {},
     taskQueue: [],
@@ -55,4 +56,35 @@ test("project context store reads defaults and applies domain patches", async ()
     updated.taskQueue.map((task) => `${task.id}:${task.status}`),
     ["task-1:in_progress", "task-2:pending"],
   );
+  assert.equal(updated.schemaVersion, 1);
+});
+
+test("project context parser merges missing root keys with defaults", async () => {
+  const root = await mkdtemp(resolve(tmpdir(), "ai-ops-project-context-"));
+  const filePath = resolve(root, "project-context.json");
+  const store = new FileSystemProjectContextStore({ filePath });
+
+  await writeFile(
+    filePath,
+    `${JSON.stringify(
+      {
+        taskQueue: [
+          {
+            id: "task-1",
+            title: "Migrate",
+            status: "pending",
+          },
+        ],
+      },
+      null,
+      2,
+    )}\n`,
+    "utf8",
+  );
+
+  const state = await store.readState();
+  assert.equal(state.schemaVersion, 1);
+  assert.deepEqual(state.globalFlags, {});
+  assert.deepEqual(state.artifactPointers, {});
+  assert.equal(state.taskQueue[0]?.id, "task-1");
 });