@stackmemoryai/stackmemory 0.5.38 → 0.5.40

package/dist/cli/commands/setup.js

@@ -0,0 +1,327 @@
+import { fileURLToPath as __fileURLToPath } from 'url';
+import { dirname as __pathDirname } from 'path';
+const __filename = __fileURLToPath(import.meta.url);
+const __dirname = __pathDirname(__filename);
+import { Command } from "commander";
+import chalk from "chalk";
+import { existsSync, readFileSync, writeFileSync, mkdirSync } from "fs";
+import { join } from "path";
+import { homedir } from "os";
+import { execSync } from "child_process";
+const CLAUDE_DIR = join(homedir(), ".claude");
+const CLAUDE_CONFIG_FILE = join(CLAUDE_DIR, "config.json");
+const MCP_CONFIG_FILE = join(CLAUDE_DIR, "stackmemory-mcp.json");
+const HOOKS_JSON = join(CLAUDE_DIR, "hooks.json");
+function createSetupMCPCommand() {
+  return new Command("setup-mcp").description("Auto-configure Claude Code MCP integration").option("--dry-run", "Show what would be configured without making changes").option("--reset", "Reset MCP configuration to defaults").action(async (options) => {
+    console.log(chalk.cyan("\nStackMemory MCP Setup\n"));
+    if (options.dryRun) {
+      console.log(chalk.yellow("[DRY RUN] No changes will be made.\n"));
+    }
+    if (!existsSync(CLAUDE_DIR)) {
+      if (options.dryRun) {
+        console.log(chalk.gray(`Would create: ${CLAUDE_DIR}`));
+      } else {
+        mkdirSync(CLAUDE_DIR, { recursive: true });
+        console.log(chalk.green("[OK]") + " Created ~/.claude directory");
+      }
+    }
+    const mcpConfig = {
+      mcpServers: {
+        stackmemory: {
+          command: "stackmemory",
+          args: ["mcp-server"],
+          env: {
+            NODE_ENV: "production"
+          }
+        }
+      }
+    };
+    if (options.dryRun) {
+      console.log(
+        chalk.gray(`Would write MCP config to: ${MCP_CONFIG_FILE}`)
+      );
+      console.log(chalk.gray(JSON.stringify(mcpConfig, null, 2)));
+    } else {
+      writeFileSync(MCP_CONFIG_FILE, JSON.stringify(mcpConfig, null, 2));
+      console.log(chalk.green("[OK]") + " Created MCP server configuration");
+    }
+    let claudeConfig = {};
+    if (existsSync(CLAUDE_CONFIG_FILE)) {
+      try {
+        claudeConfig = JSON.parse(readFileSync(CLAUDE_CONFIG_FILE, "utf8"));
+      } catch {
+        console.log(
+          chalk.yellow("[WARN]") + " Could not parse existing config.json, creating new"
+        );
+      }
+    }
+    if (!claudeConfig.mcp) {
+      claudeConfig.mcp = {};
+    }
+    const mcp = claudeConfig.mcp;
+    if (!mcp.configFiles) {
+      mcp.configFiles = [];
+    }
+    const configFiles = mcp.configFiles;
+    if (!configFiles.includes(MCP_CONFIG_FILE)) {
+      configFiles.push(MCP_CONFIG_FILE);
+    }
+    if (options.dryRun) {
+      console.log(chalk.gray(`Would update: ${CLAUDE_CONFIG_FILE}`));
+    } else {
+      writeFileSync(
+        CLAUDE_CONFIG_FILE,
+        JSON.stringify(claudeConfig, null, 2)
+      );
+      console.log(chalk.green("[OK]") + " Updated Claude config.json");
+    }
+    console.log(chalk.cyan("\nValidating configuration..."));
+    try {
+      execSync("stackmemory --version", { stdio: "pipe" });
+      console.log(chalk.green("[OK]") + " stackmemory CLI is installed");
+    } catch {
+      console.log(chalk.yellow("[WARN]") + " stackmemory CLI not in PATH");
+      console.log(chalk.gray("  You may need to restart your terminal"));
+    }
+    try {
+      execSync("claude --version", { stdio: "pipe" });
+      console.log(chalk.green("[OK]") + " Claude Code is installed");
+    } catch {
+      console.log(chalk.yellow("[WARN]") + " Claude Code not found");
+      console.log(chalk.gray("  Install from: https://claude.ai/code"));
+    }
+    if (!options.dryRun) {
+      console.log(chalk.green("\nMCP setup complete!"));
+      console.log(chalk.cyan("\nNext steps:"));
+      console.log(chalk.white("  1. Restart Claude Code"));
+      console.log(
+        chalk.white(
+          "  2. The StackMemory MCP tools will be available automatically"
+        )
+      );
+      console.log(
+        chalk.gray(
+          '\nTo verify: Run "stackmemory doctor" to check all integrations'
+        )
+      );
+    }
+  });
+}
+function createDoctorCommand() {
+  return new Command("doctor").description("Diagnose StackMemory configuration and common issues").option("--fix", "Attempt to automatically fix issues").action(async (options) => {
+    console.log(chalk.cyan("\nStackMemory Doctor\n"));
+    console.log(chalk.gray("Checking configuration and dependencies...\n"));
+    const results = [];
+    const projectDir = join(process.cwd(), ".stackmemory");
+    const dbPath = join(projectDir, "context.db");
+    if (existsSync(dbPath)) {
+      results.push({
+        name: "Project Initialization",
+        status: "ok",
+        message: "StackMemory is initialized in this project"
+      });
+    } else if (existsSync(projectDir)) {
+      results.push({
+        name: "Project Initialization",
+        status: "warn",
+        message: ".stackmemory directory exists but database not found",
+        fix: "Run: stackmemory init"
+      });
+    } else {
+      results.push({
+        name: "Project Initialization",
+        status: "error",
+        message: "StackMemory not initialized in this project",
+        fix: "Run: stackmemory init"
+      });
+    }
+    if (existsSync(dbPath)) {
+      try {
+        const Database = (await import("better-sqlite3")).default;
+        const db = new Database(dbPath, { readonly: true });
+        const tables = db.prepare("SELECT name FROM sqlite_master WHERE type='table'").all();
+        db.close();
+        const hasFrames = tables.some((t) => t.name === "frames");
+        if (hasFrames) {
+          results.push({
+            name: "Database Integrity",
+            status: "ok",
+            message: `Database has ${tables.length} tables`
+          });
+        } else {
+          results.push({
+            name: "Database Integrity",
+            status: "warn",
+            message: "Database exists but missing expected tables",
+            fix: "Run: stackmemory init --interactive"
+          });
+        }
+      } catch (error) {
+        results.push({
+          name: "Database Integrity",
+          status: "error",
+          message: `Database error: ${error.message}`,
+          fix: "Remove .stackmemory/context.db and run: stackmemory init"
+        });
+      }
+    }
+    if (existsSync(MCP_CONFIG_FILE)) {
+      try {
+        const config = JSON.parse(readFileSync(MCP_CONFIG_FILE, "utf8"));
+        if (config.mcpServers?.stackmemory) {
+          results.push({
+            name: "MCP Configuration",
+            status: "ok",
+            message: "MCP server configured"
+          });
+        } else {
+          results.push({
+            name: "MCP Configuration",
+            status: "warn",
+            message: "MCP config file exists but stackmemory server not configured",
+            fix: "Run: stackmemory setup-mcp"
+          });
+        }
+      } catch {
+        results.push({
+          name: "MCP Configuration",
+          status: "error",
+          message: "Invalid MCP configuration file",
+          fix: "Run: stackmemory setup-mcp --reset"
+        });
+      }
+    } else {
+      results.push({
+        name: "MCP Configuration",
+        status: "warn",
+        message: "MCP not configured for Claude Code",
+        fix: "Run: stackmemory setup-mcp"
+      });
+    }
+    if (existsSync(HOOKS_JSON)) {
+      try {
+        const hooks = JSON.parse(readFileSync(HOOKS_JSON, "utf8"));
+        const hasTraceHook = !!hooks["tool-use-approval"];
+        if (hasTraceHook) {
+          results.push({
+            name: "Claude Hooks",
+            status: "ok",
+            message: "Tool tracing hook installed"
+          });
+        } else {
+          results.push({
+            name: "Claude Hooks",
+            status: "warn",
+            message: "Hooks file exists but tracing not configured",
+            fix: "Run: stackmemory hooks install"
+          });
+        }
+      } catch {
+        results.push({
+          name: "Claude Hooks",
+          status: "warn",
+          message: "Could not read hooks.json"
+        });
+      }
+    } else {
+      results.push({
+        name: "Claude Hooks",
+        status: "warn",
+        message: "Claude hooks not installed (optional)",
+        fix: "Run: stackmemory hooks install"
+      });
+    }
+    const envChecks = [
+      { key: "LINEAR_API_KEY", name: "Linear API Key", optional: true },
+      { key: "TWILIO_ACCOUNT_SID", name: "Twilio Account", optional: true }
+    ];
+    for (const check of envChecks) {
+      const value = process.env[check.key];
+      if (value) {
+        results.push({
+          name: check.name,
+          status: "ok",
+          message: "Environment variable set"
+        });
+      } else if (!check.optional) {
+        results.push({
+          name: check.name,
+          status: "error",
+          message: "Required environment variable not set",
+          fix: `Set ${check.key} in your .env file`
+        });
+      }
+    }
+    const homeStackmemory = join(homedir(), ".stackmemory");
+    if (existsSync(homeStackmemory)) {
+      try {
+        const testFile = join(homeStackmemory, ".write-test");
+        writeFileSync(testFile, "test");
+        const { unlinkSync } = await import("fs");
+        unlinkSync(testFile);
+        results.push({
+          name: "File Permissions",
+          status: "ok",
+          message: "~/.stackmemory is writable"
+        });
+      } catch {
+        results.push({
+          name: "File Permissions",
+          status: "error",
+          message: "~/.stackmemory is not writable",
+          fix: "Run: chmod 700 ~/.stackmemory"
+        });
+      }
+    }
+    let hasErrors = false;
+    let hasWarnings = false;
+    for (const result of results) {
+      const icon = result.status === "ok" ? chalk.green("[OK]") : result.status === "warn" ? chalk.yellow("[WARN]") : chalk.red("[ERROR]");
+      console.log(`${icon} ${result.name}`);
+      console.log(chalk.gray(`    ${result.message}`));
+      if (result.fix) {
+        console.log(chalk.cyan(`    Fix: ${result.fix}`));
+        if (options.fix && result.status !== "ok") {
+          if (result.fix.includes("stackmemory setup-mcp")) {
+            console.log(chalk.gray("    Attempting auto-fix..."));
+            try {
+              execSync("stackmemory setup-mcp", { stdio: "inherit" });
+            } catch {
+              console.log(chalk.red("    Auto-fix failed"));
+            }
+          }
+        }
+      }
+      if (result.status === "error") hasErrors = true;
+      if (result.status === "warn") hasWarnings = true;
+    }
+    console.log("");
+    if (hasErrors) {
+      console.log(
+        chalk.red("Some issues need attention. Run suggested fixes above.")
+      );
+      process.exit(1);
+    } else if (hasWarnings) {
+      console.log(
+        chalk.yellow(
+          "StackMemory is working but some optional features are not configured."
+        )
+      );
+    } else {
+      console.log(
+        chalk.green("All checks passed! StackMemory is properly configured.")
+      );
+    }
+  });
+}
+function registerSetupCommands(program) {
+  program.addCommand(createSetupMCPCommand());
+  program.addCommand(createDoctorCommand());
+}
+export {
+  createDoctorCommand,
+  createSetupMCPCommand,
+  registerSetupCommands
+};
+//# sourceMappingURL=setup.js.map

package/dist/cli/commands/setup.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../../src/cli/commands/setup.ts"],
+  "sourcesContent": ["/**\n * Setup commands for StackMemory onboarding\n * - setup-mcp: Auto-configure Claude Code MCP integration\n * - doctor: Diagnose common issues\n */\n\nimport { Command } from 'commander';\nimport chalk from 'chalk';\nimport { existsSync, readFileSync, writeFileSync, mkdirSync } from 'fs';\nimport { join } from 'path';\nimport { homedir } from 'os';\nimport { execSync } from 'child_process';\n\n// Claude config paths\nconst CLAUDE_DIR = join(homedir(), '.claude');\nconst CLAUDE_CONFIG_FILE = join(CLAUDE_DIR, 'config.json');\nconst MCP_CONFIG_FILE = join(CLAUDE_DIR, 'stackmemory-mcp.json');\nconst HOOKS_JSON = join(CLAUDE_DIR, 'hooks.json');\n\ninterface DiagnosticResult {\n  name: string;\n  status: 'ok' | 'warn' | 'error';\n  message: string;\n  fix?: string;\n}\n\n/**\n * Create setup-mcp command\n */\nexport function createSetupMCPCommand(): Command {\n  return new Command('setup-mcp')\n    .description('Auto-configure Claude Code MCP integration')\n    .option('--dry-run', 'Show what would be configured without making changes')\n    .option('--reset', 'Reset MCP configuration to defaults')\n    .action(async (options) => {\n      console.log(chalk.cyan('\\nStackMemory MCP Setup\\n'));\n\n      if (options.dryRun) {\n        console.log(chalk.yellow('[DRY RUN] No changes will be made.\\n'));\n      }\n\n      // Step 1: Ensure Claude directory exists\n      if (!existsSync(CLAUDE_DIR)) {\n        if (options.dryRun) {\n          console.log(chalk.gray(`Would create: ${CLAUDE_DIR}`));\n        } else {\n          mkdirSync(CLAUDE_DIR, { recursive: true });\n          console.log(chalk.green('[OK]') + ' Created ~/.claude directory');\n        }\n      }\n\n      // Step 2: Create MCP server configuration\n      const mcpConfig = {\n        mcpServers: {\n          stackmemory: {\n            command: 'stackmemory',\n            args: ['mcp-server'],\n            env: {\n              NODE_ENV: 'production',\n            },\n          },\n        },\n      };\n\n      if (options.dryRun) {\n        console.log(\n          chalk.gray(`Would write MCP config to: ${MCP_CONFIG_FILE}`)\n        );\n        console.log(chalk.gray(JSON.stringify(mcpConfig, null, 2)));\n      } else {\n        writeFileSync(MCP_CONFIG_FILE, JSON.stringify(mcpConfig, null, 2));\n        console.log(chalk.green('[OK]') + ' Created MCP server configuration');\n      }\n\n      // Step 3: Update Claude config.json to reference MCP config\n      let claudeConfig: Record<string, unknown> = {};\n      if (existsSync(CLAUDE_CONFIG_FILE)) {\n        try {\n          claudeConfig = JSON.parse(readFileSync(CLAUDE_CONFIG_FILE, 'utf8'));\n        } catch {\n          console.log(\n            chalk.yellow('[WARN]') +\n              ' Could not parse existing config.json, creating new'\n          );\n        }\n      }\n\n      // Ensure mcp.configFiles array includes our config\n      if (!claudeConfig.mcp) {\n        claudeConfig.mcp = {};\n      }\n      const mcp = claudeConfig.mcp as Record<string, unknown>;\n      if (!mcp.configFiles) {\n        mcp.configFiles = [];\n      }\n      const configFiles = mcp.configFiles as string[];\n      if (!configFiles.includes(MCP_CONFIG_FILE)) {\n        configFiles.push(MCP_CONFIG_FILE);\n      }\n\n      if (options.dryRun) {\n        console.log(chalk.gray(`Would update: ${CLAUDE_CONFIG_FILE}`));\n      } else {\n        writeFileSync(\n          CLAUDE_CONFIG_FILE,\n          JSON.stringify(claudeConfig, null, 2)\n        );\n        console.log(chalk.green('[OK]') + ' Updated Claude config.json');\n      }\n\n      // Step 4: Validate configuration\n      console.log(chalk.cyan('\\nValidating configuration...'));\n\n      // Check stackmemory command is available\n      try {\n        execSync('stackmemory --version', { stdio: 'pipe' });\n        console.log(chalk.green('[OK]') + ' stackmemory CLI is installed');\n      } catch {\n        console.log(chalk.yellow('[WARN]') + ' stackmemory CLI not in PATH');\n        console.log(chalk.gray('  You may need to restart your terminal'));\n      }\n\n      // Check Claude Code is available\n      try {\n        execSync('claude --version', { stdio: 'pipe' });\n        console.log(chalk.green('[OK]') + ' Claude Code is installed');\n      } catch {\n        console.log(chalk.yellow('[WARN]') + ' Claude Code not found');\n        console.log(chalk.gray('  Install from: https://claude.ai/code'));\n      }\n\n      // Final instructions\n      if (!options.dryRun) {\n        console.log(chalk.green('\\nMCP setup complete!'));\n        console.log(chalk.cyan('\\nNext steps:'));\n        console.log(chalk.white('  1. Restart Claude Code'));\n        console.log(\n          chalk.white(\n            '  2. The StackMemory MCP tools will be available automatically'\n          )\n        );\n        console.log(\n          chalk.gray(\n            '\\nTo verify: Run \"stackmemory doctor\" to check all integrations'\n          )\n        );\n      }\n    });\n}\n\n/**\n * Create doctor command for diagnostics\n */\nexport function createDoctorCommand(): Command {\n  return new Command('doctor')\n    .description('Diagnose StackMemory configuration and common issues')\n    .option('--fix', 'Attempt to automatically fix issues')\n    .action(async (options) => {\n      console.log(chalk.cyan('\\nStackMemory Doctor\\n'));\n      console.log(chalk.gray('Checking configuration and dependencies...\\n'));\n\n      const results: DiagnosticResult[] = [];\n\n      // 1. Check project initialization\n      const projectDir = join(process.cwd(), '.stackmemory');\n      const dbPath = join(projectDir, 'context.db');\n      if (existsSync(dbPath)) {\n        results.push({\n          name: 'Project Initialization',\n          status: 'ok',\n          message: 'StackMemory is initialized in this project',\n        });\n      } else if (existsSync(projectDir)) {\n        results.push({\n          name: 'Project Initialization',\n          status: 'warn',\n          message: '.stackmemory directory exists but database not found',\n          fix: 'Run: stackmemory init',\n        });\n      } else {\n        results.push({\n          name: 'Project Initialization',\n          status: 'error',\n          message: 'StackMemory not initialized in this project',\n          fix: 'Run: stackmemory init',\n        });\n      }\n\n      // 2. Check database integrity\n      if (existsSync(dbPath)) {\n        try {\n          const Database = (await import('better-sqlite3')).default;\n          const db = new Database(dbPath, { readonly: true });\n          const tables = db\n            .prepare(\"SELECT name FROM sqlite_master WHERE type='table'\")\n            .all() as { name: string }[];\n          db.close();\n\n          const hasFrames = tables.some((t) => t.name === 'frames');\n          if (hasFrames) {\n            results.push({\n              name: 'Database Integrity',\n              status: 'ok',\n              message: `Database has ${tables.length} tables`,\n            });\n          } else {\n            results.push({\n              name: 'Database Integrity',\n              status: 'warn',\n              message: 'Database exists but missing expected tables',\n              fix: 'Run: stackmemory init --interactive',\n            });\n          }\n        } catch (error) {\n          results.push({\n            name: 'Database Integrity',\n            status: 'error',\n            message: `Database error: ${(error as Error).message}`,\n            fix: 'Remove .stackmemory/context.db and run: stackmemory init',\n          });\n        }\n      }\n\n      // 3. Check MCP configuration\n      if (existsSync(MCP_CONFIG_FILE)) {\n        try {\n          const config = JSON.parse(readFileSync(MCP_CONFIG_FILE, 'utf8'));\n          if (config.mcpServers?.stackmemory) {\n            results.push({\n              name: 'MCP Configuration',\n              status: 'ok',\n              message: 'MCP server configured',\n            });\n          } else {\n            results.push({\n              name: 'MCP Configuration',\n              status: 'warn',\n              message:\n                'MCP config file exists but stackmemory server not configured',\n              fix: 'Run: stackmemory setup-mcp',\n            });\n          }\n        } catch {\n          results.push({\n            name: 'MCP Configuration',\n            status: 'error',\n            message: 'Invalid MCP configuration file',\n            fix: 'Run: stackmemory setup-mcp --reset',\n          });\n        }\n      } else {\n        results.push({\n          name: 'MCP Configuration',\n          status: 'warn',\n          message: 'MCP not configured for Claude Code',\n          fix: 'Run: stackmemory setup-mcp',\n        });\n      }\n\n      // 4. Check Claude hooks\n      if (existsSync(HOOKS_JSON)) {\n        try {\n          const hooks = JSON.parse(readFileSync(HOOKS_JSON, 'utf8'));\n          const hasTraceHook = !!hooks['tool-use-approval'];\n          if (hasTraceHook) {\n            results.push({\n              name: 'Claude Hooks',\n              status: 'ok',\n              message: 'Tool tracing hook installed',\n            });\n          } else {\n            results.push({\n              name: 'Claude Hooks',\n              status: 'warn',\n              message: 'Hooks file exists but tracing not configured',\n              fix: 'Run: stackmemory hooks install',\n            });\n          }\n        } catch {\n          results.push({\n            name: 'Claude Hooks',\n            status: 'warn',\n            message: 'Could not read hooks.json',\n          });\n        }\n      } else {\n        results.push({\n          name: 'Claude Hooks',\n          status: 'warn',\n          message: 'Claude hooks not installed (optional)',\n          fix: 'Run: stackmemory hooks install',\n        });\n      }\n\n      // 5. Check environment variables\n      const envChecks = [\n        { key: 'LINEAR_API_KEY', name: 'Linear API Key', optional: true },\n        { key: 'TWILIO_ACCOUNT_SID', name: 'Twilio Account', optional: true },\n      ];\n\n      for (const check of envChecks) {\n        const value = process.env[check.key];\n        if (value) {\n          results.push({\n            name: check.name,\n            status: 'ok',\n            message: 'Environment variable set',\n          });\n        } else if (!check.optional) {\n          results.push({\n            name: check.name,\n            status: 'error',\n            message: 'Required environment variable not set',\n            fix: `Set ${check.key} in your .env file`,\n          });\n        }\n        // Skip optional env vars that aren't set\n      }\n\n      // 6. Check file permissions\n      const homeStackmemory = join(homedir(), '.stackmemory');\n      if (existsSync(homeStackmemory)) {\n        try {\n          const testFile = join(homeStackmemory, '.write-test');\n          writeFileSync(testFile, 'test');\n          const { unlinkSync } = await import('fs');\n          unlinkSync(testFile);\n          results.push({\n            name: 'File Permissions',\n            status: 'ok',\n            message: '~/.stackmemory is writable',\n          });\n        } catch {\n          results.push({\n            name: 'File Permissions',\n            status: 'error',\n            message: '~/.stackmemory is not writable',\n            fix: 'Run: chmod 700 ~/.stackmemory',\n          });\n        }\n      }\n\n      // Display results\n      let hasErrors = false;\n      let hasWarnings = false;\n\n      for (const result of results) {\n        const icon =\n          result.status === 'ok'\n            ? chalk.green('[OK]')\n            : result.status === 'warn'\n              ? chalk.yellow('[WARN]')\n              : chalk.red('[ERROR]');\n\n        console.log(`${icon} ${result.name}`);\n        console.log(chalk.gray(`    ${result.message}`));\n\n        if (result.fix) {\n          console.log(chalk.cyan(`    Fix: ${result.fix}`));\n\n          if (options.fix && result.status !== 'ok') {\n            // Auto-fix logic for specific issues\n            if (result.fix.includes('stackmemory setup-mcp')) {\n              console.log(chalk.gray('    Attempting auto-fix...'));\n              try {\n                execSync('stackmemory setup-mcp', { stdio: 'inherit' });\n              } catch {\n                console.log(chalk.red('    Auto-fix failed'));\n              }\n            }\n          }\n        }\n\n        if (result.status === 'error') hasErrors = true;\n        if (result.status === 'warn') hasWarnings = true;\n      }\n\n      // Summary\n      console.log('');\n      if (hasErrors) {\n        console.log(\n          chalk.red('Some issues need attention. Run suggested fixes above.')\n        );\n        process.exit(1);\n      } else if (hasWarnings) {\n        console.log(\n          chalk.yellow(\n            'StackMemory is working but some optional features are not configured.'\n          )\n        );\n      } else {\n        console.log(\n          chalk.green('All checks passed! StackMemory is properly configured.')\n        );\n      }\n    });\n}\n\n/**\n * Register setup commands\n */\nexport function registerSetupCommands(program: Command): void {\n  program.addCommand(createSetupMCPCommand());\n  program.addCommand(createDoctorCommand());\n}\n"],
+  "mappings": 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+  "names": []
+}

package/dist/cli/index.js

@@ -50,17 +50,14 @@ import { createSettingsCommand } from "./commands/settings.js";
 import { createRetrievalCommands } from "./commands/retrieval.js";
 import { createDiscoveryCommands } from "./commands/discovery.js";
 import { createModelCommand } from "./commands/model.js";
+import { registerSetupCommands } from "./commands/setup.js";
 import { ProjectManager } from "../core/projects/project-manager.js";
 import Database from "better-sqlite3";
 import { join } from "path";
 import { existsSync, mkdirSync } from "fs";
 import inquirer from "inquirer";
 import chalk from "chalk";
-import {
-  loadStorageConfig,
-  enableChromaDB,
-  getStorageModeDescription
-} from "../core/config/storage-config.js";
+import { enableChromaDB } from "../core/config/storage-config.js";
 import { spawn } from "child_process";
 import { homedir } from "os";
 import { createRequire } from "module";
@@ -131,69 +128,77 @@ program.name("stackmemory").description(
   "Lossless memory runtime for AI coding tools - organizes context as a call stack instead of linear chat logs, with team collaboration and infinite retention"
 ).version(VERSION);
 program.command("init").description(
-  `Initialize StackMemory in current project
+  `Initialize StackMemory in current project (zero-config by default)
 
-Storage Modes:
-  SQLite (default): Local only, fast, no setup required
-  ChromaDB (hybrid): Adds semantic search and cloud backup, requires API key`
-).option("--sqlite", "Use SQLite-only storage (default, skip prompts)").option(
+Options:
+  --interactive    Ask configuration questions
+  --chromadb       Enable ChromaDB semantic search (prompts for API key)`
+).option("-i, --interactive", "Interactive mode with configuration prompts").option(
   "--chromadb",
   "Enable ChromaDB for semantic search (prompts for API key)"
-).option("--skip-storage-prompt", "Skip storage configuration prompt").action(async (options) => {
+).action(async (options) => {
   try {
     const projectRoot = process.cwd();
     const dbDir = join(projectRoot, ".stackmemory");
+    const alreadyInit = existsSync(join(dbDir, "context.db"));
+    if (alreadyInit && !options.interactive) {
+      console.log(chalk.yellow("StackMemory already initialized."));
+      console.log(chalk.gray("Run with --interactive to reconfigure."));
+      return;
+    }
     if (!existsSync(dbDir)) {
       mkdirSync(dbDir, { recursive: true });
     }
-    let storageConfig = loadStorageConfig();
-    const isFirstTimeSetup = !storageConfig.chromadb.enabled && storageConfig.mode === "sqlite";
-    if (options.sqlite || options.skipStoragePrompt) {
-      console.log(chalk.gray("Using SQLite-only storage mode."));
-    } else if (options.chromadb) {
+    if (options.chromadb) {
       await promptAndEnableChromaDB();
-    } else if (isFirstTimeSetup && process.stdin.isTTY) {
+    } else if (options.interactive && process.stdin.isTTY) {
       console.log(chalk.cyan("\nStorage Configuration"));
-      console.log(chalk.gray("StackMemory supports two storage modes:\n"));
-      console.log(chalk.white("  SQLite (default):"));
-      console.log(chalk.gray("    - Local storage only"));
-      console.log(chalk.gray("    - Fast and simple"));
-      console.log(chalk.gray("    - No external dependencies\n"));
-      console.log(chalk.white("  ChromaDB (hybrid):"));
-      console.log(chalk.gray("    - Semantic search across your context"));
-      console.log(chalk.gray("    - Cloud backup capability"));
-      console.log(chalk.gray("    - Requires ChromaDB API key\n"));
+      console.log(
+        chalk.gray("SQLite (default) is fast and requires no setup.")
+      );
+      console.log(
+        chalk.gray("ChromaDB adds semantic search but requires an API key.\n")
+      );
       const { enableChroma } = await inquirer.prompt([
         {
           type: "confirm",
           name: "enableChroma",
-          message: "Enable ChromaDB for semantic search? (requires API key)",
+          message: "Enable ChromaDB for semantic search?",
           default: false
         }
       ]);
       if (enableChroma) {
         await promptAndEnableChromaDB();
-      } else {
-        console.log(chalk.gray("Using SQLite-only storage mode."));
       }
     }
     const dbPath = join(dbDir, "context.db");
     const db = new Database(dbPath);
     new FrameManager(db, "cli-project");
     logger.info("StackMemory initialized successfully", { projectRoot });
+    console.log(chalk.green("\n[OK] StackMemory initialized"));
+    console.log(chalk.gray(`    Project: ${projectRoot}`));
+    console.log(chalk.gray(`    Storage: SQLite (local)`));
+    console.log(chalk.cyan("\nNext steps:"));
+    console.log(
+      chalk.white("  1. stackmemory setup-mcp") + chalk.gray("  # Configure Claude Code integration")
+    );
+    console.log(
+      chalk.white("  2. stackmemory status") + chalk.gray("     # Check status")
+    );
     console.log(
-      chalk.green("\n[OK] StackMemory initialized in"),
-      projectRoot
+      chalk.white("  3. stackmemory doctor") + chalk.gray("     # Diagnose issues")
     );
-    storageConfig = loadStorageConfig();
-    console.log(chalk.gray(`Storage mode: ${getStorageModeDescription()}`));
     db.close();
   } catch (error) {
     logger.error("Failed to initialize StackMemory", error);
+    console.error(chalk.red("\n[ERROR] Initialization failed"));
+    console.error(chalk.gray(`  Reason: ${error.message}`));
     console.error(
-      chalk.red("[ERROR] Initialization failed:"),
-      error.message
+      chalk.gray(
+        "  Fix: Ensure you have write permissions to the current directory"
+      )
     );
+    console.error(chalk.gray("  Run: stackmemory doctor"));
     process.exit(1);
   }
 });
@@ -517,6 +522,7 @@ if (isFeatureEnabled("whatsapp")) {
 program.addCommand(createRetrievalCommands());
 program.addCommand(createDiscoveryCommands());
 program.addCommand(createModelCommand());
+registerSetupCommands(program);
 program.command("dashboard").description("Display monitoring dashboard in terminal").option("-w, --watch", "Auto-refresh dashboard").option("-i, --interval <seconds>", "Refresh interval in seconds", "5").action(async (options) => {
   const { dashboardCommand } = await import("./commands/dashboard.js");
   await dashboardCommand.handler(options);