@ncukondo/reference-manager 0.25.0 → 0.27.0

package/dist/chunks/{index-QTYx5RaF.js → index-B8ST0WLa.js}

@@ -5,7 +5,7 @@ import { promises, readFileSync, existsSync, mkdirSync, writeFileSync } from "no
 import * as os from "node:os";
 import * as path from "node:path";
 import path__default, { join, basename, dirname } from "node:path";
-import { n as normalizePathForOutput, d as deleteDirectoryIfEmpty, p as parseFilename, i as isReservedRole, e as ensureDirectory, a as addAttachment, R as RESERVED_ROLES, b as generateFilename, c as findFulltextFiles, h as findFulltextFile, j as extensionToFormat, k as fulltextAttach, l as fulltextGet, m as fulltextDiscover, o as fulltextFetch, q as fulltextConvert, r as getExtension, s as getDefaultExportFromCjs, B as BUILTIN_STYLES, t as getFulltextAttachmentTypes, u as startServerWithFileWatcher } from "./index-D2HsxXnK.js";
+import { n as normalizePathForOutput, d as deleteDirectoryIfEmpty, p as parseFilename, i as isReservedRole, e as ensureDirectory, a as addAttachment, R as RESERVED_ROLES, b as generateFilename, c as findFulltextFiles, h as findFulltextFile, j as extensionToFormat, k as fulltextAttach, l as fulltextDiscover, m as fulltextFetch, o as fulltextConvert, q as fulltextGet, r as getExtension, s as getDefaultExportFromCjs, B as BUILTIN_STYLES, t as getFulltextAttachmentTypes, u as startServerWithFileWatcher } from "./index-DUpYvm-W.js";
 import { readFile, unlink, stat, readdir, rename } from "node:fs/promises";
 import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-B-fte1uv.js";
 import { spawn, spawnSync } from "node:child_process";
@@ -19,7 +19,7 @@ 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 = "0.25.0";
+const version$1 = "0.27.0";
 const description$1 = "A local reference management tool using CSL-JSON as the single source of truth";
 const packageJson = {
   name,
@@ -902,15 +902,15 @@ class OperationsLibrary {
   }
   // High-level operations
   async search(options) {
-    const { searchReferences } = await import("./index-D2HsxXnK.js").then((n) => n.E);
+    const { searchReferences } = await import("./index-DUpYvm-W.js").then((n) => n.E);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-D2HsxXnK.js").then((n) => n.D);
+    const { listReferences } = await import("./index-DUpYvm-W.js").then((n) => n.D);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-D2HsxXnK.js").then((n) => n.C);
+    const { citeReferences } = await import("./index-DUpYvm-W.js").then((n) => n.C);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -921,36 +921,36 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-D2HsxXnK.js").then((n) => n.z);
+    const { addReferences } = await import("./index-DUpYvm-W.js").then((n) => n.z);
     return addReferences(inputs, this.library, options ?? {});
   }
   async check(options) {
-    const { checkReferences } = await import("./index-D2HsxXnK.js").then((n) => n.A);
+    const { checkReferences } = await import("./index-DUpYvm-W.js").then((n) => n.A);
     return checkReferences(this.library, options);
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-PQkbePWV.js");
+    const { addAttachment: addAttachment2 } = await import("./index-F4gbDFWf.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-PQkbePWV.js");
+    const { listAttachments: listAttachments2 } = await import("./index-F4gbDFWf.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-PQkbePWV.js");
+    const { getAttachment: getAttachment2 } = await import("./index-F4gbDFWf.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-PQkbePWV.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-F4gbDFWf.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-PQkbePWV.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-F4gbDFWf.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-PQkbePWV.js");
+    const { openAttachment: openAttachment2 } = await import("./index-F4gbDFWf.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1806,7 +1806,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Qpgt9cbN.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DtzpiOvp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2312,9 +2312,12 @@ function buildCheckOptions(options, appConfig) {
   if (options.days !== void 0) {
     opOptions.skipDays = options.days;
   }
-  if (options.noSave) {
+  if (options.save === false) {
     opOptions.save = false;
   }
+  if (options.metadata === false) {
+    opOptions.metadata = false;
+  }
   if (appConfig) {
     const pubmed = {};
     if (appConfig.pubmed.email) pubmed.email = appConfig.pubmed.email;
@@ -2332,45 +2335,109 @@ async function executeCheck(options, context, appConfig) {
 function getStatusLabel(result) {
   if (result.status === "skipped") return "[SKIPPED]";
   if (result.status === "ok") return "[OK]";
-  const finding = result.findings[0];
-  if (!finding) return "[WARNING]";
-  switch (finding.type) {
+  if (result.findings.length === 0) return "[WARNING]";
+  const priorityOrder = {
+    retracted: 0,
+    concern: 1,
+    version_changed: 2,
+    metadata_mismatch: 3,
+    metadata_outdated: 4
+  };
+  let highestPriority = Number.MAX_SAFE_INTEGER;
+  let highestType = "unknown";
+  for (const finding of result.findings) {
+    const priority = priorityOrder[finding.type] ?? 99;
+    if (priority < highestPriority) {
+      highestPriority = priority;
+      highestType = finding.type;
+    }
+  }
+  switch (highestType) {
     case "retracted":
       return "[RETRACTED]";
     case "concern":
       return "[CONCERN]";
     case "version_changed":
       return "[VERSION]";
-    case "metadata_changed":
-      return "[METADATA]";
+    case "metadata_mismatch":
+      return "[MISMATCH]";
+    case "metadata_outdated":
+      return "[OUTDATED]";
     default:
       return "[WARNING]";
   }
 }
-function formatFindingDetails(finding) {
+function formatFieldDiff(diff) {
+  const local = diff.local ?? "(none)";
+  const remote = diff.remote ?? "(none)";
+  return `  ${diff.field}: "${local}" → "${remote}"`;
+}
+function formatFindingDetails(finding, refId) {
   const lines = [];
-  lines.push(`  ${finding.message}`);
-  if (finding.details?.retractionDoi) {
-    lines.push(`  Retraction notice: https://doi.org/${finding.details.retractionDoi}`);
+  if (finding.details?.fieldDiffs && finding.details.fieldDiffs.length > 0) {
+    for (const diff of finding.details.fieldDiffs) {
+      lines.push(formatFieldDiff(diff));
+    }
   }
-  if (finding.details?.newDoi) {
-    lines.push(`  New DOI: https://doi.org/${finding.details.newDoi}`);
+  if (finding.type === "metadata_mismatch" || finding.type === "metadata_outdated") {
+    const icon = finding.type === "metadata_mismatch" ? "⚠" : "ℹ";
+    lines.push(`  ${icon} ${finding.message}`);
+    lines.push(`  → Run: ref update ${refId}`);
+  } else {
+    lines.push(`  ${finding.message}`);
+    if (finding.details?.retractionDoi) {
+      lines.push(`  Retraction notice: https://doi.org/${finding.details.retractionDoi}`);
+    }
+    if (finding.details?.newDoi) {
+      lines.push(`  New DOI: https://doi.org/${finding.details.newDoi}`);
+    }
   }
   return lines;
 }
+const FINDING_TYPE_KEYS = {
+  retracted: "retracted",
+  concern: "concern",
+  metadata_mismatch: "mismatch",
+  metadata_outdated: "outdated",
+  version_changed: "versionChanged"
+};
+function countFindingTypes(result) {
+  const counts = {};
+  const allFindings = result.results.flatMap((r) => r.findings);
+  for (const f of allFindings) {
+    const key = FINDING_TYPE_KEYS[f.type] ?? f.type;
+    counts[key] = (counts[key] ?? 0) + 1;
+  }
+  return counts;
+}
 function formatCheckTextOutput(result) {
   const lines = [];
   for (const r of result.results) {
     const label = getStatusLabel(r);
     lines.push(`${label} ${r.id}`);
     for (const finding of r.findings) {
-      lines.push(...formatFindingDetails(finding));
+      lines.push(...formatFindingDetails(finding, r.id));
     }
     lines.push("");
   }
   const { summary } = result;
   const parts = [`${summary.total} checked`];
-  if (summary.warnings > 0) parts.push(`${summary.warnings} warning(s)`);
+  const fc = countFindingTypes(result);
+  const summaryItems = [
+    ["retracted", "retracted"],
+    ["concern", "concern"],
+    ["mismatch", "mismatch"],
+    ["outdated", "outdated"],
+    ["versionChanged", "version changed"]
+  ];
+  const knownKeys = new Set(summaryItems.map(([key]) => key));
+  for (const [key, label] of summaryItems) {
+    const count = fc[key] ?? 0;
+    if (count > 0) parts.push(`${count} ${label}`);
+  }
+  for (const [key, count] of Object.entries(fc)) {
+    if (!knownKeys.has(key) && count > 0) parts.push(`${count} ${key}`);
+  }
   if (summary.ok > 0) parts.push(`${summary.ok} ok`);
   if (summary.skipped > 0) parts.push(`${summary.skipped} skipped`);
   lines.push(`Summary: ${parts.join(", ")}`);
@@ -2404,7 +2471,7 @@ async function handleCheckAction(identifiers, options, globalOpts) {
     const jsonOptions = buildJsonOptionsFromRefs(options, outputFormat, result, allRefs);
     outputCheckResult(result, outputFormat, jsonOptions);
     if (options.fix && result.summary.warnings > 0 && allRefs) {
-      const { runFixInteraction } = await import("./fix-interaction-BpfMLRNY.js");
+      const { runFixInteraction } = await import("./fix-interaction-CTIvq9t4.js");
       const findItem = (id2) => allRefs.find((item) => item.id === id2);
       const fixResult = await runFixInteraction(result.results, context.library, findItem);
       const removedSuffix = fixResult.removed.length > 0 ? `, ${fixResult.removed.length} removed` : "";
@@ -2472,7 +2539,7 @@ function outputCheckError(error, format2) {
 }
 async function selectReferencesInteractively(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Qpgt9cbN.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-DtzpiOvp.js");
   const allReferences = await context.library.getAll();
   if (allReferences.length === 0) {
     process.stderr.write("No references in library.\n");
@@ -2540,8 +2607,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-CYEise6v.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-mEMoWbM2.js");
+  const { runCiteFlow } = await import("./index-Bo1JIDmF.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-BT-HOyFf.js");
   const { search } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.B);
   const { tokenize } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.A);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
@@ -7142,7 +7209,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Qpgt9cbN.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DtzpiOvp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10681,14 +10748,14 @@ function formatFulltextConvertOutput(result) {
 function getFulltextExitCode(result) {
   return result.success ? 0 : 1;
 }
-async function executeInteractiveSelect$1(context, config2) {
+async function executeInteractiveSelect$1(context, config2, multiSelect = false) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Qpgt9cbN.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DtzpiOvp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
-    () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
+    () => selectReferencesOrExit(allReferences, { multiSelect }, config2.cli.tui)
   );
-  return identifiers[0];
+  return identifiers;
 }
 function isValidFilePath(value) {
   return typeof value === "string" && value !== "" && value !== "true";
@@ -10720,7 +10787,7 @@ async function handleFulltextAttachAction(identifierArg, filePathArg, options, g
         setExitCode(ExitCode.ERROR);
         return;
       }
-      identifier = await executeInteractiveSelect$1(context, config2);
+      identifier = (await executeInteractiveSelect$1(context, config2))[0];
     }
     const { type: type2, filePath } = parseFulltextAttachTypeAndPath(filePathArg, options);
     const stdinContent = !filePath && type2 ? await readStdinBuffer() : void 0;
@@ -10745,6 +10812,48 @@ async function handleFulltextAttachAction(identifierArg, filePathArg, options, g
     setExitCode(ExitCode.INTERNAL_ERROR);
   }
 }
+function formatMultiFulltextGetOutput(results) {
+  const isSingle = results.length === 1;
+  if (isSingle) {
+    const { result } = results[0];
+    const formatted = formatFulltextGetOutput(result);
+    return {
+      stdout: result.success ? formatted : "",
+      stderr: result.success ? "" : formatted
+    };
+  }
+  const stdoutLines = [];
+  const stderrLines = [];
+  for (const { id: id2, result } of results) {
+    if (result.success) {
+      stdoutLines.push(`${id2}:`);
+      if (result.paths?.pdf) {
+        stdoutLines.push(`  pdf: ${result.paths.pdf}`);
+      }
+      if (result.paths?.markdown) {
+        stdoutLines.push(`  markdown: ${result.paths.markdown}`);
+      }
+    } else {
+      stderrLines.push(`Error: ${result.error}`);
+    }
+  }
+  return {
+    stdout: stdoutLines.join("\n"),
+    stderr: stderrLines.join("\n")
+  };
+}
+function formatFulltextGetJsonOutput(results) {
+  const toJsonItem = ({ id: id2, result }) => {
+    if (result.success) {
+      return { id: id2, success: true, paths: result.paths };
+    }
+    return { id: id2, success: false, error: result.error };
+  };
+  if (results.length === 1) {
+    return JSON.stringify(toJsonItem(results[0]), null, 2);
+  }
+  return JSON.stringify(results.map(toJsonItem), null, 2);
+}
 function outputFulltextGetResult(result, useStdout) {
   if (result.success && result.content && useStdout) {
     process.stdout.write(result.content);
@@ -10759,27 +10868,26 @@ function outputFulltextGetResult(result, useStdout) {
 `);
   }
 }
-async function handleFulltextGetAction(identifierArg, options, globalOpts) {
-  try {
-    const config2 = await loadConfigWithOverrides({ ...globalOpts, ...options });
-    const context = await createExecutionContext(config2, Library.load);
-    let identifier;
-    if (identifierArg) {
-      identifier = identifierArg;
-    } else if (isTTY()) {
-      identifier = await executeInteractiveSelect$1(context, config2);
-    } else {
-      const stdinId = await readIdentifierFromStdin();
-      if (!stdinId) {
-        process.stderr.write(
-          "Error: No identifier provided. Provide an ID, pipe one via stdin, or run interactively in a TTY.\n"
-        );
-        setExitCode(ExitCode.ERROR);
-        return;
-      }
-      identifier = stdinId;
-    }
-    const preferValue = options.prefer ?? config2.fulltext.preferredType;
+async function resolveGetIdentifiers(identifierArgs, context, config2) {
+  if (identifierArgs.length > 0) {
+    return identifierArgs;
+  }
+  if (isTTY()) {
+    return executeInteractiveSelect$1(context, config2, true);
+  }
+  const stdinIds = await readIdentifiersFromStdin();
+  if (stdinIds.length === 0) {
+    process.stderr.write(
+      "Error: No identifier provided. Provide an ID, pipe one via stdin, or run interactively in a TTY.\n"
+    );
+    return null;
+  }
+  return stdinIds;
+}
+async function collectFulltextGetResults(identifiers, options, config2, context) {
+  const preferValue = options.prefer ?? config2.fulltext.preferredType;
+  const results = [];
+  for (const identifier of identifiers) {
     const getOptions = {
       identifier,
       fulltextDirectory: config2.attachments.directory,
@@ -10790,8 +10898,48 @@ async function handleFulltextGetAction(identifierArg, options, globalOpts) {
       ...preferValue && { preferredType: preferValue }
     };
     const result = await executeFulltextGet(getOptions, context);
-    outputFulltextGetResult(result, Boolean(options.stdout));
-    setExitCode(getFulltextExitCode(result));
+    results.push({ id: identifier, result });
+  }
+  return results;
+}
+function outputFulltextGetResults(results, options) {
+  if (options.output === "json") {
+    process.stdout.write(`${formatFulltextGetJsonOutput(results)}
+`);
+    return;
+  }
+  if (results.length === 1) {
+    outputFulltextGetResult(results[0].result, Boolean(options.stdout));
+    return;
+  }
+  const output = formatMultiFulltextGetOutput(results);
+  if (output.stdout) {
+    process.stdout.write(`${output.stdout}
+`);
+  }
+  if (output.stderr) {
+    process.stderr.write(`${output.stderr}
+`);
+  }
+}
+async function handleFulltextGetAction(identifierArgs, options, globalOpts) {
+  try {
+    const config2 = await loadConfigWithOverrides({ ...globalOpts, ...options });
+    const context = await createExecutionContext(config2, Library.load);
+    const identifiers = await resolveGetIdentifiers(identifierArgs, context, config2);
+    if (!identifiers) {
+      setExitCode(ExitCode.ERROR);
+      return;
+    }
+    if (options.stdout && identifiers.length > 1) {
+      process.stderr.write("Error: --stdout cannot be used with multiple identifiers\n");
+      setExitCode(ExitCode.ERROR);
+      return;
+    }
+    const results = await collectFulltextGetResults(identifiers, options, config2, context);
+    outputFulltextGetResults(results, options);
+    const hasFailure = results.some((r) => !r.result.success);
+    setExitCode(hasFailure ? ExitCode.ERROR : ExitCode.SUCCESS);
   } catch (error) {
     process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}
 `);
@@ -10806,7 +10954,7 @@ async function handleFulltextDetachAction(identifierArg, options, globalOpts) {
     if (identifierArg) {
       identifier = identifierArg;
     } else if (isTTY()) {
-      identifier = await executeInteractiveSelect$1(context, config2);
+      identifier = (await executeInteractiveSelect$1(context, config2))[0];
     } else {
       const stdinId = await readIdentifierFromStdin();
       if (!stdinId) {
@@ -10846,7 +10994,7 @@ async function handleFulltextOpenAction(identifierArg, options, globalOpts) {
     if (identifierArg) {
       identifier = identifierArg;
     } else if (isTTY()) {
-      identifier = await executeInteractiveSelect$1(context, config2);
+      identifier = (await executeInteractiveSelect$1(context, config2))[0];
     } else {
       const stdinId = await readIdentifierFromStdin();
       if (!stdinId) {
@@ -10886,7 +11034,7 @@ async function handleFulltextDiscoverAction(identifierArg, options, globalOpts)
     if (identifierArg) {
       identifier = identifierArg;
     } else if (isTTY()) {
-      identifier = await executeInteractiveSelect$1(context, config2);
+      identifier = (await executeInteractiveSelect$1(context, config2))[0];
     } else {
       const stdinId = await readIdentifierFromStdin();
       if (!stdinId) {
@@ -10926,7 +11074,7 @@ async function handleFulltextFetchAction(identifierArg, options, globalOpts) {
     if (identifierArg) {
       identifier = identifierArg;
     } else if (isTTY()) {
-      identifier = await executeInteractiveSelect$1(context, config2);
+      identifier = (await executeInteractiveSelect$1(context, config2))[0];
     } else {
       const stdinId = await readIdentifierFromStdin();
       if (!stdinId) {
@@ -10966,7 +11114,7 @@ async function handleFulltextConvertAction(identifierArg, options, globalOpts) {
     if (identifierArg) {
       identifier = identifierArg;
     } else if (isTTY()) {
-      identifier = await executeInteractiveSelect$1(context, config2);
+      identifier = (await executeInteractiveSelect$1(context, config2))[0];
     } else {
       const stdinId = await readIdentifierFromStdin();
       if (!stdinId) {
@@ -11008,8 +11156,10 @@ const fulltext = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProp
   formatFulltextDetachOutput,
   formatFulltextDiscoverOutput,
   formatFulltextFetchOutput,
+  formatFulltextGetJsonOutput,
   formatFulltextGetOutput,
   formatFulltextOpenOutput,
+  formatMultiFulltextGetOutput,
   getFulltextExitCode,
   handleFulltextAttachAction,
   handleFulltextConvertAction,
@@ -31561,7 +31711,8 @@ function registerCheckTool(server, getLibraryOperations) {
         ids: z.array(z.string()).optional().describe("Array of reference IDs to check. Omit if using 'all'."),
         all: z.boolean().optional().describe("Check all references in library"),
         skipDays: z.number().optional().describe("Skip references checked within n days (default: 7)"),
-        save: z.boolean().optional().describe("Whether to save results to library (default: true)")
+        save: z.boolean().optional().describe("Whether to save results to library (default: true)"),
+        metadata: z.boolean().optional().describe("Compare metadata against remote sources (default: true)")
       }
     },
     async (args) => {
@@ -31571,6 +31722,7 @@ function registerCheckTool(server, getLibraryOperations) {
       if (args.all) options.all = true;
       if (args.skipDays !== void 0) options.skipDays = args.skipDays;
       if (args.save !== void 0) options.save = args.save;
+      if (args.metadata !== void 0) options.metadata = args.metadata;
       const result = await libraryOps.check(options);
       const text = formatCheckResult(result);
       return {
@@ -32031,7 +32183,7 @@ async function mcpStart(options) {
 async function executeRemove(options, context) {
   const { identifier, idType = "id", fulltextDirectory, deleteFulltext = false } = options;
   if (context.mode === "local" && deleteFulltext && fulltextDirectory) {
-    const { removeReference } = await import("./index-D2HsxXnK.js").then((n) => n.x);
+    const { removeReference } = await import("./index-DUpYvm-W.js").then((n) => n.x);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -32086,7 +32238,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Qpgt9cbN.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-DtzpiOvp.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32311,7 +32463,7 @@ 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-CYEise6v.js");
+  const { runSearchFlow } = await import("./index-Bo1JIDmF.js");
   const { search } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.B);
   const { tokenize } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.A);
   checkTTY();
@@ -32330,7 +32482,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-DD0RtNVD.js");
+    const { isSideEffectAction } = await import("./action-menu-DP1rmCkH.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32733,7 +32885,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Qpgt9cbN.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DtzpiOvp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33028,7 +33180,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Qpgt9cbN.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DtzpiOvp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33561,7 +33713,7 @@ function shouldAutoFetch(cliFlag, configEnabled) {
   return configEnabled;
 }
 async function performAutoFetch(addedItems, context, config2) {
-  const { fulltextFetch: fulltextFetch2 } = await import("./index-D2HsxXnK.js").then((n) => n.w);
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-DUpYvm-W.js").then((n) => n.w);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -33642,7 +33794,9 @@ function registerEditCommand(program) {
   });
 }
 function registerCheckCommand(program) {
-  program.command("check").description("Check references for retractions, expressions of concern, and version changes").argument("[ids...]", "Citation keys or UUIDs to check (interactive selection if omitted)").option("--all", "Check all references in library").option("--search <query>", "Check references matching search query").option("--uuid", "Interpret identifiers as UUIDs").option("-o, --output <format>", "Output format: text|json", "text").option("--full", "Include full details in JSON output").option("--no-save", "Report only, do not save results to library").option("--days <n>", "Skip references checked within n days (default: 7)", Number.parseInt).option("--fix", "Interactive repair for findings (TTY only)").action(async (ids, options) => {
+  program.command("check").description(
+    "Check references for retractions, expressions of concern, version changes, and metadata drift"
+  ).argument("[ids...]", "Citation keys or UUIDs to check (interactive selection if omitted)").option("--all", "Check all references in library").option("--search <query>", "Check references matching search query").option("--uuid", "Interpret identifiers as UUIDs").option("-o, --output <format>", "Output format: text|json", "text").option("--full", "Include full details in JSON output").option("--no-save", "Report only, do not save results to library").option("--days <n>", "Skip references checked within n days (default: 7)", Number.parseInt).option("--fix", "Interactive repair for findings (TTY only)").option("--no-metadata", "Skip metadata comparison against remote sources").action(async (ids, options) => {
     await handleCheckAction(ids, options, program.opts());
   });
 }
@@ -33787,10 +33941,12 @@ function registerFulltextCommand(program) {
   fulltextCmd.command("attach").description("Attach a full-text file to a reference").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").argument("[file-path]", "Path to the file to attach").option("--pdf [path]", "Attach as PDF (path optional if provided as argument)").option("--markdown [path]", "Attach as Markdown (path optional if provided as argument)").option("--move", "Move file instead of copy").option("-f, --force", "Overwrite existing attachment").option("--uuid", "Interpret identifier as UUID").action(async (identifier, filePath, options) => {
     await handleFulltextAttachAction(identifier, filePath, options, program.opts());
   });
-  fulltextCmd.command("get").description("Get full-text file path or content").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--pdf", "Get PDF file only").option("--markdown", "Get Markdown file only").addOption(
+  fulltextCmd.command("get").description("Get full-text file path or content").argument("[identifiers...]", "Citation keys or UUIDs (interactive selection if omitted)").option("--pdf", "Get PDF file only").option("--markdown", "Get Markdown file only").addOption(
     new Option("--prefer <type>", "Preferred fulltext type").choices(["pdf", "markdown"])
-  ).option("--stdout", "Output file content to stdout").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
-    await handleFulltextGetAction(identifier, options, program.opts());
+  ).option("--stdout", "Output file content to stdout").option("--uuid", "Interpret identifiers as UUIDs").addOption(
+    new Option("-o, --output <format>", "Output format: json|text").choices(["json", "text"]).default("text")
+  ).action(async (identifiers, options) => {
+    await handleFulltextGetAction(identifiers, options, program.opts());
   });
   fulltextCmd.command("detach").description("Detach full-text file from a reference").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--pdf", "Detach PDF only").option("--markdown", "Detach Markdown only").option("--remove-files", "Also delete the file from disk").option("-f, --force", "Skip confirmation for file removal").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
     await handleFulltextDetachAction(identifier, options, program.opts());
@@ -33845,4 +34001,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-QTYx5RaF.js.map
+//# sourceMappingURL=index-B8ST0WLa.js.map