@ncukondo/search-hub 0.21.0 → 0.23.0

package/dist/cli/commands/init.js

@@ -3,8 +3,27 @@ import { join } from "node:path";
 import { stringify } from "@iarna/toml";
 import "../../config/schema.js";
 import { getDefaultConfig } from "../../config/defaults.js";
-import { getConfigDir, getDataDir } from "../../config/paths.js";
+import { getConfigDir, getProjectDir } from "../../config/paths.js";
 import "node:os";
+const FULL_PROVIDERS = ["pubmed", "eric", "arxiv", "scopus"];
+const MINIMAL_PROVIDERS = ["wos", "embase"];
+function buildProvidersToml(config) {
+  const providers = {};
+  for (const name of FULL_PROVIDERS) {
+    const p = config.providers[name];
+    providers[name] = {
+      enabled: p.enabled,
+      rate_limit: p.rate_limit,
+      timeout: p.timeout,
+      retries: p.retries,
+      max_results: p.max_results
+    };
+  }
+  for (const name of MINIMAL_PROVIDERS) {
+    providers[name] = { enabled: config.providers[name].enabled };
+  }
+  return providers;
+}
 async function exists(path) {
   try {
     await access(path, constants.F_OK);
@@ -13,11 +32,20 @@ async function exists(path) {
     return false;
   }
 }
-function configToToml(config) {
+function localConfigToToml(config) {
   return {
-    session: {
-      directory: config.session.directory
-    },
+    providers: buildProvidersToml(config),
+    integration: {
+      reference_manager: {
+        enabled: config.integration.reference_manager.enabled,
+        command: config.integration.reference_manager.command,
+        auto_register: config.integration.reference_manager.auto_register
+      }
+    }
+  };
+}
+function generateGlobalConfigContent(config) {
+  const tomlObj = {
     log: {
       level: config.log.level
     },
@@ -25,55 +53,7 @@ function configToToml(config) {
       color: config.output.color,
       progress_bar: config.output.progress_bar
     },
-    providers: {
-      pubmed: {
-        enabled: config.providers.pubmed.enabled,
-        api_key: config.providers.pubmed.api_key ?? "",
-        email: config.providers.pubmed.email ?? "",
-        rate_limit: config.providers.pubmed.rate_limit,
-        timeout: config.providers.pubmed.timeout,
-        retries: config.providers.pubmed.retries,
-        max_results: config.providers.pubmed.max_results
-      },
-      eric: {
-        enabled: config.providers.eric.enabled,
-        rate_limit: config.providers.eric.rate_limit,
-        timeout: config.providers.eric.timeout,
-        retries: config.providers.eric.retries,
-        max_results: config.providers.eric.max_results
-      },
-      arxiv: {
-        enabled: config.providers.arxiv.enabled,
-        rate_limit: config.providers.arxiv.rate_limit,
-        timeout: config.providers.arxiv.timeout,
-        retries: config.providers.arxiv.retries,
-        max_results: config.providers.arxiv.max_results
-      },
-      scopus: {
-        enabled: config.providers.scopus.enabled,
-        api_key: config.providers.scopus.api_key ?? "",
-        inst_token: config.providers.scopus.inst_token ?? "",
-        rate_limit: config.providers.scopus.rate_limit,
-        timeout: config.providers.scopus.timeout,
-        retries: config.providers.scopus.retries,
-        max_results: config.providers.scopus.max_results
-      },
-      wos: {
-        enabled: config.providers.wos.enabled,
-        api_key: config.providers.wos.api_key ?? "",
-        rate_limit: config.providers.wos.rate_limit,
-        timeout: config.providers.wos.timeout,
-        retries: config.providers.wos.retries,
-        max_results: config.providers.wos.max_results
-      },
-      embase: {
-        enabled: config.providers.embase.enabled,
-        rate_limit: config.providers.embase.rate_limit,
-        timeout: config.providers.embase.timeout,
-        retries: config.providers.embase.retries,
-        max_results: config.providers.embase.max_results
-      }
-    },
+    providers: buildProvidersToml(config),
     integration: {
       reference_manager: {
         enabled: config.integration.reference_manager.enabled,
@@ -82,54 +62,114 @@ function configToToml(config) {
       }
     }
   };
-}
-function generateConfigContent(config) {
-  const tomlObj = configToToml(config);
-  const header = `# search-hub configuration file
+  const header = `# search-hub global configuration
 # See: https://github.com/search-hub/search-hub for documentation
+#
+# [session]
+# directory = ""  # Override default session directory (empty = platform default)
+
+`;
+  const tomlContent = stringify(tomlObj);
+  const lines = tomlContent.split("\n");
+  const result = [];
+  for (const line of lines) {
+    result.push(line);
+    if (line.startsWith("[providers.pubmed]")) {
+      result.push('# api_key = ""    # Optional but recommended (NCBI E-utilities)');
+      result.push('# email = ""      # Required by NCBI for tracking');
+    } else if (line.startsWith("[providers.scopus]")) {
+      result.push('# api_key = ""    # Required for Scopus access');
+      result.push('# inst_token = "" # Optional institutional token');
+    } else if (line.startsWith("[providers.wos]")) {
+      result.push('# api_key = ""    # Required for Web of Science');
+    }
+  }
+  return header + result.join("\n");
+}
+function generateLocalConfigContent(config) {
+  const tomlObj = localConfigToToml(config);
+  const header = `# search-hub project configuration
+# Project-specific overrides (no secrets - use env vars or global config for API keys)
 
 `;
   return header + stringify(tomlObj);
 }
-async function init(options = {}) {
-  const {
-    configDir = getConfigDir(),
-    dataDir = getDataDir(),
-    force = false
-  } = options;
-  const configPath = join(configDir, "config.toml");
-  const sessionsDir = join(dataDir, "sessions");
-  const queriesDir = join(dataDir, "queries");
+async function initLocal(directory, force) {
+  const projectDir = getProjectDir(directory);
+  const configPath = join(projectDir, "config.toml");
+  const sessionsDir = join(projectDir, "sessions");
+  const queriesDir = join(projectDir, "queries");
   const result = {
     success: false,
     configPath,
-    sessionsDir,
-    configDir,
-    dataDir
+    projectDir
   };
-  if (await exists(configDir)) {
+  if (await exists(projectDir)) {
     if (!force) {
       return {
         ...result,
         alreadyExists: true,
-        message: `Configuration directory already exists at ${configDir}. Use --force to overwrite.`
+        message: `Project directory already exists at ${projectDir}. Use --force to overwrite.`
       };
     }
     result.overwritten = true;
   }
-  await mkdir(configDir, { recursive: true });
+  await mkdir(projectDir, { recursive: true });
   await mkdir(sessionsDir, { recursive: true });
   await mkdir(queriesDir, { recursive: true });
   const defaultConfig = getDefaultConfig();
-  defaultConfig.session.directory = sessionsDir;
-  const configContent = generateConfigContent(defaultConfig);
+  const configContent = generateLocalConfigContent(defaultConfig);
   await writeFile(configPath, configContent, "utf-8");
   return {
     ...result,
     success: true,
-    message: result.overwritten ? `Configuration overwritten at ${configDir}` : `Configuration created at ${configDir}`
+    message: result.overwritten ? `Project re-initialized at ${projectDir}` : `Project initialized at ${projectDir}`,
+    hints: [
+      "Set up global credentials: search-hub init --global",
+      "Or use environment variables: see search-hub config --env-vars",
+      "API keys can also be set via .env file in the project root"
+    ]
   };
 }
+async function initGlobal(configDir, force) {
+  const configPath = join(configDir, "config.toml");
+  const result = {
+    success: false,
+    configPath
+  };
+  if (await exists(configDir)) {
+    if (!force) {
+      return {
+        ...result,
+        alreadyExists: true,
+        message: `Global configuration already exists at ${configDir}. Use --force to overwrite.`
+      };
+    }
+    result.overwritten = true;
+  }
+  await mkdir(configDir, { recursive: true });
+  const defaultConfig = getDefaultConfig();
+  const configContent = generateGlobalConfigContent(defaultConfig);
+  await writeFile(configPath, configContent, "utf-8");
+  return {
+    ...result,
+    success: true,
+    message: result.overwritten ? `Global configuration overwritten at ${configDir}` : `Global configuration created at ${configDir}`,
+    hints: [
+      `Edit credentials: search-hub config --global set providers.pubmed.api_key <key>`,
+      `Or edit directly: ${configPath}`
+    ]
+  };
+}
+async function init(options = {}) {
+  const { force = false } = options;
+  if (options.global) {
+    const configDir = options.configDir ?? getConfigDir();
+    return initGlobal(configDir, force);
+  }
+  const directory = options.directory ?? process.cwd();
+  return initLocal(directory, force);
+}
 export {
   init
 };

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

@@ -1 +1 @@
-{"version":3,"file":"init.js","sources":["../../../src/cli/commands/init.ts"],"sourcesContent":["import { mkdir, writeFile, access, constants } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { stringify as stringifyToml } from '@iarna/toml';\nimport { getDefaultConfig } from '../../config/index.js';\nimport { getConfigDir, getDataDir } from '../../config/paths.js';\nimport type { Config } from '../../config/index.js';\n\n/**\n * Options for the init command.\n */\nexport interface InitOptions {\n  /** Config directory (defaults to platform-specific via getConfigDir()) */\n  configDir?: string;\n  /** Data directory (defaults to platform-specific via getDataDir()) */\n  dataDir?: string;\n  /** Force overwrite if directory already exists */\n  force?: boolean;\n}\n\n/**\n * Result of the init command.\n */\nexport interface InitResult {\n  /** Whether initialization was successful */\n  success: boolean;\n  /** Path to the created config file */\n  configPath: string;\n  /** Path to the sessions directory */\n  sessionsDir: string;\n  /** Path to the config directory */\n  configDir: string;\n  /** Path to the data directory */\n  dataDir: string;\n  /** Whether files already existed (only when success=false) */\n  alreadyExists?: boolean;\n  /** Whether existing files were overwritten (only when force=true) */\n  overwritten?: boolean;\n  /** Message describing the result */\n  message?: string;\n}\n\n/**\n * Check if a file or directory exists.\n */\nasync function exists(path: string): Promise<boolean> {\n  try {\n    await access(path, constants.F_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Convert Config to TOML-compatible object.\n * Removes undefined values and converts to the expected format.\n */\nfunction configToToml(config: Config): Record<string, unknown> {\n  return {\n    session: {\n      directory: config.session.directory,\n    },\n    log: {\n      level: config.log.level,\n    },\n    output: {\n      color: config.output.color,\n      progress_bar: config.output.progress_bar,\n    },\n    providers: {\n      pubmed: {\n        enabled: config.providers.pubmed.enabled,\n        api_key: config.providers.pubmed.api_key ?? '',\n        email: config.providers.pubmed.email ?? '',\n        rate_limit: config.providers.pubmed.rate_limit,\n        timeout: config.providers.pubmed.timeout,\n        retries: config.providers.pubmed.retries,\n        max_results: config.providers.pubmed.max_results,\n      },\n      eric: {\n        enabled: config.providers.eric.enabled,\n        rate_limit: config.providers.eric.rate_limit,\n        timeout: config.providers.eric.timeout,\n        retries: config.providers.eric.retries,\n        max_results: config.providers.eric.max_results,\n      },\n      arxiv: {\n        enabled: config.providers.arxiv.enabled,\n        rate_limit: config.providers.arxiv.rate_limit,\n        timeout: config.providers.arxiv.timeout,\n        retries: config.providers.arxiv.retries,\n        max_results: config.providers.arxiv.max_results,\n      },\n      scopus: {\n        enabled: config.providers.scopus.enabled,\n        api_key: config.providers.scopus.api_key ?? '',\n        inst_token: config.providers.scopus.inst_token ?? '',\n        rate_limit: config.providers.scopus.rate_limit,\n        timeout: config.providers.scopus.timeout,\n        retries: config.providers.scopus.retries,\n        max_results: config.providers.scopus.max_results,\n      },\n      wos: {\n        enabled: config.providers.wos.enabled,\n        api_key: config.providers.wos.api_key ?? '',\n        rate_limit: config.providers.wos.rate_limit,\n        timeout: config.providers.wos.timeout,\n        retries: config.providers.wos.retries,\n        max_results: config.providers.wos.max_results,\n      },\n      embase: {\n        enabled: config.providers.embase.enabled,\n        rate_limit: config.providers.embase.rate_limit,\n        timeout: config.providers.embase.timeout,\n        retries: config.providers.embase.retries,\n        max_results: config.providers.embase.max_results,\n      },\n    },\n    integration: {\n      reference_manager: {\n        enabled: config.integration.reference_manager.enabled,\n        command: config.integration.reference_manager.command,\n        auto_register: config.integration.reference_manager.auto_register,\n      },\n    },\n  };\n}\n\n/**\n * Generate TOML config file content with comments.\n */\nfunction generateConfigContent(config: Config): string {\n  const tomlObj = configToToml(config);\n  const header = `# search-hub configuration file\n# See: https://github.com/search-hub/search-hub for documentation\n\n`;\n  return header + stringifyToml(tomlObj as Parameters<typeof stringifyToml>[0]);\n}\n\n/**\n * Initialize the search-hub configuration directory.\n *\n * Creates:\n * - Config directory with config.toml\n * - Data directory with sessions/ subdirectory\n *\n * On Linux (XDG):\n * - ~/.config/search-hub/config.toml\n * - ~/.local/share/search-hub/sessions/\n */\nexport async function init(options: InitOptions = {}): Promise<InitResult> {\n  const {\n    configDir = getConfigDir(),\n    dataDir = getDataDir(),\n    force = false,\n  } = options;\n\n  const configPath = join(configDir, 'config.toml');\n  const sessionsDir = join(dataDir, 'sessions');\n  const queriesDir = join(dataDir, 'queries');\n\n  const result: InitResult = {\n    success: false,\n    configPath,\n    sessionsDir,\n    configDir,\n    dataDir,\n  };\n\n  // Check if config directory already exists\n  if (await exists(configDir)) {\n    if (!force) {\n      return {\n        ...result,\n        alreadyExists: true,\n        message: `Configuration directory already exists at ${configDir}. 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+{"version":3,"file":"init.js","sources":["../../../src/cli/commands/init.ts"],"sourcesContent":["import { mkdir, writeFile, access, constants } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { stringify as stringifyToml } from '@iarna/toml';\nimport { getDefaultConfig } from '../../config/index.js';\nimport { getConfigDir, getProjectDir } from '../../config/paths.js';\nimport type { Config, ProviderConfig } from '../../config/index.js';\n\n/** Provider names that carry full settings (rate_limit, timeout, etc.) in generated configs. */\nconst FULL_PROVIDERS = ['pubmed', 'eric', 'arxiv', 'scopus'] as const;\n/** Provider names that only carry the enabled flag in generated configs. */\nconst MINIMAL_PROVIDERS = ['wos', 'embase'] as const;\n\n/**\n * Build the providers TOML object from a Config, excluding secrets.\n */\nfunction buildProvidersToml(config: Config): Record<string, Partial<ProviderConfig>> {\n  const providers: Record<string, Partial<ProviderConfig>> = {};\n  for (const name of FULL_PROVIDERS) {\n    const p = config.providers[name];\n    providers[name] = {\n      enabled: p.enabled,\n      rate_limit: p.rate_limit,\n      timeout: p.timeout,\n      retries: p.retries,\n      max_results: p.max_results,\n    };\n  }\n  for (const name of MINIMAL_PROVIDERS) {\n    providers[name] = { enabled: config.providers[name].enabled };\n  }\n  return providers;\n}\n\n/**\n * Options for the init command.\n */\nexport interface InitOptions {\n  /** Directory to create .search-hub/ in (defaults to cwd) */\n  directory?: string;\n  /** Initialize global config instead of local project */\n  global?: boolean;\n  /** Config directory for global init (defaults to platform-specific via getConfigDir()) */\n  configDir?: string;\n  /** Force overwrite if directory already exists */\n  force?: boolean;\n}\n\n/**\n * Result of the init command.\n */\nexport interface InitResult {\n  /** Whether initialization was successful */\n  success: boolean;\n  /** Path to the created config file */\n  configPath: string;\n  /** Path to the .search-hub/ project directory (local init only) */\n  projectDir?: string;\n  /** Whether files already existed (only when success=false) */\n  alreadyExists?: boolean;\n  /** Whether existing files were overwritten (only when force=true) */\n  overwritten?: boolean;\n  /** Message describing the result */\n  message?: string;\n  /** Actionable hints for the user */\n  hints?: string[];\n}\n\n/**\n * Check if a file or directory exists.\n */\nasync function exists(path: string): Promise<boolean> {\n  try {\n    await access(path, constants.F_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Convert Config to TOML-compatible object for local project config.\n * Excludes secrets (api_key, email, inst_token).\n */\nfunction localConfigToToml(config: Config): Record<string, unknown> {\n  return {\n    providers: buildProvidersToml(config),\n    integration: {\n      reference_manager: {\n        enabled: config.integration.reference_manager.enabled,\n        command: config.integration.reference_manager.command,\n        auto_register: config.integration.reference_manager.auto_register,\n      },\n    },\n  };\n}\n\n/**\n * Generate TOML config content for global config with credential hints as comments.\n */\nfunction generateGlobalConfigContent(config: Config): string {\n  const tomlObj = {\n    log: {\n      level: config.log.level,\n    },\n    output: {\n      color: config.output.color,\n      progress_bar: config.output.progress_bar,\n    },\n    providers: buildProvidersToml(config),\n    integration: {\n      reference_manager: {\n        enabled: config.integration.reference_manager.enabled,\n        command: config.integration.reference_manager.command,\n        auto_register: config.integration.reference_manager.auto_register,\n      },\n    },\n  };\n\n  const header = `# search-hub global configuration\n# See: https://github.com/search-hub/search-hub for documentation\n#\n# [session]\n# directory = \"\"  # Override default session directory (empty = platform default)\n\n`;\n\n  const tomlContent = stringifyToml(tomlObj as Parameters<typeof stringifyToml>[0]);\n\n  // Add credential hints as comments after provider sections\n  const lines = tomlContent.split('\\n');\n  const result: string[] = [];\n  for (const line of lines) {\n    result.push(line);\n    if (line.startsWith('[providers.pubmed]')) {\n      result.push('# api_key = \"\"    # Optional but recommended (NCBI E-utilities)');\n      result.push('# email = \"\"      # Required by NCBI for tracking');\n    } else if (line.startsWith('[providers.scopus]')) {\n      result.push('# api_key = \"\"    # Required for Scopus access');\n      result.push('# inst_token = \"\" # Optional institutional token');\n    } else if (line.startsWith('[providers.wos]')) {\n      result.push('# api_key = \"\"    # Required for Web of Science');\n    }\n  }\n\n  return header + result.join('\\n');\n}\n\n/**\n * Generate TOML config file content for local project config.\n */\nfunction generateLocalConfigContent(config: Config): string {\n  const tomlObj = localConfigToToml(config);\n  const header = `# search-hub project configuration\n# Project-specific overrides (no secrets - use env vars or global config for API keys)\n\n`;\n  return header + stringifyToml(tomlObj as Parameters<typeof stringifyToml>[0]);\n}\n\n/**\n * Initialize a local .search-hub/ project directory.\n */\nasync function initLocal(directory: string, force: boolean): Promise<InitResult> {\n  const projectDir = getProjectDir(directory);\n  const configPath = join(projectDir, 'config.toml');\n  const sessionsDir = join(projectDir, 'sessions');\n  const queriesDir = join(projectDir, 'queries');\n\n  const result: InitResult = {\n    success: false,\n    configPath,\n    projectDir,\n  };\n\n  // Check if .search-hub/ already exists\n  if (await exists(projectDir)) {\n    if (!force) {\n      return {\n        ...result,\n        alreadyExists: true,\n        message: `Project directory already exists at ${projectDir}. Use --force to overwrite.`,\n      };\n    }\n    result.overwritten = true;\n  }\n\n  // Create directories\n  await mkdir(projectDir, { recursive: true });\n  await mkdir(sessionsDir, { recursive: true });\n  await mkdir(queriesDir, { recursive: true });\n\n  // Generate and write local config (no secrets)\n  const defaultConfig = getDefaultConfig();\n  const configContent = generateLocalConfigContent(defaultConfig);\n  await writeFile(configPath, configContent, 'utf-8');\n\n  return {\n    ...result,\n    success: true,\n    message: result.overwritten\n      ? `Project re-initialized at ${projectDir}`\n      : `Project initialized at ${projectDir}`,\n    hints: [\n      'Set up global credentials: search-hub init --global',\n      'Or use environment variables: see search-hub config --env-vars',\n      'API keys can also be set via .env file in the project root',\n    ],\n  };\n}\n\n/**\n * Initialize the global search-hub configuration.\n */\nasync function initGlobal(configDir: string, force: boolean): Promise<InitResult> {\n  const configPath = join(configDir, 'config.toml');\n\n  const result: InitResult = {\n    success: false,\n    configPath,\n  };\n\n  // Check if config directory already exists\n  if (await exists(configDir)) {\n    if (!force) {\n      return {\n        ...result,\n        alreadyExists: true,\n        message: `Global configuration already exists at ${configDir}. 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package/dist/cli/entry-bun.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=entry-bun.d.ts.map

package/dist/cli/entry-bun.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"entry-bun.d.ts","sourceRoot":"","sources":["../../src/cli/entry-bun.ts"],"names":[],"mappings":""}

package/dist/cli/index.d.ts.map

@@ -1 +1 @@
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package/dist/cli/index.js

@@ -4,11 +4,12 @@ import { Command, Option } from "commander";
 import { VERSION } from "../version.js";
 import { init } from "./commands/init.js";
 import { EXIT_CODES } from "./exit-codes.js";
-import { loadConfig, saveConfig } from "../config/loader.js";
+import { loadConfig, loadTomlFile, saveConfig } from "../config/loader.js";
 import "../config/schema.js";
 import { getDefaultConfig } from "../config/defaults.js";
-import { getDefaultConfigPath } from "../config/paths.js";
-import { viewConfig, viewConfigKey, setConfigKey } from "./commands/config.js";
+import { isInsideProject, getDefaultConfigPath, getLocalConfigPath } from "../config/paths.js";
+import { formatEnvVars, viewConfigAllOrigins, viewConfigFiltered, viewConfig, formatShowOrigin, getNestedValue, viewConfigKey, resolveWriteScope, checkSecretKeyWarning, setConfigKey, parseValue, setNestedValue } from "./commands/config.js";
+import { ENV_VAR_MAP } from "../config/env.js";
 import { detectSchemaLink, validateQueryCommand, formatValidateResult, formatVocabValidationOutput, hasVocabErrors } from "./commands/query/validate.js";
 import { MeSHLookupClient } from "../query/mesh-lookup.js";
 import { RateLimiter } from "../providers/base/rate-limiter.js";
@@ -82,16 +83,23 @@ Quick Start:
   $ search-hub search my-search --count-only     # Check hit counts
   $ search-hub search my-search                  # Execute search
   $ search-hub results <session>                 # Review titles`);
-  program.command("init").description("Initialize configuration directory").option("-f, --force", "overwrite existing configuration", false).addHelpText("after", `
+  program.command("init").description("Initialize search-hub project (local) or global config").option("-f, --force", "overwrite existing configuration", false).option("-g, --global", "initialize global config instead of local project", false).addHelpText("after", `
 Examples:
-  $ search-hub init                 # Initialize with default settings
+  $ search-hub init                 # Create .search-hub/ in current directory
+  $ search-hub init --global        # Create global config (~/.config/search-hub/)
   $ search-hub init --force         # Overwrite existing configuration`).action(async (options) => {
     const globalOpts = program.opts();
     try {
-      const result = await init({ force: options.force });
+      const result = await init({ force: options.force, global: options.global });
       if (!globalOpts.quiet) {
         if (result.success) {
           console.log(result.message);
+          if (result.hints) {
+            console.log("");
+            for (const hint of result.hints) {
+              console.log(`  ${hint}`);
+            }
+          }
         } else {
           console.error(result.message);
         }
@@ -107,13 +115,91 @@ Examples:
       process.exitCode = EXIT_CODES.GENERAL_ERROR;
     }
   });
-  program.command("config").description("View and edit configuration").argument("[key]", "configuration key to view or set").argument("[value]", "value to set for the key").addHelpText("after", `
+  program.command("config").description("View and edit configuration").argument("[key]", "configuration key to view or set").argument("[value]", "value to set for the key").option("--global", "Use global config scope").option("--local", "Use local project config scope").option("--show-origin", "Show where each config value comes from").option("--list", "List all config values (default when no key given)").option("--env-vars", "Show environment variable mappings").option("--force", "Force write even for secret keys in local scope").addHelpText("after", `
 Examples:
-  $ search-hub config                              # Show all config
-  $ search-hub config providers.pubmed             # Show PubMed config
-  $ search-hub config providers.pubmed.api_key KEY # Set API key`).action(async (key, value) => {
+  $ search-hub config                                     # Show all config
+  $ search-hub config providers.pubmed                    # Show PubMed config
+  $ search-hub config --global providers.pubmed.api_key KEY # Set API key globally
+  $ search-hub config --local output.color false          # Set in project config
+  $ search-hub config --show-origin providers.pubmed.api_key # Show value origin
+  $ search-hub config --list --global                     # Show only global values
+  $ search-hub config --env-vars                          # Show env var mappings`).action(async (key, value, cmdOpts) => {
     const globalOpts = program.opts();
     try {
+      if (cmdOpts.envVars) {
+        if (!globalOpts.quiet) {
+          console.log(formatEnvVars());
+        }
+        process.exitCode = EXIT_CODES.SUCCESS;
+        return;
+      }
+      const inProject = await isInsideProject();
+      if (cmdOpts.list || !key && !value) {
+        if (cmdOpts.global && cmdOpts.local) {
+          if (!globalOpts.quiet) {
+            console.error("Error: --global and --local are mutually exclusive");
+          }
+          process.exitCode = EXIT_CODES.CONFIG_ERROR;
+          return;
+        }
+        if (cmdOpts.showOrigin && !cmdOpts.global && !cmdOpts.local) {
+          let config22;
+          try {
+            config22 = await loadConfig(
+              globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}
+            );
+          } catch {
+            config22 = getDefaultConfig();
+          }
+          const globalPath = expandPath(getDefaultConfigPath());
+          const globalCfg = await loadTomlFile(globalPath);
+          const localPath = inProject ? getLocalConfigPath() : "";
+          const localCfg = inProject ? await loadTomlFile(localPath) : {};
+          if (!globalOpts.quiet) {
+            console.log(viewConfigAllOrigins(
+              config22,
+              ENV_VAR_MAP,
+              localCfg,
+              localPath,
+              globalCfg,
+              globalPath
+            ));
+          }
+        } else if (cmdOpts.global) {
+          const globalConfig = await loadTomlFile(expandPath(getDefaultConfigPath()));
+          if (!globalOpts.quiet) {
+            const output = viewConfigFiltered(globalConfig);
+            console.log(output || "(no global config values set)");
+          }
+        } else if (cmdOpts.local) {
+          if (!inProject) {
+            if (!globalOpts.quiet) {
+              console.error('Error: --local requires a project directory (.search-hub/). Run "search-hub init" first.');
+            }
+            process.exitCode = EXIT_CODES.CONFIG_ERROR;
+            return;
+          }
+          const localConfig = await loadTomlFile(getLocalConfigPath());
+          if (!globalOpts.quiet) {
+            const output = viewConfigFiltered(localConfig);
+            console.log(output || "(no local config values set)");
+          }
+        } else {
+          let config22;
+          try {
+            config22 = await loadConfig(
+              globalOpts.config ? { explicitConfigPath: globalOpts.config } : {}
+            );
+          } catch {
+            config22 = getDefaultConfig();
+          }
+          if (!globalOpts.quiet) {
+            console.log(viewConfig(config22));
+          }
+        }
+        process.exitCode = EXIT_CODES.SUCCESS;
+        return;
+      }
       let config2;
       try {
         config2 = await loadConfig(
@@ -122,29 +208,103 @@ Examples:
       } catch {
         config2 = getDefaultConfig();
       }
-      if (!key) {
-        if (!globalOpts.quiet) {
-          console.log(viewConfig(config2));
+      if (key && !value) {
+        if (cmdOpts.showOrigin) {
+          const envEntry = Object.entries(ENV_VAR_MAP).find(([, path]) => path === key);
+          if (envEntry && process.env[envEntry[0]] !== void 0) {
+            if (!globalOpts.quiet) {
+              console.log(formatShowOrigin(key, process.env[envEntry[0]], "env", envEntry[0]));
+            }
+            process.exitCode = EXIT_CODES.SUCCESS;
+            return;
+          }
+          if (inProject) {
+            const localConfig = await loadTomlFile(getLocalConfigPath());
+            const localVal = getNestedValue(localConfig, key);
+            if (localVal !== void 0) {
+              if (!globalOpts.quiet) {
+                console.log(formatShowOrigin(key, String(localVal), "local", getLocalConfigPath()));
+              }
+              process.exitCode = EXIT_CODES.SUCCESS;
+              return;
+            }
+          }
+          const globalConfigPath = expandPath(getDefaultConfigPath());
+          const globalConfig = await loadTomlFile(globalConfigPath);
+          const globalVal = getNestedValue(globalConfig, key);
+          if (globalVal !== void 0) {
+            if (!globalOpts.quiet) {
+              console.log(formatShowOrigin(key, String(globalVal), "global", globalConfigPath));
+            }
+            process.exitCode = EXIT_CODES.SUCCESS;
+            return;
+          }
+          const mergedVal = getNestedValue(config2, key);
+          if (mergedVal !== void 0) {
+            if (!globalOpts.quiet) {
+              console.log(formatShowOrigin(key, String(mergedVal), "default", ""));
+            }
+          } else {
+            if (!globalOpts.quiet) {
+              console.error(`Error: Key "${key}" not found in configuration`);
+            }
+            process.exitCode = EXIT_CODES.CONFIG_ERROR;
+            return;
+          }
+        } else {
+          const result = viewConfigKey(config2, key);
+          if (result.success) {
+            if (!globalOpts.quiet) {
+              console.log(result.value);
+            }
+          } else {
+            if (!globalOpts.quiet) {
+              console.error(`Error: ${result.error}`);
+            }
+            process.exitCode = EXIT_CODES.CONFIG_ERROR;
+            return;
+          }
         }
-      } else if (!value) {
-        const result = viewConfigKey(config2, key);
-        if (result.success) {
+      } else if (key && value) {
+        const scopeResult = resolveWriteScope({
+          global: !!cmdOpts.global,
+          local: !!cmdOpts.local,
+          insideProject: inProject
+        });
+        if (scopeResult.scope === "error") {
           if (!globalOpts.quiet) {
-            console.log(result.value);
+            console.error(`Error: ${scopeResult.error}`);
           }
-        } else {
+          process.exitCode = EXIT_CODES.CONFIG_ERROR;
+          return;
+        }
+        const warning = checkSecretKeyWarning(key, scopeResult.scope);
+        if (warning && !cmdOpts.force) {
           if (!globalOpts.quiet) {
-            console.error(`Error: ${result.error}`);
+            console.error(`Error: ${warning} Use --force to override.`);
           }
           process.exitCode = EXIT_CODES.CONFIG_ERROR;
           return;
         }
-      } else {
         const result = setConfigKey(config2, key, value);
         if (result.success) {
-          const configPath = globalOpts.config ? expandPath(globalOpts.config) : getDefaultConfigPath();
+          let configPath;
+          if (globalOpts.config) {
+            configPath = expandPath(globalOpts.config);
+          } else if (scopeResult.scope === "local") {
+            configPath = expandPath(getLocalConfigPath());
+          } else {
+            configPath = expandPath(getDefaultConfigPath());
+          }
           try {
-            await saveConfig(config2, { path: configPath });
+            const existing = await loadTomlFile(configPath);
+            const existingValue = getNestedValue(
+              config2,
+              key
+            );
+            const parsedValue = parseValue(value, existingValue);
+            setNestedValue(existing, key, parsedValue);
+            await saveConfig(existing, { path: configPath });
             if (!globalOpts.quiet) {
               console.log(`Set ${key} = ${result.value}`);
               console.log(`Saved to ${configPath}`);
@@ -2204,11 +2364,18 @@ async function main() {
 const currentFile = fileURLToPath(import.meta.url);
 const executedFile = process.argv[1];
 if (executedFile) {
-  if (realpathSync(executedFile) === realpathSync(currentFile)) {
-    main().catch((error) => {
-      console.error("Fatal error:", error);
-      process.exit(EXIT_CODES.GENERAL_ERROR);
-    });
+  try {
+    if (realpathSync(executedFile) === realpathSync(currentFile)) {
+      main().catch((error) => {
+        console.error("Fatal error:", error);
+        process.exit(EXIT_CODES.GENERAL_ERROR);
+      });
+    }
+  } catch (e) {
+    const code = e instanceof Error ? e.code : void 0;
+    if (code !== "ENOENT" && code !== "ERR_INVALID_ARG_TYPE") {
+      console.error("[debug] Unexpected error resolving entry path:", e);
+    }
   }
 }
 export {