@quiltdata/benchling-webhook 0.9.0-20251127T032721Z → 0.9.0-20251129T063536Z

package/README.md

@@ -65,12 +65,70 @@ If the App Canvas is not already part of your standard notebook template, Benchl
 
 ![App Canvas - Insert](imgs/benchling-insert.png)
 
-## Architecture (v0.9.0)
+## Architecture (v1.0.0)
 
-- **API Gateway HTTP API** terminates TLS and forwards requests through a **VPC Link** to **Cloud Map** service discovery
-- **ECS Fargate** tasks register in `benchling.local` and serve FastAPI on port **8080** (no ALB hop)
-- **S3 + SQS** remain the storage and queue backends for package creation
-- **CloudWatch Logs** capture API access logs (`/aws/apigateway/benchling-webhook-http`) and container logs (stack name)
+AWS CDK application with defense-in-depth security:
+
+```
+Benchling Webhook
+        |
+        | HTTPS POST
+        v
+API Gateway (HTTP API v2)
+        |
+        | Extract headers + body
+        v
+Lambda Authorizer ←─────────────┐
+        |                        │
+        | Verify HMAC signature  │ Defense-in-Depth:
+        | - Valid → Allow        │ Both Lambda and
+        | - Invalid → 403        │ FastAPI verify
+        v                        │ HMAC signatures
+VPC Link                         │
+        |                        │
+        v                        │
+Cloud Map (benchling.local)      │
+        |                        │
+        v                        │
+ECS Fargate (FastAPI)   ─────────┘
+        |
+        | Re-verify HMAC
+        | Process webhook
+        v
+S3 + SQS → Quilt Package
+```
+
+### Components
+
+- **API Gateway (HTTP API v2)** - HTTPS webhook routing with Lambda Authorizer integration
+- **Lambda Authorizer** - HMAC signature verification (first line of defense, logs to CloudWatch)
+- **VPC Link + Cloud Map** - Private service discovery to ECS tasks
+- **ECS Fargate** - FastAPI application (auto-scales 2-10 tasks, second line of defense)
+- **S3** - Payload and package storage
+- **SQS** - Quilt package creation queue
+- **Secrets Manager** - Benchling OAuth credentials
+- **CloudWatch** - Logging and monitoring for all components
+
+### Security Features
+
+**Defense-in-Depth HMAC Verification:**
+
+1. **Lambda Authorizer Layer** - Verifies webhook signatures before request reaches ECS, rejecting invalid requests with 403 Forbidden
+2. **Application Layer** - FastAPI re-verifies signatures for defense-in-depth protection
+
+**Why HTTP API v2?**
+
+- REST API Lambda Authorizers cannot access request body (HMAC verification impossible)
+- HTTP API v2 Lambda Authorizers can access body via `event['body']` field
+- Benchling HMAC signatures are computed over entire request body
+- HTTP API v2 is the only architecture that supports proper webhook signature verification
+
+**Additional Security:**
+
+- Private network (ECS in private subnets, no public IPs)
+- TLS 1.2+ encryption on all API Gateway endpoints
+- CloudWatch audit trail for all authorization events
+- Least-privilege IAM roles
 
 ## Installation
 
@@ -115,6 +173,8 @@ The wizard will guide you through:
 
 Add the webhook URL (displayed after setup) to your [Benchling app settings](https://docs.benchling.com/docs/getting-started-benchling-apps#installing-your-app).
 
+**Important**: The endpoint URL format is `https://{api-id}.execute-api.{region}.amazonaws.com/webhook` (no stage prefix in path).
+
 ### 4. Test Integration
 
 In Benchling:
@@ -126,6 +186,25 @@ In Benchling:
 A Quilt package will be automatically created and linked to your notebook entry.
 If you run into problems, contact [Quilt Support](support@quilt.bio)
 
+## Monitoring
+
+### CloudWatch Logs
+
+- `/aws/apigateway/benchling-webhook-http` - API Gateway access logs
+- `/aws/lambda/BenchlingWebhookAuthorizer` - Lambda Authorizer logs (HMAC verification)
+- `/ecs/benchling-webhook` - ECS container logs (application logs)
+
+### View Logs
+
+```bash
+# Via AWS CLI
+aws logs tail /aws/lambda/BenchlingWebhookAuthorizer --follow
+aws logs tail /ecs/benchling-webhook --follow
+
+# Via NPX (all logs combined)
+npx @quiltdata/benchling-webhook@latest logs --profile default
+```
+
 ## Additional Commands
 
 ```bash
@@ -135,8 +214,38 @@ npx @quiltdata/benchling-webhook@latest deploy [--profile <name>]
 # Check CloudFormation stack status
 npx @quiltdata/benchling-webhook@latest status [--profile <name>]
 
+# View CloudWatch logs
+npx @quiltdata/benchling-webhook@latest logs [--profile <name>]
+
 # Show all available commands
 npx @quiltdata/benchling-webhook@latest --help
+
+# Validate Lambda authorizer bundle locally (offline-friendly)
+npm run test:lambda-bundle
+```
+
+## Upgrading from v0.8.x or v0.9.0
+
+Version 1.0.0 introduces HTTP API v2 with Lambda Authorizer for proper HMAC signature verification. **This is a breaking change that requires stack recreation.**
+
+See [MIGRATION.md](./MIGRATION.md) for detailed upgrade instructions.
+
+**Quick migration:**
+
+```bash
+# 1. Backup configuration
+cp ~/.config/benchling-webhook/{profile}/config.json ~/backup-config.json
+
+# 2. Destroy old stack
+npx cdk destroy --profile {profile} --context stage={stage}
+
+# 3. Deploy new stack
+npm run deploy:{stage} -- --profile {profile} --yes
+
+# 4. Update webhook URL in Benchling app settings
+
+# 5. Test
+npm run test:{stage} -- --profile {profile}
 ```
 
 ## License

package/dist/bin/benchling-webhook.js

@@ -175,6 +175,12 @@ if (require.main === module) {
             account: process.env.CDK_DEFAULT_ACCOUNT,
             ecrRepository: process.env.ECR_REPOSITORY_NAME || "quiltdata/benchling",
             imageTag: process.env.IMAGE_TAG || "latest",
+            // Include VPC configuration if specified
+            ...(process.env.VPC_ID && {
+                vpc: {
+                    vpcId: process.env.VPC_ID,
+                },
+            }),
         },
         logging: {
             level: process.env.LOG_LEVEL || "INFO",

package/dist/bin/benchling-webhook.js.map

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+{"version":3,"file":"benchling-webhook.js","sourceRoot":"","sources":["../../bin/benchling-webhook.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAgCA,8CAyCC;AAsDD,kCAoBC;AAlJD,iDAAmC;AACnC,4EAAuE;AACvE,iDAAyC;AAyBzC;;;GAGG;AACI,KAAK,UAAU,iBAAiB,CACnC,OAAe,EACf,MAAc;IAEd,IAAI,CAAC;QACD,MAAM,MAAM,GAAG,IAAA,wBAAQ,EACnB,+CAA+C,MAAM,6EAA6E,EAClI,EAAE,QAAQ,EAAE,OAAO,EAAE,CACxB,CAAC;QAEF,MAAM,WAAW,GAAG,MAAM,CAAC,IAAI,EAAE,CAAC;QAElC,IACI,WAAW,CAAC,QAAQ,CAAC,gBAAgB,CAAC;YACtC,WAAW,CAAC,QAAQ,CAAC,iBAAiB,CAAC,EACzC,CAAC;YACC,OAAO;gBACH,YAAY,EAAE,KAAK;gBACnB,OAAO,EAAE,uCAAuC,OAAO,cAAc,MAAM,EAAE;gBAC7E,OAAO,EAAE,2BAA2B,OAAO,IAAI,MAAM,EAAE;aAC1D,CAAC;QACN,CAAC;QAED,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;YACpC,OAAO;gBACH,YAAY,EAAE,IAAI;gBAClB,MAAM,EAAE,WAAW;gBACnB,OAAO,EAAE,iCAAiC,WAAW,qCAAqC;aAC7F,CAAC;QACN,CAAC;QAED,OAAO;YACH,YAAY,EAAE,IAAI;YAClB,MAAM,EAAE,WAAW;SACtB,CAAC;IACN,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACb,OAAO;YACH,YAAY,EAAE,KAAK;YACnB,OAAO,EAAE,0CAA2C,KAAe,CAAC,OAAO,EAAE;SAChF,CAAC;IACN,CAAC;AACL,CAAC;AAED;;;GAGG;AACH,SAAS,2BAA2B,CAAC,MAAc;IAC/C,OAAO;QACH,KAAK,EAAE;YACH,QAAQ,EAAE,MAAM,CAAC,aAAa,IAAI,EAAE;YACpC,OAAO,EAAE,MAAM,CAAC,YAAY;YAC5B,QAAQ,EAAE,MAAM,CAAC,aAAa;YAC9B,QAAQ,EAAE,MAAM,CAAC,QAAQ;YACzB,MAAM,EAAE,MAAM,CAAC,SAAS;SAC3B;QACD,SAAS,EAAE;YACP,MAAM,EAAE,MAAM,CAAC,eAAe;YAC9B,QAAQ,EAAE,MAAM,CAAC,iBAAiB;YAClC,YAAY,EAAE,MAAM,CAAC,qBAAqB;YAC1C,SAAS,EAAE,MAAM,CAAC,eAAe;YACjC,eAAe,EAAE,MAAM,CAAC,wBAAwB;SACnD;QACD,QAAQ,EAAE;YACN,MAAM,EAAE,MAAM,CAAC,eAAe;YAC9B,MAAM,EAAE,MAAM,CAAC,SAAS,IAAI,WAAW;YACvC,WAAW,EAAE,MAAM,CAAC,MAAM,IAAI,eAAe;SAChD;QACD,UAAU,EAAE;YACR,MAAM,EAAE,MAAM,CAAC,SAAS;YACxB,OAAO,EAAE,MAAM,CAAC,UAAU;YAC1B,aAAa,EAAE,MAAM,CAAC,iBAAiB,IAAI,qBAAqB;YAChE,QAAQ,EAAE,MAAM,CAAC,QAAQ,IAAI,QAAQ;SACxC;QACD,OAAO,EAAE;YACL,KAAK,EAAG,MAAM,CAAC,QAAmD,IAAI,MAAM;SAC/E;QACD,QAAQ,EAAE;YACN,gBAAgB,EAAE,MAAM,CAAC,gBAAgB,IAAI,EAAE;YAC/C,kBAAkB,EAAE,MAAM,CAAC,yBAAyB,KAAK,OAAO;SACnE;QACD,SAAS,EAAE;YACP,OAAO,EAAE,iBAAiB;YAC1B,SAAS,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;YACnC,SAAS,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;YACnC,MAAM,EAAE,KAAK;SAChB;KACJ,CAAC;AACN,CAAC;AAED;;;;GAIG;AACH,SAAgB,WAAW,CAAC,MAAc;IACtC,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,GAAG,EAAE,CAAC;IAE1B,yCAAyC;IACzC,MAAM,aAAa,GAAG,2BAA2B,CAAC,MAAM,CAAC,CAAC;IAE1D,MAAM,KAAK,GAAG,IAAI,+CAAqB,CAAC,GAAG,EAAE,uBAAuB,EAAE;QAClE,GAAG,EAAE;YACD,OAAO,EAAE,MAAM,CAAC,UAAU;YAC1B,MAAM,EAAE,MAAM,CAAC,SAAS;SAC3B;QACD,MAAM,EAAE,aAAa;KACxB,CAAC,CAAC;IAEH,OAAO;QACH,GAAG;QACH,KAAK;QACL,SAAS,EAAE,KAAK,CAAC,SAAS;QAC1B,OAAO,EAAE,KAAK,CAAC,OAAO;KACzB,CAAC;AACN,CAAC;AAED,6CAA6C;AAC7C,uCAAuC;AACvC,gEAAgE;AAChE,IAAI,OAAO,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;IAC1B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,GAAG,EAAE,CAAC;IAE1B,0EAA0E;IAC1E,sFAAsF;IACtF,MAAM,cAAc,GAAG,OAAO,CAAC,GAAG,CAAC,sBAAsB,KAAK,MAAM,CAAC;IACrE,MAAM,aAAa,GAAkB;QACjC,KAAK,EAAE;YACH,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,eAAe,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC;YAC9E,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,aAAa,IAAI,EAAE;YACxC,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,cAAc,IAAI,EAAE;YAC1C,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,IAAI,EAAE;YACrC,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,kBAAkB,IAAI,WAAW;SACxD;QACD,SAAS,EAAE;YACP,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,EAAE;YAC1C,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,mBAAmB,IAAI,EAAE;YAC/C,SAAS,EAAE,OAAO,CAAC,GAAG,CAAC,gBAAgB,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC;YACvF,eAAe,EAAE,OAAO,CAAC,GAAG,CAAC,2BAA2B,IAAI,EAAE;SACjE;QACD,QAAQ,EAAE;YACN,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,iBAAiB,IAAI,EAAE;YAC3C,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,UAAU,IAAI,WAAW;YAC7C,WAAW,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,IAAI,eAAe;SACtD;QACD,UAAU,EAAE;YACR,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,kBAAkB,IAAI,WAAW;YACrD,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,mBAAmB;YACxC,aAAa,EAAE,OAAO,CAAC,GAAG,CAAC,mBAAmB,IAAI,qBAAqB;YACvE,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,IAAI,QAAQ;YAC3C,yCAAyC;YACzC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,MAAM,IAAI;gBACtB,GAAG,EAAE;oBACD,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,MAAM;iBAC5B;aACJ,CAAC;SACL;QACD,OAAO,EAAE;YACL,KAAK,EAAG,OAAO,CAAC,GAAG,CAAC,SAAoD,IAAI,MAAM;SACrF;QACD,QAAQ,EAAE;YACN,gBAAgB,EAAE,OAAO,CAAC,GAAG,CAAC,kBAAkB,IAAI,EAAE;YACtD,kBAAkB,EAAE,OAAO,CAAC,GAAG,CAAC,2BAA2B,KAAK,OAAO;SAC1E;QACD,SAAS,EAAE;YACP,OAAO,EAAE,OAAO;YAChB,SAAS,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;YACnC,SAAS,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;YACnC,MAAM,EAAE,KAAK;SAChB;KACJ,CAAC;IAEF,IAAI,+CAAqB,CAAC,GAAG,EAAE,uBAAuB,EAAE;QACpD,GAAG,EAAE;YACD,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,mBAAmB;YACxC,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,kBAAkB;SACzC;QACD,MAAM,EAAE,aAAa;KACxB,CAAC,CAAC;AACP,CAAC"}

package/dist/bin/cli.js

@@ -95,6 +95,7 @@ program
     .option("--region <region>", "AWS region to deploy to")
     .option("--image-tag <tag>", "Docker image tag to deploy (default: latest)")
     .option("--yes", "Skip confirmation prompts")
+    .option("--force", "Force deployment despite legacy architecture warning (DANGEROUS - use with caution)")
     .addHelpText("after", `
 
 Examples:

package/dist/bin/cli.js.map

@@ -1 +1 @@
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package/dist/bin/commands/deploy.d.ts

@@ -19,6 +19,7 @@ export declare function deployCommand(options: {
     imageTag?: string;
     region?: string;
     envFile?: string;
+    force?: boolean;
 }): Promise<void>;
 /**
  * Deploy the Benchling webhook stack
@@ -32,5 +33,6 @@ export declare function deploy(stackArn: string, benchlingSecret: string, config
     imageTag: string;
     region?: string;
     envFile?: string;
+    force?: boolean;
 }): Promise<void>;
 //# sourceMappingURL=deploy.d.ts.map

package/dist/bin/commands/deploy.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"deploy.d.ts","sourceRoot":"","sources":["../../../bin/commands/deploy.ts"],"names":[],"mappings":"AAaA,OAAO,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAC;AA0HvD;;;;;;;;GAQG;AACH,wBAAsB,aAAa,CAAC,OAAO,EAAE;IACzC,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,KAAK,GAAG,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;CACpB,GAAG,OAAO,CAAC,IAAI,CAAC,CA8FhB;AAED;;GAEG;AACH,wBAAsB,MAAM,CACxB,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EACvB,MAAM,EAAE,aAAa,EACrB,OAAO,EAAE;IACL,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,KAAK,EAAE,KAAK,GAAG,MAAM,CAAC;IACtB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;CACpB,GACF,OAAO,CAAC,IAAI,CAAC,CAkYf"}
+{"version":3,"file":"deploy.d.ts","sourceRoot":"","sources":["../../../bin/commands/deploy.ts"],"names":[],"mappings":"AAaA,OAAO,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAC;AA6LvD;;;;;;;;GAQG;AACH,wBAAsB,aAAa,CAAC,OAAO,EAAE;IACzC,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,KAAK,GAAG,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACnB,GAAG,OAAO,CAAC,IAAI,CAAC,CA8FhB;AAED;;GAEG;AACH,wBAAsB,MAAM,CACxB,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EACvB,MAAM,EAAE,aAAa,EACrB,OAAO,EAAE;IACL,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,KAAK,EAAE,KAAK,GAAG,MAAM,CAAC;IACtB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACnB,GACF,OAAO,CAAC,IAAI,CAAC,CA8af"}

package/dist/bin/commands/deploy.js

@@ -61,12 +61,12 @@ function suggestSetup(profileName, message) {
     console.log();
 }
 /**
- * Detect if the existing stack is v0.8.x (REST API + ALB architecture)
- * Returns true if v0.8.x stack detected, false otherwise
+ * Check if the existing stack is in a problematic state (rollback, failed, etc.)
  *
- * Also handles stacks in failed/rollback states by examining existing resources
+ * Note: v0.8.8+ all use the same architecture (REST API + ALB + VPC Link), so there's
+ * no "legacy architecture" to detect. CloudFormation handles in-place updates seamlessly.
  */
-async function detectLegacyStack(region) {
+async function checkStackStatus(region) {
     try {
         const cloudformation = new client_cloudformation_1.CloudFormationClient({ region });
         const stackName = "BenchlingWebhookStack";
@@ -74,51 +74,106 @@ async function detectLegacyStack(region) {
         const describeCommand = new client_cloudformation_1.DescribeStacksCommand({ StackName: stackName });
         const describeResponse = await cloudformation.send(describeCommand);
         if (!describeResponse.Stacks || describeResponse.Stacks.length === 0) {
-            return false; // No stack exists
+            return {
+                stackExists: false,
+                statusCategory: "none",
+            };
         }
         const stack = describeResponse.Stacks[0];
         const stackStatus = stack.StackStatus || "";
-        // Check if stack is in a rollback/failed state that blocks updates
-        // These states indicate a previous deployment attempt failed
-        const blockingStates = [
-            "UPDATE_ROLLBACK_COMPLETE",
+        const inProgressStates = [
             "UPDATE_ROLLBACK_COMPLETE_CLEANUP_IN_PROGRESS",
             "UPDATE_ROLLBACK_IN_PROGRESS",
-            "UPDATE_ROLLBACK_FAILED",
-            "ROLLBACK_COMPLETE",
             "ROLLBACK_IN_PROGRESS",
-            "ROLLBACK_FAILED",
         ];
-        if (blockingStates.includes(stackStatus)) {
-            // Stack is in a failed state - can't determine architecture reliably
-            // User needs to destroy and redeploy regardless
-            // Return true to trigger migration warning which tells them to destroy
-            return true;
-        }
-        // Get stack resources to check architecture
-        const resourcesCommand = new client_cloudformation_1.DescribeStackResourcesCommand({ StackName: stackName });
-        const resourcesResponse = await cloudformation.send(resourcesCommand);
-        if (!resourcesResponse.StackResources) {
-            return false;
-        }
-        // v0.8.x indicators:
-        // - Has AWS::ElasticLoadBalancingV2::LoadBalancer (ALB)
-        // - Has AWS::ApiGateway::RestApi (REST API)
-        // v0.9.0 indicators:
-        // - Has AWS::ApiGatewayV2::VpcLink (VPC Link)
-        // - Has AWS::ApiGatewayV2::Api (HTTP API)
-        const hasALB = resourcesResponse.StackResources.some(r => r.ResourceType === "AWS::ElasticLoadBalancingV2::LoadBalancer");
-        const hasRestAPI = resourcesResponse.StackResources.some(r => r.ResourceType === "AWS::ApiGateway::RestApi");
-        const hasVpcLink = resourcesResponse.StackResources.some(r => r.ResourceType === "AWS::ApiGatewayV2::VpcLink");
-        const hasHttpAPI = resourcesResponse.StackResources.some(r => r.ResourceType === "AWS::ApiGatewayV2::Api");
-        // If has ALB or REST API but not VPC Link or HTTP API, it's v0.8.x
-        return (hasALB || hasRestAPI) && !hasVpcLink && !hasHttpAPI;
+        const failedStates = ["ROLLBACK_FAILED", "UPDATE_ROLLBACK_FAILED"];
+        const rolledBackStates = ["UPDATE_ROLLBACK_COMPLETE", "ROLLBACK_COMPLETE"];
+        const statusCategory = inProgressStates.includes(stackStatus)
+            ? "in_progress"
+            : failedStates.includes(stackStatus)
+                ? "failed"
+                : rolledBackStates.includes(stackStatus)
+                    ? "rolled_back"
+                    : "none";
+        return {
+            stackExists: true,
+            stackStatus,
+            statusCategory,
+        };
+    }
+    catch (_error) {
+        // Stack doesn't exist or error checking
+        return {
+            stackExists: false,
+            statusCategory: "none",
+        };
+    }
+}
+/**
+ * Detect if existing stack uses legacy REST API Gateway (v0.8.x)
+ * Returns true if REST API detected, indicating need for stack recreation
+ */
+async function detectLegacyRestApi(stackName, region) {
+    const client = new client_cloudformation_1.CloudFormationClient({ region });
+    try {
+        const response = await client.send(new client_cloudformation_1.DescribeStackResourcesCommand({ StackName: stackName }));
+        const hasRestApi = response.StackResources?.some((resource) => resource.ResourceType === "AWS::ApiGateway::RestApi");
+        return hasRestApi || false;
     }
     catch (_error) {
-        // Stack doesn't exist or error checking - not a v0.8.x stack
+        // Stack doesn't exist - first deployment
         return false;
     }
 }
+/**
+ * Prompt user about legacy stack migration
+ * Returns true if user wants to abort deployment
+ * Returns false if user wants to proceed anyway
+ */
+async function promptLegacyMigration(profileName, stage, yes) {
+    const migrationMessage = `${chalk_1.default.red.bold("⚠️  BREAKING CHANGE DETECTED")}\n\n` +
+        `Your existing stack uses ${chalk_1.default.yellow("v0.8.x architecture (REST API Gateway)")}.\n` +
+        `v1.0.0 uses ${chalk_1.default.green("HTTP API v2")} (required for Lambda Authorizer body access).\n\n` +
+        `${chalk_1.default.bold("Technical reason:")} REST API Lambda Authorizers cannot access request body,\n` +
+        "breaking HMAC signature verification. HTTP API v2 provides body access.\n\n" +
+        `${chalk_1.default.bold("Stack resources that will be REPLACED:")}\n` +
+        "  - API Gateway REST API → HTTP API v2\n" +
+        "  - Network Load Balancer → (removed, direct VPC Link)\n" +
+        "  - Endpoint URL format → (stage removed from path)\n\n" +
+        `${chalk_1.default.bold("You must destroy the existing stack before deploying v1.0.0:")}\n\n` +
+        `  ${chalk_1.default.cyan(`npx cdk destroy --profile ${profileName} --context stage=${stage}`)}\n\n` +
+        `${chalk_1.default.bold("After destruction, redeploy with:")}\n\n` +
+        `  ${chalk_1.default.cyan(`npm run deploy:${stage} -- --profile ${profileName} --yes`)}\n\n` +
+        `${chalk_1.default.bold("Update your Benchling webhook URL after deployment.")}`;
+    console.log();
+    console.log((0, boxen_1.default)(migrationMessage, {
+        padding: 1,
+        borderColor: "red",
+        borderStyle: "round",
+    }));
+    console.log();
+    if (yes) {
+        console.log(chalk_1.default.yellow("⚠️  --yes flag detected, but migration requires manual intervention."));
+        console.log(chalk_1.default.yellow("    Deployment aborted. Run destroy command to proceed with v1.0.0 upgrade."));
+        return true; // Abort deployment
+    }
+    const { shouldProceed } = await (0, enquirer_1.prompt)({
+        type: "confirm",
+        name: "shouldProceed",
+        message: "Continue with deployment anyway? (Stack will likely fail to update)",
+        initial: false,
+    });
+    if (shouldProceed) {
+        console.log();
+        console.log(chalk_1.default.yellow("⚠️  Proceeding despite legacy architecture warning."));
+        console.log(chalk_1.default.yellow("    Deployment may fail due to incompatible resource types."));
+        console.log();
+        return false; // Don't abort, let user try
+    }
+    console.log();
+    console.log(chalk_1.default.yellow("Deployment aborted. Run destroy command to proceed with v1.0.0 upgrade."));
+    return true; // Abort deployment
+}
 /**
  * Get the most recent dev version tag (without 'v' prefix)
  * Returns null if no dev tags found
@@ -352,37 +407,74 @@ async function deploy(stackArn, benchlingSecret, config, options) {
             spinner.succeed(`CDK is bootstrapped (${bootstrapStatus.status})`);
         }
     }
-    // Check for v0.8.x stack and warn about migration
-    spinner.start("Checking for legacy stack or failed deployment...");
-    const isLegacyStack = await detectLegacyStack(deployRegion);
-    if (isLegacyStack) {
-        spinner.fail("Stack must be destroyed before deploying v0.9.0");
-        console.log();
-        console.log((0, boxen_1.default)(`${chalk_1.default.red.bold("⚠ Stack Destruction Required")}\n\n` +
-            `${chalk_1.default.yellow("The existing BenchlingWebhookStack must be destroyed before deploying v0.9.0.")}\n\n` +
-            `${chalk_1.default.bold("This could be due to:")}\n` +
-            "  • v0.8.x → v0.9.0 migration (REST API + ALB → HTTP API + VPC Link)\n" +
-            "  • Failed deployment in rollback state (UPDATE_ROLLBACK_COMPLETE)\n" +
-            "  • Incomplete stack that needs cleanup\n\n" +
-            `${chalk_1.default.red.bold("⚠ CloudFormation cannot update stacks in these states.")}\n\n` +
-            `${chalk_1.default.yellow("To proceed, you must first destroy the existing stack.")}`, { padding: 1, borderColor: "red", borderStyle: "double" }));
-        console.log();
-        console.log(chalk_1.default.bold("Required steps:"));
-        console.log();
-        console.log(`  ${chalk_1.default.cyan("1. Destroy the existing v0.8.x stack:")}`);
-        console.log(chalk_1.default.dim(`     npx @quiltdata/benchling-webhook destroy --profile ${options.profileName} --stage ${options.stage}`));
-        console.log();
-        console.log(`  ${chalk_1.default.cyan("2. Deploy v0.9.0:")}`);
-        console.log(chalk_1.default.dim(`     npx @quiltdata/benchling-webhook deploy --profile ${options.profileName} --stage ${options.stage}`));
+    // Check for rollback or failed state
+    spinner.start("Checking stack status...");
+    const stackCheck = await checkStackStatus(deployRegion);
+    const needsAttention = ["in_progress", "failed", "rolled_back"].includes(stackCheck.statusCategory);
+    if (needsAttention) {
+        const isActiveRollback = stackCheck.statusCategory === "in_progress";
+        const borderColor = isActiveRollback ? "red" : "yellow";
+        const title = isActiveRollback ? "Stack is rolling back" : "Stack in problematic state";
+        spinner[isActiveRollback ? "fail" : "warn"]("Stack state may block update");
         console.log();
-        console.log(`  ${chalk_1.default.cyan("3. Update Benchling webhook URL")} to the new HTTP API endpoint`);
+        console.log((0, boxen_1.default)(`${chalk_1.default.red.bold(title)}\n\n` +
+            `${chalk_1.default.bold("Stack status:")} ${stackCheck.stackStatus}\n\n` +
+            `${chalk_1.default.bold("Options:")}\n` +
+            (isActiveRollback
+                ? "  1) Wait/abort (recommended while rollback is in progress)\n  2) Destroy and redeploy if stuck\n  3) Proceed anyway (likely to fail)\n"
+                : "  1) Proceed with deploy\n  2) Destroy and redeploy clean\n  3) Abort\n"), { padding: 1, borderColor, borderStyle: "round" }));
         console.log();
-        console.log(chalk_1.default.dim("See MIGRATION.md for full details:"));
-        console.log(chalk_1.default.dim("https://github.com/quiltdata/benchling-webhook/blob/main/MIGRATION.md"));
-        console.log();
-        process.exit(1);
+        const { proceedChoice } = await (0, enquirer_1.prompt)([
+            {
+                type: "select",
+                name: "proceedChoice",
+                message: "How would you like to proceed?",
+                choices: isActiveRollback
+                    ? [
+                        { name: "abort", message: "Abort / wait for rollback to finish (recommended)" },
+                        { name: "destroy", message: "Destroy existing stack then redeploy clean" },
+                        { name: "proceed", message: "Proceed anyway (likely to fail while rollback active)" },
+                    ]
+                    : [
+                        { name: "proceed", message: "Proceed with deployment" },
+                        { name: "destroy", message: "Destroy existing stack then redeploy clean" },
+                        { name: "abort", message: "Abort now" },
+                    ],
+                initial: isActiveRollback ? 0 : 0,
+            },
+        ]);
+        if (proceedChoice === "destroy") {
+            console.log();
+            console.log(chalk_1.default.bold("Run destroy then redeploy:"));
+            console.log(chalk_1.default.cyan(`  npx @quiltdata/benchling-webhook destroy --profile ${options.profileName} --stage ${options.stage}`));
+            console.log(chalk_1.default.cyan(`  npx @quiltdata/benchling-webhook deploy --profile ${options.profileName} --stage ${options.stage}`));
+            console.log();
+            process.exit(1);
+        }
+        if (proceedChoice === "abort") {
+            console.log(chalk_1.default.yellow("Aborting by user choice."));
+            process.exit(1);
+        }
+        spinner.warn("Proceeding despite stack state; deployment may fail.");
+    }
+    else {
+        spinner.succeed("Stack status OK - ready for deployment");
+    }
+    // Check for legacy REST API architecture (v0.8.x)
+    if (stackCheck.stackExists && !options.force) {
+        spinner.start("Checking for legacy architecture...");
+        const hasLegacyRestApi = await detectLegacyRestApi("BenchlingWebhookStack", deployRegion);
+        if (hasLegacyRestApi) {
+            spinner.fail("Legacy REST API Gateway detected (v0.8.x)");
+            const shouldAbort = await promptLegacyMigration(options.profileName, options.stage, options.yes || false);
+            if (shouldAbort) {
+                process.exit(1);
+            }
+        }
+        else {
+            spinner.succeed("No legacy architecture detected");
+        }
     }
-    spinner.succeed("Stack status OK - ready for deployment");
     // Load Quilt configuration from config.quilt.*
     spinner.start("Loading Quilt configuration...");
     // Validate required fields
@@ -533,6 +625,8 @@ async function deploy(stackArn, benchlingSecret, config, options) {
                 CDK_DEFAULT_REGION: deployRegion,
                 QUILT_STACK_ARN: stackArn,
                 BENCHLING_SECRET: benchlingSecret,
+                // Pass VPC configuration if specified in profile
+                ...(config.deployment.vpc?.vpcId && { VPC_ID: config.deployment.vpc.vpcId }),
             },
         });
         console.log();