@quiltdata/benchling-webhook 0.6.3-20251104T182406Z → 0.7.1-20251106T100426Z

package/dist/bin/commands/health-check.js

@@ -0,0 +1,357 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * Configuration Health Check Command
+ *
+ * Post-setup validation that checks:
+ * - Configuration file integrity
+ * - Secrets synchronization status
+ * - Deployment configuration
+ *
+ * @module commands/health-check
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.runHealthChecks = runHealthChecks;
+exports.healthCheckCommand = healthCheckCommand;
+const xdg_config_1 = require("../../lib/xdg-config");
+const fs_1 = require("fs");
+const client_secrets_manager_1 = require("@aws-sdk/client-secrets-manager");
+const chalk_1 = __importDefault(require("chalk"));
+const path_1 = require("path");
+/**
+ * Checks XDG configuration file integrity
+ */
+async function checkXDGIntegrity(xdgConfig, profile) {
+    try {
+        // Check if profile exists
+        if (!xdgConfig.profileExists(profile)) {
+            return {
+                check: "xdg-integrity",
+                status: "fail",
+                message: "Profile does not exist",
+                details: { profile, recommendation: "Run setup wizard to create configuration" },
+            };
+        }
+        // Try to read and validate profile config
+        try {
+            const config = xdgConfig.readProfile(profile);
+            // Validate required fields
+            if (!config.quilt || !config.benchling || !config.packages || !config.deployment) {
+                return {
+                    check: "xdg-integrity",
+                    status: "fail",
+                    message: "Configuration is missing required sections",
+                    details: { profile },
+                };
+            }
+            return {
+                check: "xdg-integrity",
+                status: "pass",
+                message: "XDG configuration integrity verified",
+                details: { profile },
+            };
+        }
+        catch (error) {
+            return {
+                check: "xdg-integrity",
+                status: "fail",
+                message: `Configuration validation failed: ${error.message}`,
+                details: { profile, error: error.message },
+            };
+        }
+    }
+    catch (error) {
+        return {
+            check: "xdg-integrity",
+            status: "fail",
+            message: `Integrity check failed: ${error.message}`,
+            details: { error: error.message },
+        };
+    }
+}
+/**
+ * Checks if local config and remote secrets are in sync
+ */
+async function checkSecretsSync(xdgConfig, profile) {
+    try {
+        // Check if profile exists
+        if (!xdgConfig.profileExists(profile)) {
+            return {
+                check: "secrets-sync",
+                status: "warn",
+                message: "No configuration found",
+                details: { profile, recommendation: "Run setup wizard first" },
+            };
+        }
+        // Load profile config
+        const config = xdgConfig.readProfile(profile);
+        if (!config.benchling.secretArn) {
+            return {
+                check: "secrets-sync",
+                status: "warn",
+                message: "No secrets configured",
+                details: { profile, recommendation: "Run 'benchling-webhook sync-secrets' to sync secrets" },
+            };
+        }
+        // Get local config modification time
+        const configPath = (0, path_1.join)(xdgConfig["baseDir"], profile, "config.json");
+        const configStats = (0, fs_1.statSync)(configPath);
+        const localModifiedAt = configStats.mtime;
+        // Get remote secret modification time
+        const region = config.deployment.region;
+        const clientConfig = { region };
+        // If AWS profile is configured, use it
+        if (process.env.AWS_PROFILE) {
+            const { fromIni } = await Promise.resolve().then(() => __importStar(require("@aws-sdk/credential-providers")));
+            clientConfig.credentials = fromIni({ profile: process.env.AWS_PROFILE });
+        }
+        const client = new client_secrets_manager_1.SecretsManagerClient(clientConfig);
+        const command = new client_secrets_manager_1.DescribeSecretCommand({ SecretId: config.benchling.secretArn });
+        const secretMetadata = await client.send(command);
+        if (!secretMetadata.LastChangedDate) {
+            return {
+                check: "secrets-sync",
+                status: "warn",
+                message: "Cannot determine secret modification time",
+                details: { secretArn: config.benchling.secretArn },
+            };
+        }
+        const remoteModifiedAt = secretMetadata.LastChangedDate;
+        // Compare times (allow 1 second tolerance for filesystem precision)
+        const timeDiffMs = Math.abs(localModifiedAt.getTime() - remoteModifiedAt.getTime());
+        const timeDiffSeconds = Math.floor(timeDiffMs / 1000);
+        if (localModifiedAt > remoteModifiedAt && timeDiffMs > 1000) {
+            // Local is newer - secrets need to be synced
+            const ageMinutes = Math.floor(timeDiffMs / (1000 * 60));
+            const ageHours = Math.floor(ageMinutes / 60);
+            const ageDays = Math.floor(ageHours / 24);
+            let ageDescription;
+            if (ageDays > 0) {
+                ageDescription = `${ageDays} day${ageDays > 1 ? "s" : ""}`;
+            }
+            else if (ageHours > 0) {
+                ageDescription = `${ageHours} hour${ageHours > 1 ? "s" : ""}`;
+            }
+            else {
+                ageDescription = `${ageMinutes} minute${ageMinutes > 1 ? "s" : ""}`;
+            }
+            return {
+                check: "secrets-sync",
+                status: "warn",
+                message: `Local config is ${ageDescription} newer than remote secrets`,
+                details: {
+                    localModifiedAt: localModifiedAt.toISOString(),
+                    remoteModifiedAt: remoteModifiedAt.toISOString(),
+                    timeDiffSeconds,
+                    recommendation: "Run 'benchling-webhook sync-secrets --force' to sync changes",
+                },
+            };
+        }
+        return {
+            check: "secrets-sync",
+            status: "pass",
+            message: "Local config and remote secrets are in sync",
+            details: {
+                localModifiedAt: localModifiedAt.toISOString(),
+                remoteModifiedAt: remoteModifiedAt.toISOString(),
+                timeDiffSeconds,
+            },
+        };
+    }
+    catch (error) {
+        return {
+            check: "secrets-sync",
+            status: "fail",
+            message: `Sync check failed: ${error.message}`,
+            details: { error: error.message },
+        };
+    }
+}
+/**
+ * Checks deployment configuration
+ */
+async function checkDeploymentConfig(xdgConfig, profile) {
+    try {
+        // Check for active deployment
+        const deployment = xdgConfig.getActiveDeployment(profile, "prod");
+        if (!deployment) {
+            return {
+                check: "deployment-config",
+                status: "warn",
+                message: "No deployment found",
+                details: {
+                    profile,
+                    recommendation: "Run 'benchling-webhook deploy' to deploy the stack",
+                },
+            };
+        }
+        // Check for webhook endpoint
+        if (!deployment.endpoint) {
+            return {
+                check: "deployment-config",
+                status: "warn",
+                message: "Webhook endpoint not configured",
+                details: { profile },
+            };
+        }
+        // Check deployment age
+        const deployedDate = new Date(deployment.timestamp);
+        const ageInDays = (Date.now() - deployedDate.getTime()) / (1000 * 60 * 60 * 24);
+        if (ageInDays > 30) {
+            return {
+                check: "deployment-config",
+                status: "warn",
+                message: `Deployment is ${Math.floor(ageInDays)} days old`,
+                details: {
+                    deployedAt: deployment.timestamp,
+                    ageInDays: Math.floor(ageInDays),
+                    recommendation: "Consider updating deployment",
+                },
+            };
+        }
+        return {
+            check: "deployment-config",
+            status: "pass",
+            message: "Deployment configuration valid",
+            details: {
+                endpoint: deployment.endpoint,
+                deployedAt: deployment.timestamp,
+                stackName: deployment.stackName,
+                region: deployment.region,
+            },
+        };
+    }
+    catch (error) {
+        return {
+            check: "deployment-config",
+            status: "fail",
+            message: `Deployment check failed: ${error.message}`,
+            details: { error: error.message },
+        };
+    }
+}
+/**
+ * Runs all health checks
+ */
+async function runHealthChecks(profile = "default") {
+    const xdgConfig = new xdg_config_1.XDGConfig();
+    const checks = [];
+    // Run all checks in parallel
+    const results = await Promise.all([
+        checkXDGIntegrity(xdgConfig, profile),
+        checkSecretsSync(xdgConfig, profile),
+        checkDeploymentConfig(xdgConfig, profile),
+    ]);
+    checks.push(...results);
+    // Determine overall status
+    const failCount = checks.filter((c) => c.status === "fail").length;
+    const warnCount = checks.filter((c) => c.status === "warn").length;
+    let overall;
+    if (failCount > 0) {
+        overall = "unhealthy";
+    }
+    else if (warnCount > 0) {
+        overall = "degraded";
+    }
+    else {
+        overall = "healthy";
+    }
+    return {
+        overall,
+        checks,
+        timestamp: new Date().toISOString(),
+        profile,
+    };
+}
+/**
+ * Formats health status for console output
+ */
+function formatHealthStatus(status) {
+    const lines = [];
+    lines.push("╔═══════════════════════════════════════════════════════════╗");
+    lines.push("║   Configuration Health Check                              ║");
+    lines.push("╚═══════════════════════════════════════════════════════════╝");
+    lines.push("");
+    lines.push(`Profile: ${status.profile}`);
+    lines.push(`Timestamp: ${status.timestamp}`);
+    const overallColor = status.overall === "healthy" ? chalk_1.default.green : status.overall === "degraded" ? chalk_1.default.yellow : chalk_1.default.red;
+    lines.push(`Overall Status: ${overallColor(status.overall.toUpperCase())}`);
+    lines.push("");
+    lines.push("Checks:");
+    for (const check of status.checks) {
+        const icon = check.status === "pass" ? chalk_1.default.green("✓") : check.status === "warn" ? chalk_1.default.yellow("⚠") : chalk_1.default.red("❌");
+        lines.push(`  ${icon} ${check.check}: ${check.message}`);
+        if (check.details) {
+            Object.entries(check.details).forEach(([key, value]) => {
+                if (key !== "error" && key !== "recommendation") {
+                    lines.push(`    ${chalk_1.default.dim(`${key}: ${value}`)}`);
+                }
+            });
+            if (check.details.recommendation) {
+                lines.push(`    ${chalk_1.default.cyan(`→ ${check.details.recommendation}`)}`);
+            }
+        }
+        lines.push("");
+    }
+    return lines.join("\n");
+}
+/**
+ * Health check command handler
+ */
+async function healthCheckCommand(options = {}) {
+    const { profile = "default", json = false } = options;
+    const status = await runHealthChecks(profile);
+    if (json) {
+        console.log(JSON.stringify(status, null, 2));
+    }
+    else {
+        console.log(formatHealthStatus(status));
+    }
+    // Exit with appropriate code
+    if (status.overall === "unhealthy") {
+        process.exit(1);
+    }
+    else if (status.overall === "degraded") {
+        process.exit(2);
+    }
+    else {
+        process.exit(0);
+    }
+}
+//# sourceMappingURL=health-check.js.map

package/dist/bin/commands/health-check.js.map

@@ -0,0 +1 @@
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package/dist/{scripts → bin/commands}/infer-quilt-config.d.ts

@@ -9,18 +9,16 @@
  *
  * @module scripts/infer-quilt-config
  */
-import { DerivedConfig } from "../lib/types/config";
 /**
  * Result of Quilt configuration inference
  */
 interface InferenceResult {
-    catalogUrl?: string;
-    quiltUserBucket?: string;
-    quiltDatabase?: string;
-    quiltStackArn?: string;
-    quiltRegion?: string;
-    queueArn?: string;
-    registryUrl?: string;
+    catalog?: string;
+    database?: string;
+    stackArn?: string;
+    region?: string;
+    account?: string;
+    queueUrl?: string;
     source: string;
 }
 /**
@@ -39,12 +37,5 @@ export declare function inferQuiltConfig(options: {
     profile?: string;
     interactive?: boolean;
 }): Promise<InferenceResult>;
-/**
- * Converts inference result to DerivedConfig
- *
- * @param result - Inference result
- * @returns DerivedConfig object
- */
-export declare function inferenceResultToDerivedConfig(result: InferenceResult): DerivedConfig;
 export {};
 //# sourceMappingURL=infer-quilt-config.d.ts.map

package/dist/bin/commands/infer-quilt-config.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"infer-quilt-config.d.ts","sourceRoot":"","sources":["../../../bin/commands/infer-quilt-config.ts"],"names":[],"mappings":";AACA;;;;;;;;;GASG;AA4BH;;GAEG;AACH,UAAU,eAAe;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;CAClB;AAmJD;;;;;;;;;;GAUG;AACH,wBAAsB,gBAAgB,CAAC,OAAO,EAAE;IAC5C,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,OAAO,CAAC;CACzB,GAAG,OAAO,CAAC,eAAe,CAAC,CA8F3B"}

package/dist/{scripts → bin/commands}/infer-quilt-config.js

@@ -45,10 +45,10 @@ var __importStar = (this && this.__importStar) || (function () {
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.inferQuiltConfig = inferQuiltConfig;
-exports.inferenceResultToDerivedConfig = inferenceResultToDerivedConfig;
 const child_process_1 = require("child_process");
 const readline = __importStar(require("readline"));
 const client_cloudformation_1 = require("@aws-sdk/client-cloudformation");
+const sqs_1 = require("../../lib/utils/sqs");
 /**
  * Executes quilt3 config command to get current catalog URL
  *
@@ -113,6 +113,12 @@ async function findQuiltStacks(region = "us-east-1", profile) {
                     stackArn: stackDetail.StackId || "",
                     region: region,
                 };
+                // Extract AWS Account ID from Stack ARN
+                // ARN format: arn:aws:cloudformation:REGION:ACCOUNT_ID:stack/STACK_NAME/STACK_ID
+                const arnMatch = stackInfo.stackArn.match(/^arn:aws:cloudformation:[^:]+:(\d{12}):/);
+                if (arnMatch) {
+                    stackInfo.account = arnMatch[1];
+                }
                 // Extract outputs
                 for (const output of outputs) {
                     const key = output.OutputKey || "";
@@ -120,14 +126,13 @@ async function findQuiltStacks(region = "us-east-1", profile) {
                     if (key === "QuiltWebHost") {
                         stackInfo.catalogUrl = value;
                     }
-                    else if (key.includes("ucket")) {
-                        stackInfo.bucket = value;
-                    }
                     else if (key === "UserAthenaDatabaseName" || key.includes("Database")) {
                         stackInfo.database = value;
                     }
                     else if (key.includes("Queue")) {
-                        stackInfo.queueArn = value;
+                        if ((0, sqs_1.isQueueUrl)(value)) {
+                            stackInfo.queueUrl = value;
+                        }
                     }
                 }
                 stackInfos.push(stackInfo);
@@ -192,7 +197,7 @@ async function inferQuiltConfig(options) {
     console.log("Checking quilt3 CLI configuration...");
     const quilt3Config = getQuilt3Catalog();
     if (quilt3Config?.catalogUrl) {
-        result.catalogUrl = quilt3Config.catalogUrl;
+        result.catalog = quilt3Config.catalogUrl;
         result.source = "quilt3-cli";
     }
     else {
@@ -208,10 +213,10 @@ async function inferQuiltConfig(options) {
     console.log(`Found ${stacks.length} Quilt stack(s):\n`);
     let selectedStack;
     // If we have a catalog URL from quilt3, try to find matching stack
-    if (result.catalogUrl && stacks.length > 1) {
+    if (result.catalog && stacks.length > 1) {
         // Normalize URLs for comparison (remove protocol and trailing slashes)
         const normalizeUrl = (url) => url.replace(/^https?:\/\//, "").replace(/\/$/, "");
-        const targetUrl = normalizeUrl(result.catalogUrl);
+        const targetUrl = normalizeUrl(result.catalog);
         const matchingStack = stacks.find((s) => s.catalogUrl && normalizeUrl(s.catalogUrl) === targetUrl);
         if (matchingStack) {
             selectedStack = matchingStack;
@@ -219,7 +224,7 @@ async function inferQuiltConfig(options) {
         }
         else {
             // No match found, prompt user
-            console.log(`No stack found matching catalog URL: ${result.catalogUrl}`);
+            console.log(`No stack found matching catalog URL: ${result.catalog}`);
             if (interactive) {
                 const options = stacks.map((s) => `${s.stackName} (${s.region})`);
                 const selectedIndex = await promptCatalogSelection(options);
@@ -248,19 +253,22 @@ async function inferQuiltConfig(options) {
     }
     // Populate result from selected stack
     if (selectedStack.stackArn) {
-        result.quiltStackArn = selectedStack.stackArn;
+        result.stackArn = selectedStack.stackArn;
     }
-    if (selectedStack.bucket) {
-        result.quiltUserBucket = selectedStack.bucket;
+    if (selectedStack.account) {
+        result.account = selectedStack.account;
     }
-    if (selectedStack.queueArn) {
-        result.queueArn = selectedStack.queueArn;
+    if (selectedStack.database) {
+        result.database = selectedStack.database;
     }
-    if (selectedStack.catalogUrl && !result.catalogUrl) {
-        result.catalogUrl = selectedStack.catalogUrl;
+    if (selectedStack.queueUrl) {
+        result.queueUrl = selectedStack.queueUrl;
+    }
+    if (selectedStack.catalogUrl && !result.catalog) {
+        result.catalog = selectedStack.catalogUrl;
     }
     if (selectedStack.region) {
-        result.quiltRegion = selectedStack.region;
+        result.region = selectedStack.region;
     }
     if (result.source === "quilt3-cli") {
         result.source = "quilt3-cli+cloudformation";
@@ -270,39 +278,6 @@ async function inferQuiltConfig(options) {
     }
     return result;
 }
-/**
- * Converts inference result to DerivedConfig
- *
- * @param result - Inference result
- * @returns DerivedConfig object
- */
-function inferenceResultToDerivedConfig(result) {
-    const config = {
-        _metadata: {
-            inferredAt: new Date().toISOString(),
-            inferredFrom: result.source,
-            source: "infer-quilt-config",
-            version: "0.6.0",
-        },
-    };
-    if (result.catalogUrl) {
-        config.catalogUrl = result.catalogUrl;
-        config.quiltCatalog = result.catalogUrl;
-    }
-    if (result.quiltUserBucket) {
-        config.quiltUserBucket = result.quiltUserBucket;
-    }
-    if (result.quiltStackArn) {
-        config.quiltStackArn = result.quiltStackArn;
-    }
-    if (result.quiltRegion) {
-        config.quiltRegion = result.quiltRegion;
-    }
-    if (result.queueArn) {
-        config.queueArn = result.queueArn;
-    }
-    return config;
-}
 /**
  * Main execution for CLI usage
  */
@@ -329,19 +304,18 @@ async function main() {
     const result = await inferQuiltConfig(options);
     console.log("\n=== Inference Results ===");
     console.log(`Source: ${result.source}`);
-    if (result.catalogUrl)
-        console.log(`Catalog URL: ${result.catalogUrl}`);
-    if (result.quiltUserBucket)
-        console.log(`User Bucket: ${result.quiltUserBucket}`);
-    if (result.quiltStackArn)
-        console.log(`Stack ARN: ${result.quiltStackArn}`);
-    if (result.quiltRegion)
-        console.log(`Region: ${result.quiltRegion}`);
-    if (result.queueArn)
-        console.log(`Queue ARN: ${result.queueArn}`);
-    const derivedConfig = inferenceResultToDerivedConfig(result);
-    console.log("\n=== Derived Configuration ===");
-    console.log(JSON.stringify(derivedConfig, null, 4));
+    if (result.catalog)
+        console.log(`Catalog URL: ${result.catalog}`);
+    if (result.database)
+        console.log(`Database: ${result.database}`);
+    if (result.stackArn)
+        console.log(`Stack ARN: ${result.stackArn}`);
+    if (result.region)
+        console.log(`Region: ${result.region}`);
+    if (result.account)
+        console.log(`AWS Account ID: ${result.account}`);
+    if (result.queueUrl)
+        console.log(`Queue URL: ${result.queueUrl}`);
 }
 // Run main if executed directly
 if (require.main === module) {

package/dist/bin/commands/infer-quilt-config.js.map

@@ -0,0 +1 @@
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package/dist/bin/commands/init.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../bin/commands/init.ts"],"names":[],"mappings":"AAQA,UAAU,WAAW;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;CACnB;AAED,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAiLrE"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../../bin/commands/init.ts"],"names":[],"mappings":"AAMA,UAAU,WAAW;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;CACnB;AAED,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAgJrE"}

package/dist/bin/commands/init.js

@@ -7,10 +7,8 @@ exports.initCommand = initCommand;
 const fs_1 = require("fs");
 const path_1 = require("path");
 const chalk_1 = __importDefault(require("chalk"));
-const ora_1 = __importDefault(require("ora"));
 const boxen_1 = __importDefault(require("boxen"));
 const enquirer_1 = require("enquirer");
-const benchling_webhook_1 = require("../benchling-webhook");
 async function initCommand(options) {
     console.log((0, boxen_1.default)(chalk_1.default.bold("Benchling Webhook Setup"), {
         padding: 1,
@@ -102,36 +100,8 @@ async function initCommand(options) {
     envLines.push(`BENCHLING_CLIENT_SECRET=${answers.clientSecret}`);
     envLines.push(`BENCHLING_APP_DEFINITION_ID=${answers.appId}`);
     envLines.push("");
-    // Attempt inference if requested
-    let inferredVars = {};
-    if (options.infer !== false) {
-        console.log();
-        const spinner = (0, ora_1.default)("Inferring additional configuration from catalog...").start();
-        const inferenceResult = await (0, benchling_webhook_1.inferConfiguration)(answers.catalog);
-        if (inferenceResult.success) {
-            inferredVars = inferenceResult.inferredVars;
-            spinner.succeed("Successfully inferred additional configuration");
-            if (inferredVars.CDK_DEFAULT_ACCOUNT) {
-                envLines.push("# AWS Configuration (inferred)");
-                envLines.push(`CDK_DEFAULT_ACCOUNT=${inferredVars.CDK_DEFAULT_ACCOUNT}`);
-                envLines.push(`CDK_DEFAULT_REGION=${inferredVars.CDK_DEFAULT_REGION}`);
-                envLines.push("");
-            }
-            if (inferredVars.QUEUE_ARN) {
-                envLines.push("# SQS Configuration (inferred)");
-                envLines.push(`QUEUE_ARN=${inferredVars.QUEUE_ARN}`);
-                envLines.push("");
-            }
-            if (inferredVars.QUILT_DATABASE) {
-                envLines.push("# Quilt Database (inferred)");
-                envLines.push(`QUILT_DATABASE=${inferredVars.QUILT_DATABASE}`);
-                envLines.push("");
-            }
-        }
-        else {
-            spinner.warn(`Could not infer additional configuration: ${inferenceResult.error}`);
-        }
-    }
+    // Note: Inference is deprecated in secrets-only mode (v0.6.0+)
+    // Configuration is now stored in AWS Secrets Manager and CloudFormation parameters
     // Add optional configuration section
     if (!options.minimal) {
         envLines.push("# Optional Configuration");