@ncukondo/reference-manager 0.17.1 → 0.18.0

package/dist/chunks/{index-wb8zgPJ0.js → index-BPhIwqHO.js}

@@ -8,7 +8,7 @@ import * as path from "node:path";
 import path__default, { extname, join, basename, dirname } from "node:path";
 import fs__default, { stat, rename, copyFile, readFile, unlink, readdir, mkdir, rm } from "node:fs/promises";
 import { g as getExtension, i as isValidFulltextFiles, a as isReservedRole, F as FULLTEXT_ROLE, b as formatToExtension, c as findFulltextFiles, d as findFulltextFile, e as extensionToFormat, B as BUILTIN_STYLES, h as getFulltextAttachmentTypes, s as startServerWithFileWatcher } from "./index-B4gr0P83.js";
-import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-Ds4s8UO0.js";
+import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-BtW20O32.js";
 import { spawn, spawnSync } from "node:child_process";
 import process$1, { stdin, stdout } from "node:process";
 import * as readline from "node:readline";
@@ -20,7 +20,7 @@ import "@citation-js/plugin-csl";
 import { ZodOptional as ZodOptional$2, z } from "zod";
 import { serve } from "@hono/node-server";
 const name = "@ncukondo/reference-manager";
-const version$1 = "0.17.1";
+const version$1 = "0.18.0";
 const description$1 = "A local reference management tool using CSL-JSON as the single source of truth";
 const packageJson = {
   name,
@@ -1056,27 +1056,27 @@ class OperationsLibrary {
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-DWEWWvFO.js");
+    const { addAttachment: addAttachment2 } = await import("./index-iYPq6D80.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-DWEWWvFO.js");
+    const { listAttachments: listAttachments2 } = await import("./index-iYPq6D80.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-DWEWWvFO.js");
+    const { getAttachment: getAttachment2 } = await import("./index-iYPq6D80.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-DWEWWvFO.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-iYPq6D80.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-DWEWWvFO.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-iYPq6D80.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-DWEWWvFO.js");
+    const { openAttachment: openAttachment2 } = await import("./index-iYPq6D80.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1092,8 +1092,8 @@ class ServerClient {
    * @returns Array of CSL items
    */
   async getAll() {
-    const url = `${this.baseUrl}/api/references`;
-    const response = await fetch(url);
+    const url2 = `${this.baseUrl}/api/references`;
+    const response = await fetch(url2);
     if (!response.ok) {
       throw new Error(await response.text());
     }
@@ -1107,8 +1107,8 @@ class ServerClient {
    */
   async find(identifier, options = {}) {
     const { idType = "id" } = options;
-    const url = idType === "uuid" ? `${this.baseUrl}/api/references/uuid/${encodeURIComponent(identifier)}` : `${this.baseUrl}/api/references/id/${encodeURIComponent(identifier)}`;
-    const response = await fetch(url);
+    const url2 = idType === "uuid" ? `${this.baseUrl}/api/references/uuid/${encodeURIComponent(identifier)}` : `${this.baseUrl}/api/references/id/${encodeURIComponent(identifier)}`;
+    const response = await fetch(url2);
     if (response.status === 404) {
       return void 0;
     }
@@ -1126,8 +1126,8 @@ class ServerClient {
    * @returns The added CSL item (with generated ID and UUID)
    */
   async add(item) {
-    const url = `${this.baseUrl}/api/references`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/references`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(item)
@@ -1146,8 +1146,8 @@ class ServerClient {
    */
   async update(identifier, updates, options) {
     const { idType = "id", onIdCollision } = options ?? {};
-    const url = idType === "uuid" ? `${this.baseUrl}/api/references/uuid/${encodeURIComponent(identifier)}` : `${this.baseUrl}/api/references/id/${encodeURIComponent(identifier)}`;
-    const response = await fetch(url, {
+    const url2 = idType === "uuid" ? `${this.baseUrl}/api/references/uuid/${encodeURIComponent(identifier)}` : `${this.baseUrl}/api/references/id/${encodeURIComponent(identifier)}`;
+    const response = await fetch(url2, {
       method: "PUT",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify({ updates, onIdCollision })
@@ -1171,8 +1171,8 @@ class ServerClient {
    */
   async remove(identifier, options = {}) {
     const { idType = "id" } = options;
-    const url = idType === "uuid" ? `${this.baseUrl}/api/references/uuid/${encodeURIComponent(identifier)}` : `${this.baseUrl}/api/references/id/${encodeURIComponent(identifier)}`;
-    const response = await fetch(url, {
+    const url2 = idType === "uuid" ? `${this.baseUrl}/api/references/uuid/${encodeURIComponent(identifier)}` : `${this.baseUrl}/api/references/id/${encodeURIComponent(identifier)}`;
+    const response = await fetch(url2, {
       method: "DELETE"
     });
     if (!response.ok && response.status !== 404) {
@@ -1203,8 +1203,8 @@ class ServerClient {
    * @returns Result containing added, failed, and skipped items
    */
   async import(inputs, options) {
-    const url = `${this.baseUrl}/api/add`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/add`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify({ inputs, options })
@@ -1220,8 +1220,8 @@ class ServerClient {
    * @returns Cite result with per-identifier results
    */
   async cite(options) {
-    const url = `${this.baseUrl}/api/cite`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/cite`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options)
@@ -1237,8 +1237,8 @@ class ServerClient {
    * @returns List result with raw CslItem[]
    */
   async list(options) {
-    const url = `${this.baseUrl}/api/list`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/list`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options ?? {})
@@ -1254,8 +1254,8 @@ class ServerClient {
    * @returns Search result with raw CslItem[]
    */
   async search(options) {
-    const url = `${this.baseUrl}/api/search`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/search`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options)
@@ -1274,8 +1274,8 @@ class ServerClient {
    * @returns Result of the add operation
    */
   async attachAdd(options) {
-    const url = `${this.baseUrl}/api/attachments/add`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/attachments/add`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options)
@@ -1291,8 +1291,8 @@ class ServerClient {
    * @returns List of attachments
    */
   async attachList(options) {
-    const url = `${this.baseUrl}/api/attachments/list`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/attachments/list`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options)
@@ -1308,8 +1308,8 @@ class ServerClient {
    * @returns Attachment file path or content
    */
   async attachGet(options) {
-    const url = `${this.baseUrl}/api/attachments/get`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/attachments/get`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options)
@@ -1325,8 +1325,8 @@ class ServerClient {
    * @returns Result of the detach operation
    */
   async attachDetach(options) {
-    const url = `${this.baseUrl}/api/attachments/detach`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/attachments/detach`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options)
@@ -1342,8 +1342,8 @@ class ServerClient {
    * @returns Sync result
    */
   async attachSync(options) {
-    const url = `${this.baseUrl}/api/attachments/sync`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/attachments/sync`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options)
@@ -1359,8 +1359,8 @@ class ServerClient {
    * @returns Result of the open operation
    */
   async attachOpen(options) {
-    const url = `${this.baseUrl}/api/attachments/open`;
-    const response = await fetch(url, {
+    const url2 = `${this.baseUrl}/api/attachments/open`;
+    const response = await fetch(url2, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify(options)
@@ -1458,7 +1458,9 @@ function parseJsonInput(input) {
   }
 }
 async function loadConfigWithOverrides(options) {
-  const config2 = await loadConfig();
+  const config2 = await loadConfig({
+    ...options.config && { configPath: options.config }
+  });
   const overrides = {};
   if (options.library) {
     overrides.library = options.library;
@@ -1566,6 +1568,35 @@ function exitWithError(message, code2 = ExitCode.ERROR) {
 `);
   setExitCode(code2);
 }
+function resolveClipboardEnabled(options, config2, isTui) {
+  if (options.clipboard !== void 0) {
+    return options.clipboard;
+  }
+  const envVal = process.env.REFERENCE_MANAGER_CLIPBOARD_AUTO_COPY;
+  if (envVal !== void 0) {
+    return envVal === "1" || envVal === "true";
+  }
+  if (isTui) {
+    return config2.cli.tui.clipboardAutoCopy;
+  }
+  return false;
+}
+async function writeOutputWithClipboard(output, clipboardEnabled, quiet) {
+  process.stdout.write(`${output}
+`);
+  if (clipboardEnabled) {
+    const { copyToClipboard } = await import("./clipboard-KXwFSJ4w.js");
+    const result = await copyToClipboard(output);
+    if (!quiet) {
+      if (result.success) {
+        process.stderr.write("Copied to clipboard\n");
+      } else {
+        process.stderr.write(`Warning: Failed to copy to clipboard: ${result.error}
+`);
+      }
+    }
+  }
+}
 async function executeAttachOpen(options, context) {
   const operationOptions = {
     identifier: options.identifier,
@@ -1762,9 +1793,9 @@ function formatSyncPreview(result) {
 function getAttachExitCode(result) {
   return result.success ? 0 : 1;
 }
-async function executeInteractiveSelect$1(context, config2) {
+async function executeInteractiveSelect$2(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-O0PY7CRU.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DcClzkw2.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -1776,7 +1807,7 @@ async function resolveIdentifier(identifierArg, context, config2) {
     return identifierArg;
   }
   if (isTTY()) {
-    return executeInteractiveSelect$1(context, config2);
+    return executeInteractiveSelect$2(context, config2);
   }
   const stdinId = await readIdentifierFromStdin();
   if (!stdinId) {
@@ -1894,6 +1925,7 @@ async function handleAttachOpenAction(identifierArg, filenameArg, options, globa
       process.stdout.write(`${result.path}
 `);
       setExitCode(ExitCode.SUCCESS);
+      return;
     }
     if (shouldUseInteractive) {
       await runInteractiveMode(
@@ -2080,6 +2112,27 @@ async function handleAttachSyncAction(identifierArg, options, globalOpts) {
     setExitCode(ExitCode.INTERNAL_ERROR);
   }
 }
+const attach = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
+  __proto__: null,
+  executeAttachAdd,
+  executeAttachDetach,
+  executeAttachGet,
+  executeAttachList,
+  executeAttachOpen,
+  executeAttachSync,
+  formatAttachAddOutput,
+  formatAttachDetachOutput,
+  formatAttachListOutput,
+  formatAttachOpenOutput,
+  formatAttachSyncOutput,
+  getAttachExitCode,
+  handleAttachAddAction,
+  handleAttachDetachAction,
+  handleAttachGetAction,
+  handleAttachListAction,
+  handleAttachOpenAction,
+  handleAttachSyncAction
+}, Symbol.toStringTag, { value: "Module" }));
 async function validateOptions$2(options) {
   if (options.output && !["text", "html", "rtf"].includes(options.output)) {
     throw new Error(`Invalid output format '${options.output}'. Must be one of: text, html, rtf`);
@@ -2137,8 +2190,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-BigPRCTh.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-DF5kX4G6.js");
+  const { runCiteFlow } = await import("./index-B5W5srUa.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-D0bgalgW.js");
   const { search } = await import("./file-watcher-CrsNHUpz.js").then((n) => n.z);
   const { tokenize } = await import("./file-watcher-CrsNHUpz.js").then((n) => n.y);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
@@ -2180,8 +2233,10 @@ async function handleCiteAction(identifiers, options, globalOpts) {
     const config2 = await loadConfigWithOverrides({ ...globalOpts, ...options });
     const context = await createExecutionContext(config2, Library.load);
     let result;
+    let isTuiMode = false;
     if (identifiers.length === 0) {
       if (isTTY()) {
+        isTuiMode = true;
         result = await executeInteractiveCite(options, context, config2);
       } else {
         const stdinIds = await readIdentifiersFromStdin();
@@ -2199,8 +2254,8 @@ async function handleCiteAction(identifiers, options, globalOpts) {
     }
     const output = formatCiteOutput(result);
     if (output) {
-      process.stdout.write(`${output}
-`);
+      const clipboardEnabled = resolveClipboardEnabled(globalOpts, config2, isTuiMode);
+      await writeOutputWithClipboard(output, clipboardEnabled, config2.logLevel === "silent");
     }
     const errors2 = formatCiteErrors(result);
     if (errors2) {
@@ -2219,6 +2274,7 @@ const ENV_OVERRIDE_MAP = {
   REFERENCE_MANAGER_ATTACHMENTS_DIR: "attachments.directory",
   REFERENCE_MANAGER_CLI_DEFAULT_LIMIT: "cli.default_limit",
   REFERENCE_MANAGER_MCP_DEFAULT_LIMIT: "mcp.default_limit",
+  REFERENCE_MANAGER_CLIPBOARD_AUTO_COPY: "cli.tui.clipboard_auto_copy",
   PUBMED_EMAIL: "pubmed.email",
   PUBMED_API_KEY: "pubmed.api_key"
 };
@@ -2275,6 +2331,12 @@ const CONFIG_KEY_REGISTRY = [
     description: "Default format",
     enumValues: ["text", "html", "rtf"]
   },
+  {
+    key: "citation.default_key_format",
+    type: "enum",
+    description: "Default citation key format",
+    enumValues: ["pandoc", "latex"]
+  },
   // pubmed section
   { key: "pubmed.email", type: "string", description: "Email for PubMed API", optional: true },
   { key: "pubmed.api_key", type: "string", description: "API key for PubMed", optional: true },
@@ -2309,6 +2371,11 @@ const CONFIG_KEY_REGISTRY = [
     type: "integer",
     description: "Search debounce delay (ms)"
   },
+  {
+    key: "cli.tui.clipboard_auto_copy",
+    type: "boolean",
+    description: "Auto-copy TUI output to clipboard"
+  },
   // cli.edit section
   {
     key: "cli.edit.default_format",
@@ -6681,7 +6748,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-O0PY7CRU.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DcClzkw2.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -6747,6 +6814,12 @@ async function handleEditAction(identifiers, options, globalOpts) {
     setExitCode(ExitCode.INTERNAL_ERROR);
   }
 }
+const edit = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
+  __proto__: null,
+  executeEditCommand,
+  formatEditOutput,
+  handleEditAction
+}, Symbol.toStringTag, { value: "Module" }));
 const ALIAS = Symbol.for("yaml.alias");
 const DOC = Symbol.for("yaml.document");
 const MAP = Symbol.for("yaml.map");
@@ -10327,9 +10400,9 @@ function formatFulltextOpenOutput(result) {
 function getFulltextExitCode(result) {
   return result.success ? 0 : 1;
 }
-async function executeInteractiveSelect(context, config2) {
+async function executeInteractiveSelect$1(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-O0PY7CRU.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DcClzkw2.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -10366,7 +10439,7 @@ async function handleFulltextAttachAction(identifierArg, filePathArg, options, g
         setExitCode(ExitCode.ERROR);
         return;
       }
-      identifier = await executeInteractiveSelect(context, config2);
+      identifier = await executeInteractiveSelect$1(context, config2);
     }
     const { type: type2, filePath } = parseFulltextAttachTypeAndPath(filePathArg, options);
     const stdinContent = !filePath && type2 ? await readStdinBuffer() : void 0;
@@ -10413,7 +10486,7 @@ async function handleFulltextGetAction(identifierArg, options, globalOpts) {
     if (identifierArg) {
       identifier = identifierArg;
     } else if (isTTY()) {
-      identifier = await executeInteractiveSelect(context, config2);
+      identifier = await executeInteractiveSelect$1(context, config2);
     } else {
       const stdinId = await readIdentifierFromStdin();
       if (!stdinId) {
@@ -10450,7 +10523,7 @@ async function handleFulltextDetachAction(identifierArg, options, globalOpts) {
     if (identifierArg) {
       identifier = identifierArg;
     } else if (isTTY()) {
-      identifier = await executeInteractiveSelect(context, config2);
+      identifier = await executeInteractiveSelect$1(context, config2);
     } else {
       const stdinId = await readIdentifierFromStdin();
       if (!stdinId) {
@@ -10490,7 +10563,7 @@ async function handleFulltextOpenAction(identifierArg, options, globalOpts) {
     if (identifierArg) {
       identifier = identifierArg;
     } else if (isTTY()) {
-      identifier = await executeInteractiveSelect(context, config2);
+      identifier = await executeInteractiveSelect$1(context, config2);
     } else {
       const stdinId = await readIdentifierFromStdin();
       if (!stdinId) {
@@ -10520,6 +10593,22 @@ async function handleFulltextOpenAction(identifierArg, options, globalOpts) {
     setExitCode(ExitCode.INTERNAL_ERROR);
   }
 }
+const fulltext = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
+  __proto__: null,
+  executeFulltextAttach,
+  executeFulltextDetach,
+  executeFulltextGet,
+  executeFulltextOpen,
+  formatFulltextAttachOutput,
+  formatFulltextDetachOutput,
+  formatFulltextGetOutput,
+  formatFulltextOpenOutput,
+  getFulltextExitCode,
+  handleFulltextAttachAction,
+  handleFulltextDetachAction,
+  handleFulltextGetAction,
+  handleFulltextOpenAction
+}, Symbol.toStringTag, { value: "Module" }));
 function formatAuthor(author) {
   const family = author.family || "";
   const givenInitial = author.given ? `${author.given.charAt(0)}.` : "";
@@ -10572,6 +10661,10 @@ function formatItems(items2, format2) {
       return items2.filter(
         (item) => Boolean(item.custom?.uuid)
       ).map((item) => item.custom.uuid);
+    case "pandoc-key":
+      return items2.map((item) => `@${item.id}`);
+    case "latex-key":
+      return items2.map((item) => `\\cite{${item.id}}`);
     default:
       return items2.map((item) => formatPretty([item]));
   }
@@ -10610,11 +10703,14 @@ const VALID_LIST_SORT_FIELDS = /* @__PURE__ */ new Set([
   "mod",
   "pub"
 ]);
-function getOutputFormat$1(options) {
+function getOutputFormat$1(options, defaultKeyFormat) {
   if (options.output) {
     if (options.output === "ids") return "ids-only";
     return options.output;
   }
+  if (options.key) return defaultKeyFormat === "latex" ? "latex-key" : "pandoc-key";
+  if (options.pandocKey) return "pandoc-key";
+  if (options.latexKey) return "latex-key";
   if (options.json) return "json";
   if (options.idsOnly) return "ids-only";
   if (options.uuidOnly) return "uuid";
@@ -10622,12 +10718,18 @@ function getOutputFormat$1(options) {
   return "pretty";
 }
 function validateOptions$1(options) {
-  const outputOptions = [options.json, options.idsOnly, options.uuidOnly, options.bibtex].filter(
-    Boolean
-  );
+  const outputOptions = [
+    options.json,
+    options.idsOnly,
+    options.uuidOnly,
+    options.bibtex,
+    options.key,
+    options.pandocKey,
+    options.latexKey
+  ].filter(Boolean);
   if (outputOptions.length > 1) {
     throw new Error(
-      "Multiple output formats specified. Only one of --json, --ids-only, --uuid-only, --bibtex can be used."
+      "Multiple output formats specified. Only one of --json, --ids-only, --uuid-only, --bibtex, --key, --pandoc-key, --latex-key can be used."
     );
   }
   if (options.output && outputOptions.length > 0) {
@@ -10662,8 +10764,8 @@ async function executeList(options, context) {
     ...pickDefined(options, ["order", "limit", "offset"])
   });
 }
-function formatListOutput(result, options) {
-  const format2 = getOutputFormat$1(options);
+function formatListOutput(result, options, defaultKeyFormat) {
+  const format2 = getOutputFormat$1(options, defaultKeyFormat);
   if (format2 === "json") {
     return JSON.stringify({
       items: result.items,
@@ -15480,10 +15582,10 @@ const $ZodURL = /* @__PURE__ */ $constructor("$ZodURL", (inst, def) => {
   inst._zod.check = (payload) => {
     try {
       const trimmed = payload.value.trim();
-      const url = new URL(trimmed);
+      const url2 = new URL(trimmed);
       if (def.hostname) {
         def.hostname.lastIndex = 0;
-        if (!def.hostname.test(url.hostname)) {
+        if (!def.hostname.test(url2.hostname)) {
           payload.issues.push({
             code: "invalid_format",
             format: "url",
@@ -15497,7 +15599,7 @@ const $ZodURL = /* @__PURE__ */ $constructor("$ZodURL", (inst, def) => {
       }
       if (def.protocol) {
         def.protocol.lastIndex = 0;
-        if (!def.protocol.test(url.protocol.endsWith(":") ? url.protocol.slice(0, -1) : url.protocol)) {
+        if (!def.protocol.test(url2.protocol.endsWith(":") ? url2.protocol.slice(0, -1) : url2.protocol)) {
           payload.issues.push({
             code: "invalid_format",
             format: "url",
@@ -15510,7 +15612,7 @@ const $ZodURL = /* @__PURE__ */ $constructor("$ZodURL", (inst, def) => {
         }
       }
       if (def.normalize) {
-        payload.value = url.href;
+        payload.value = url2.href;
       } else {
         payload.value = trimmed;
       }
@@ -31388,7 +31490,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-O0PY7CRU.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-DcClzkw2.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -31485,6 +31587,15 @@ async function handleRemoveAction(identifierArg, options, globalOpts) {
     handleRemoveError(error, identifierArg, outputFormat);
   }
 }
+const remove = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
+  __proto__: null,
+  confirmRemoveIfNeeded,
+  executeRemove,
+  formatFulltextWarning,
+  formatRemoveOutput,
+  getFulltextAttachmentTypes,
+  handleRemoveAction
+}, Symbol.toStringTag, { value: "Module" }));
 const VALID_SEARCH_SORT_FIELDS = /* @__PURE__ */ new Set([
   "created",
   "updated",
@@ -31497,11 +31608,14 @@ const VALID_SEARCH_SORT_FIELDS = /* @__PURE__ */ new Set([
   "pub",
   "rel"
 ]);
-function getOutputFormat(options) {
+function getOutputFormat(options, defaultKeyFormat) {
   if (options.output) {
     if (options.output === "ids") return "ids-only";
     return options.output;
   }
+  if (options.key) return defaultKeyFormat === "latex" ? "latex-key" : "pandoc-key";
+  if (options.pandocKey) return "pandoc-key";
+  if (options.latexKey) return "latex-key";
   if (options.json) return "json";
   if (options.idsOnly) return "ids-only";
   if (options.uuidOnly) return "uuid";
@@ -31509,12 +31623,18 @@ function getOutputFormat(options) {
   return "pretty";
 }
 function validateOptions(options) {
-  const outputOptions = [options.json, options.idsOnly, options.uuidOnly, options.bibtex].filter(
-    Boolean
-  );
+  const outputOptions = [
+    options.json,
+    options.idsOnly,
+    options.uuidOnly,
+    options.bibtex,
+    options.key,
+    options.pandocKey,
+    options.latexKey
+  ].filter(Boolean);
   if (outputOptions.length > 1) {
     throw new Error(
-      "Multiple output formats specified. Only one of --json, --ids-only, --uuid-only, --bibtex can be used."
+      "Multiple output formats specified. Only one of --json, --ids-only, --uuid-only, --bibtex, --key, --pandoc-key, --latex-key can be used."
     );
   }
   if (options.output && outputOptions.length > 0) {
@@ -31550,8 +31670,8 @@ async function executeSearch(options, context) {
     ...pickDefined(options, ["order", "limit", "offset"])
   });
 }
-function formatSearchOutput(result, options) {
-  const format2 = getOutputFormat(options);
+function formatSearchOutput(result, options, defaultKeyFormat) {
+  const format2 = getOutputFormat(options, defaultKeyFormat);
   if (format2 === "json") {
     return JSON.stringify({
       items: result.items,
@@ -31580,11 +31700,14 @@ function validateInteractiveOptions(options) {
     options.json,
     options.idsOnly,
     options.uuidOnly,
-    options.bibtex
+    options.bibtex,
+    options.key,
+    options.pandocKey,
+    options.latexKey
   ].filter(Boolean);
   if (outputOptions.length > 0) {
     throw new Error(
-      "TUI mode cannot be combined with output format options (--output, --json, --ids-only, --uuid-only, --bibtex)"
+      "TUI mode cannot be combined with output format options (--output, --json, --ids-only, --uuid-only, --bibtex, --key, --pandoc-key, --latex-key)"
     );
   }
 }
@@ -31592,7 +31715,7 @@ async function executeInteractiveSearch(options, context, config2) {
   validateInteractiveOptions(options);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runSearchFlow } = await import("./index-BigPRCTh.js");
+  const { runSearchFlow } = await import("./index-B5W5srUa.js");
   const { search } = await import("./file-watcher-CrsNHUpz.js").then((n) => n.z);
   const { tokenize } = await import("./file-watcher-CrsNHUpz.js").then((n) => n.y);
   checkTTY();
@@ -31605,14 +31728,110 @@ async function executeInteractiveSearch(options, context, config2) {
   const result = await withAlternateScreen2(
     () => runSearchFlow(allReferences, searchFn, {
       limit: tuiConfig.limit,
-      debounceMs: tuiConfig.debounceMs
+      debounceMs: tuiConfig.debounceMs,
+      defaultKeyFormat: config2.citation.defaultKeyFormat,
+      defaultStyle: config2.citation.defaultStyle
     })
   );
+  if (result.selectedItems && !result.cancelled) {
+    const { isSideEffectAction } = await import("./action-menu-D8gSe1YM.js");
+    if (isSideEffectAction(result.action)) {
+      await executeSideEffectAction(result.action, result.selectedItems, context, config2);
+      return { output: "", cancelled: false, action: result.action };
+    }
+  }
   return {
     output: result.output,
-    cancelled: result.cancelled
+    cancelled: result.cancelled,
+    action: result.action
   };
 }
+async function executeSideEffectAction(action, items2, context, config2) {
+  switch (action) {
+    case "open-url": {
+      const { resolveDefaultUrl: resolveDefaultUrl2 } = await Promise.resolve().then(() => url);
+      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-BtW20O32.js").then((n) => n.j);
+      const item = items2[0];
+      if (!item) return;
+      const url$1 = resolveDefaultUrl2(item);
+      if (url$1) {
+        await openWithSystemApp2(url$1);
+      } else {
+        process.stderr.write(`No URL available for ${item.id}
+`);
+      }
+      break;
+    }
+    case "open-fulltext": {
+      const { executeFulltextOpen: executeFulltextOpen2 } = await Promise.resolve().then(() => fulltext);
+      const item = items2[0];
+      if (!item) return;
+      const result = await executeFulltextOpen2(
+        {
+          identifier: item.id,
+          fulltextDirectory: config2.attachments.directory
+        },
+        context
+      );
+      if (!result.success) {
+        process.stderr.write(`${result.error}
+`);
+      }
+      break;
+    }
+    case "manage-attachments": {
+      const { executeAttachOpen: executeAttachOpen2 } = await Promise.resolve().then(() => attach);
+      const item = items2[0];
+      if (!item) return;
+      await executeAttachOpen2(
+        {
+          identifier: item.id,
+          attachmentsDirectory: config2.attachments.directory
+        },
+        context
+      );
+      break;
+    }
+    case "edit": {
+      const { executeEditCommand: executeEditCommand2 } = await Promise.resolve().then(() => edit);
+      await executeEditCommand2(
+        {
+          identifiers: items2.map((i) => i.id),
+          format: config2.cli.edit.defaultFormat
+        },
+        context
+      );
+      break;
+    }
+    case "remove": {
+      const {
+        executeRemove: executeRemove2,
+        confirmRemoveIfNeeded: confirmRemoveIfNeeded2,
+        getFulltextAttachmentTypes: getFulltextAttachmentTypes2,
+        formatRemoveOutput: formatRemoveOutput2
+      } = await Promise.resolve().then(() => remove);
+      for (const item of items2) {
+        const hasFulltext = getFulltextAttachmentTypes2(item).length > 0;
+        const confirmed = await confirmRemoveIfNeeded2(item, hasFulltext, false);
+        if (!confirmed) {
+          process.stderr.write("Cancelled.\n");
+          continue;
+        }
+        const result = await executeRemove2(
+          {
+            identifier: item.id,
+            fulltextDirectory: config2.attachments.directory,
+            deleteFulltext: hasFulltext
+          },
+          context
+        );
+        process.stderr.write(`${formatRemoveOutput2(result, item.id)}
+`);
+      }
+      break;
+    }
+  }
+}
 async function serverStart(options) {
   const existingStatus = await serverStatus(options.portfilePath);
   if (existingStatus !== null) {
@@ -31906,7 +32125,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-O0PY7CRU.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DcClzkw2.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32021,6 +32240,231 @@ async function handleUpdateAction(identifierArg, file, options, globalOpts) {
 function collectSetOption(value, previous) {
   return previous.concat([value]);
 }
+function buildDoiUrl(doi) {
+  return `https://doi.org/${doi}`;
+}
+function buildPubmedUrl(pmid) {
+  return `https://pubmed.ncbi.nlm.nih.gov/${pmid}/`;
+}
+function buildPmcUrl(pmcid) {
+  return `https://www.ncbi.nlm.nih.gov/pmc/articles/${pmcid}/`;
+}
+function resolveAllUrls(item) {
+  const urls = [];
+  if (item.DOI) {
+    urls.push(buildDoiUrl(item.DOI));
+  }
+  if (item.URL) {
+    urls.push(item.URL);
+  }
+  if (item.PMID) {
+    urls.push(buildPubmedUrl(item.PMID));
+  }
+  if (item.PMCID) {
+    urls.push(buildPmcUrl(item.PMCID));
+  }
+  const additionalUrls = item.custom?.additional_urls;
+  if (additionalUrls && additionalUrls.length > 0) {
+    urls.push(...additionalUrls);
+  }
+  return urls;
+}
+function resolveDefaultUrl(item) {
+  if (item.DOI) {
+    return buildDoiUrl(item.DOI);
+  }
+  if (item.URL) {
+    return item.URL;
+  }
+  if (item.PMID) {
+    return buildPubmedUrl(item.PMID);
+  }
+  if (item.PMCID) {
+    return buildPmcUrl(item.PMCID);
+  }
+  const additionalUrls = item.custom?.additional_urls;
+  if (additionalUrls && additionalUrls.length > 0) {
+    return additionalUrls[0] ?? null;
+  }
+  return null;
+}
+function resolveUrlByType(item, type2) {
+  switch (type2) {
+    case "doi":
+      return item.DOI ? buildDoiUrl(item.DOI) : null;
+    case "url":
+      return item.URL ?? null;
+    case "pubmed":
+      return item.PMID ? buildPubmedUrl(item.PMID) : null;
+    case "pmcid":
+      return item.PMCID ? buildPmcUrl(item.PMCID) : null;
+  }
+}
+const url = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
+  __proto__: null,
+  resolveAllUrls,
+  resolveDefaultUrl,
+  resolveUrlByType
+}, Symbol.toStringTag, { value: "Module" }));
+function getUrlTypeFilter(options) {
+  if (options.doi) return "doi";
+  if (options.pubmed) return "pubmed";
+  if (options.pmcid) return "pmcid";
+  if (options.default) return "default";
+  if (options.open) return "default";
+  return null;
+}
+function getFilterLabel(filter) {
+  switch (filter) {
+    case "doi":
+      return "DOI";
+    case "pubmed":
+      return "PubMed";
+    case "pmcid":
+      return "PMC";
+    case "url":
+      return "URL";
+    case "default":
+      return "default";
+  }
+}
+function resolveUrlsForItem(item, id2, filter) {
+  if (filter === null) {
+    const urls = resolveAllUrls(item);
+    if (urls.length === 0) {
+      return { id: id2, urls: [], error: `No URLs available for ${id2}` };
+    }
+    return { id: id2, urls };
+  }
+  if (filter === "default") {
+    const url22 = resolveDefaultUrl(item);
+    if (!url22) {
+      return { id: id2, urls: [], error: `No URLs available for ${id2}` };
+    }
+    return { id: id2, urls: [url22] };
+  }
+  const url2 = resolveUrlByType(item, filter);
+  if (!url2) {
+    return { id: id2, urls: [], error: `No ${getFilterLabel(filter)} URL for ${id2}` };
+  }
+  return { id: id2, urls: [url2] };
+}
+async function executeUrlCommand(identifiers, options, context) {
+  const filter = getUrlTypeFilter(options);
+  const findOptions = options.uuid ? { idType: "uuid" } : void 0;
+  const results = [];
+  for (const identifier of identifiers) {
+    const item = await context.library.find(identifier, findOptions);
+    if (!item) {
+      results.push({ id: identifier, urls: [], error: `Reference not found: ${identifier}` });
+      continue;
+    }
+    const result = resolveUrlsForItem(item, identifier, filter);
+    results.push(result);
+  }
+  if (options.open) {
+    const firstSuccess = results.find((r) => r.urls.length > 0);
+    if (firstSuccess?.urls[0]) {
+      try {
+        await openWithSystemApp(firstSuccess.urls[0]);
+      } catch (error) {
+        return {
+          results,
+          openError: `Failed to open URL: ${error instanceof Error ? error.message : String(error)}`
+        };
+      }
+    }
+  }
+  return { results };
+}
+function hasFilter(options) {
+  return Boolean(options.default || options.doi || options.pubmed || options.pmcid || options.open);
+}
+function formatUrlOutput(result, options) {
+  const successResults = result.results.filter((r) => r.urls.length > 0);
+  if (successResults.length === 0) {
+    return "";
+  }
+  const filtered = hasFilter(options);
+  if (filtered || successResults.length === 1) {
+    const lines2 = [];
+    for (const r of successResults) {
+      for (const url2 of r.urls) {
+        lines2.push(url2);
+      }
+    }
+    return lines2.join("\n");
+  }
+  const lines = [];
+  for (const r of successResults) {
+    for (const url2 of r.urls) {
+      lines.push(`${r.id}	${url2}`);
+    }
+  }
+  return lines.join("\n");
+}
+function formatUrlErrors(result) {
+  const errorMessages = result.results.filter((r) => r.error).map((r) => `Error: ${r.error}`);
+  if (result.openError) {
+    errorMessages.push(`Error: ${result.openError}`);
+  }
+  return errorMessages.join("\n");
+}
+function getUrlExitCode(result) {
+  if (result.openError) return ExitCode.ERROR;
+  const hasSuccess = result.results.some((r) => r.urls.length > 0);
+  const hasError = result.results.some((r) => r.error);
+  if (hasSuccess) return ExitCode.SUCCESS;
+  if (hasError) return ExitCode.ERROR;
+  return ExitCode.SUCCESS;
+}
+async function executeInteractiveSelect(context, config2) {
+  const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
+  const { selectReferencesOrExit } = await import("./reference-select-DcClzkw2.js");
+  const allReferences = await context.library.getAll();
+  const identifiers = await withAlternateScreen2(
+    () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
+  );
+  return identifiers[0] ?? "";
+}
+async function handleUrlAction(identifiers, options, globalOpts) {
+  try {
+    const config2 = await loadConfigWithOverrides({ ...globalOpts, ...options });
+    const context = await createExecutionContext(config2, Library.load);
+    let resolvedIdentifiers;
+    let isTuiMode = false;
+    if (identifiers && identifiers.length > 0) {
+      resolvedIdentifiers = identifiers;
+    } else if (isTTY()) {
+      isTuiMode = true;
+      const selected = await executeInteractiveSelect(context, config2);
+      resolvedIdentifiers = [selected];
+    } else {
+      const stdinId = await readIdentifierFromStdin();
+      if (!stdinId) {
+        exitWithError("Identifier is required");
+        return;
+      }
+      resolvedIdentifiers = [stdinId];
+    }
+    const result = await executeUrlCommand(resolvedIdentifiers, options, context);
+    const output = formatUrlOutput(result, options);
+    if (output) {
+      const clipboardEnabled = resolveClipboardEnabled(globalOpts, config2, isTuiMode);
+      await writeOutputWithClipboard(output, clipboardEnabled, config2.logLevel === "silent");
+    }
+    const errors2 = formatUrlErrors(result);
+    if (errors2) {
+      process.stderr.write(`${errors2}
+`);
+    }
+    setExitCode(getUrlExitCode(result));
+  } catch (error) {
+    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}
+`);
+    setExitCode(ExitCode.INTERNAL_ERROR);
+  }
+}
 const SEARCH_SORT_FIELDS = searchSortFieldSchema.options;
 const SORT_ORDERS = sortOrderSchema.options;
 const CITATION_OUTPUT_FORMATS = ["text", "html", "rtf"];
@@ -32305,7 +32749,7 @@ function registerCompletionCommand(program) {
 function createProgram() {
   const program = new Command();
   program.name("reference-manager").version(packageJson.version).description(packageJson.description);
-  program.option("--library <path>", "Override library file path").option("--log-level <level>", "Override log level (silent|info|debug)").option("--config <path>", "Use specific config file").option("--quiet", "Suppress all non-error output").option("--verbose", "Enable verbose output").option("--no-backup", "Disable backup creation").option("--backup-dir <path>", "Override backup directory").option("--attachments-dir <path>", "Override attachments directory");
+  program.option("--library <path>", "Override library file path").option("--log-level <level>", "Override log level (silent|info|debug)").option("--config <path>", "Use specific config file").option("--quiet", "Suppress all non-error output").option("--verbose", "Enable verbose output").option("--no-backup", "Disable backup creation").option("--backup-dir <path>", "Override backup directory").option("--attachments-dir <path>", "Override attachments directory").option("--clipboard", "Copy output to system clipboard").option("--no-clipboard", "Disable clipboard copy");
   registerListCommand(program);
   registerSearchCommand(program);
   registerExportCommand(program);
@@ -32318,6 +32762,7 @@ function createProgram() {
   registerFulltextCommand(program);
   registerAttachCommand(program);
   registerMcpCommand(program);
+  registerUrlCommand(program);
   registerConfigCommand(program);
   registerCompletionCommand(program);
   return program;
@@ -32326,12 +32771,12 @@ async function handleListAction(options, program) {
   try {
     const globalOpts = program.opts();
     const config2 = await loadConfigWithOverrides({ ...globalOpts, ...options });
+    const clipboardEnabled = resolveClipboardEnabled(globalOpts, config2, false);
     const context = await createExecutionContext(config2, Library.load);
     const result = await executeList(options, context);
-    const output = formatListOutput(result, options);
+    const output = formatListOutput(result, options, config2.citation.defaultKeyFormat);
     if (output) {
-      process.stdout.write(`${output}
-`);
+      await writeOutputWithClipboard(output, clipboardEnabled, config2.logLevel === "silent");
     }
     setExitCode(ExitCode.SUCCESS);
   } catch (error) {
@@ -32339,7 +32784,10 @@ async function handleListAction(options, program) {
   }
 }
 function registerListCommand(program) {
-  program.command("list").description("List all references in the library").option("-o, --output <format>", "Output format: pretty|json|bibtex|ids|uuid").option("--json", "Alias for --output json").option("--bibtex", "Alias for --output bibtex").option("--ids-only", "Alias for --output ids").option("--uuid-only", "Alias for --output uuid").option("--sort <field>", "Sort by field: created|updated|published|author|title").option("--order <order>", "Sort order: asc|desc").option("-n, --limit <n>", "Maximum number of results", Number.parseInt).option("--offset <n>", "Number of results to skip", Number.parseInt).action(async (options) => {
+  program.command("list").description("List all references in the library").option(
+    "-o, --output <format>",
+    "Output format: pretty|json|bibtex|ids|uuid|pandoc-key|latex-key"
+  ).option("--json", "Alias for --output json").option("--bibtex", "Alias for --output bibtex").option("--ids-only", "Alias for --output ids").option("--uuid-only", "Alias for --output uuid").option("-k, --key", "Output citation keys (uses citation.default_key_format config)").option("--pandoc-key", "Alias for --output pandoc-key").option("--latex-key", "Alias for --output latex-key").option("--sort <field>", "Sort by field: created|updated|published|author|title").option("--order <order>", "Sort order: asc|desc").option("-n, --limit <n>", "Maximum number of results", Number.parseInt).option("--offset <n>", "Number of results to skip", Number.parseInt).action(async (options) => {
     await handleListAction(options, program);
   });
 }
@@ -32347,12 +32795,12 @@ async function handleExportAction(ids, options, program) {
   try {
     const globalOpts = program.opts();
     const config2 = await loadConfigWithOverrides({ ...globalOpts, ...options });
+    const clipboardEnabled = resolveClipboardEnabled(globalOpts, config2, false);
     const context = await createExecutionContext(config2, Library.load);
     const result = await executeExport({ ...options, ids }, context);
     const output = formatExportOutput(result, { ...options, ids });
     if (output) {
-      process.stdout.write(`${output}
-`);
+      await writeOutputWithClipboard(output, clipboardEnabled, config2.logLevel === "silent");
     }
     if (result.notFound.length > 0) {
       for (const id2 of result.notFound) {
@@ -32380,17 +32828,25 @@ async function handleSearchAction(query, options, program) {
     if (options.tui) {
       const result2 = await executeInteractiveSearch({ ...options, query }, context, config2);
       if (result2.output) {
-        process.stdout.write(`${result2.output}
-`);
+        const clipboardEnabled = resolveClipboardEnabled(globalOpts, config2, true);
+        await writeOutputWithClipboard(
+          result2.output,
+          clipboardEnabled,
+          config2.logLevel === "silent"
+        );
       }
       setExitCode(ExitCode.SUCCESS);
       return;
     }
     const result = await executeSearch({ ...options, query }, context);
-    const output = formatSearchOutput(result, { ...options, query });
+    const output = formatSearchOutput(
+      result,
+      { ...options, query },
+      config2.citation.defaultKeyFormat
+    );
     if (output) {
-      process.stdout.write(`${output}
-`);
+      const clipboardEnabled = resolveClipboardEnabled(globalOpts, config2, false);
+      await writeOutputWithClipboard(output, clipboardEnabled, config2.logLevel === "silent");
     }
     setExitCode(ExitCode.SUCCESS);
   } catch (error) {
@@ -32400,7 +32856,10 @@ async function handleSearchAction(query, options, program) {
   }
 }
 function registerSearchCommand(program) {
-  program.command("search").description("Search references").argument("[query]", "Search query (required unless using --tui)").option("-t, --tui", "Enable TUI (interactive) search mode").option("-o, --output <format>", "Output format: pretty|json|bibtex|ids|uuid").option("--json", "Alias for --output json").option("--bibtex", "Alias for --output bibtex").option("--ids-only", "Alias for --output ids").option("--uuid-only", "Alias for --output uuid").option("--sort <field>", "Sort by field: created|updated|published|author|title|relevance").option("--order <order>", "Sort order: asc|desc").option("-n, --limit <n>", "Maximum number of results", Number.parseInt).option("--offset <n>", "Number of results to skip", Number.parseInt).action(async (query, options) => {
+  program.command("search").description("Search references").argument("[query]", "Search query (required unless using --tui)").option("-t, --tui", "Enable TUI (interactive) search mode").option(
+    "-o, --output <format>",
+    "Output format: pretty|json|bibtex|ids|uuid|pandoc-key|latex-key"
+  ).option("--json", "Alias for --output json").option("--bibtex", "Alias for --output bibtex").option("--ids-only", "Alias for --output ids").option("--uuid-only", "Alias for --output uuid").option("-k, --key", "Output citation keys (uses citation.default_key_format config)").option("--pandoc-key", "Alias for --output pandoc-key").option("--latex-key", "Alias for --output latex-key").option("--sort <field>", "Sort by field: created|updated|published|author|title|relevance").option("--order <order>", "Sort order: asc|desc").option("-n, --limit <n>", "Maximum number of results", Number.parseInt).option("--offset <n>", "Number of results to skip", Number.parseInt).action(async (query, options) => {
     if (!options.tui && !query) {
       process.stderr.write("Error: Search query is required unless using --tui\n");
       setExitCode(ExitCode.ERROR);
@@ -32616,6 +33075,9 @@ function registerMcpCommand(program) {
 }
 function registerAttachCommand(program) {
   const attachCmd = program.command("attach").description("Manage file attachments for references");
+  attachCmd.argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
+    await handleAttachOpenAction(identifier, void 0, options, program.opts());
+  });
   attachCmd.command("open").description("Open attachments directory or specific file").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").argument("[filename]", "Specific file to open").option("--role <role>", "Open file by role").option("--print", "Output path instead of opening").option("--no-sync", "Skip interactive sync prompt").option("--uuid", "Interpret identifier as UUID").action(async (identifier, filename, options) => {
     await handleAttachOpenAction(identifier, filename, options, program.opts());
   });
@@ -32653,6 +33115,12 @@ function registerFulltextCommand(program) {
     await handleFulltextOpenAction(identifier, options, program.opts());
   });
 }
+function registerUrlCommand(program) {
+  program.command("url").description("Show URLs for references").argument("[identifiers...]", "Reference identifiers").option("--default", "Show only the best URL by priority").option("--doi", "Show only DOI URL").option("--pubmed", "Show only PubMed URL").option("--pmcid", "Show only PMC URL").option("--open", "Open URL in browser").option("--uuid", "Interpret identifiers as UUIDs").action(async (identifiers, options) => {
+    const globalOpts = program.opts();
+    await handleUrlAction(identifiers.length > 0 ? identifiers : void 0, options, globalOpts);
+  });
+}
 async function main(argv) {
   const program = createProgram();
   if (process.env.COMP_LINE) {
@@ -32670,6 +33138,7 @@ async function main(argv) {
 export {
   Select as S,
   addAttachment as a,
+  stringify as b,
   createProgram as c,
   detachAttachment as d,
   formatBibtex as f,
@@ -32681,4 +33150,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-wb8zgPJ0.js.map
+//# sourceMappingURL=index-BPhIwqHO.js.map