@ncukondo/reference-manager 0.24.1 → 0.26.0

package/dist/chunks/fix-interaction-DNXbmlPr.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fix-interaction-DNXbmlPr.js","sources":["../../src/features/check/fix-actions.ts","../../src/features/check/fix-interaction.ts"],"sourcesContent":["import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport type { CheckFinding } from \"./types.js\";\n\nexport type FixActionType =\n  | \"add_retracted_tag\"\n  | \"add_retraction_note\"\n  | \"remove_from_library\"\n  | \"update_from_published\"\n  | \"add_version_tag\"\n  | \"add_concern_tag\"\n  | \"add_concern_note\"\n  | \"update_all_fields\"\n  | \"update_selected_fields\"\n  | \"skip\";\n\nexport interface FixAction {\n  type: FixActionType;\n  label: string;\n}\n\nexport interface FixActionResult {\n  applied: boolean;\n  message: string;\n  removed?: boolean;\n}\n\nexport function getFixActionsForFinding(finding: CheckFinding): FixAction[] {\n  switch (finding.type) {\n    case \"retracted\":\n      return [\n        { type: \"add_retracted_tag\", label: 'Add tag \"retracted\"' },\n        { type: \"add_retraction_note\", label: \"Add note with retraction details\" },\n        { type: \"remove_from_library\", label: \"Remove from library\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"version_changed\":\n      return [\n        { type: \"update_from_published\", label: \"Update metadata from published version\" },\n        { type: \"add_version_tag\", label: 'Add tag \"has-published-version\"' },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"concern\":\n      return [\n        { type: \"add_concern_tag\", label: 'Add tag \"expression-of-concern\"' },\n        { type: \"add_concern_note\", label: \"Add note with concern details\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"metadata_mismatch\":\n    case \"metadata_outdated\":\n      return [\n        { type: \"update_all_fields\", label: \"Update all changed fields from remote\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    default:\n      return [];\n  }\n}\n\nfunction addTag(item: CslItem, tag: string): string[] {\n  const existing = (item.custom?.tags as string[] | undefined) ?? [];\n  if (existing.includes(tag)) {\n    return existing;\n  }\n  return [...existing, tag];\n}\n\nfunction buildNoteText(prefix: string, finding: CheckFinding): string {\n  const parts = [prefix];\n  if (finding.details?.retractionDate) {\n    parts.push(`Date: ${finding.details.retractionDate}`);\n  }\n  if (finding.details?.retractionDoi) {\n    parts.push(`DOI: ${finding.details.retractionDoi}`);\n  }\n  return parts.join(\". \");\n}\n\nfunction appendNote(existingNote: string | undefined, newNote: string): string {\n  if (existingNote) {\n    return `${existingNote}\\n\\n${newNote}`;\n  }\n  return newNote;\n}\n\nasync function applyTagAction(\n  library: ILibrary,\n  item: CslItem,\n  tag: string\n): Promise<FixActionResult> {\n  const tags = addTag(item, tag);\n  await library.update(item.id, { custom: { ...item.custom, tags } } as Partial<CslItem>, {\n    idType: \"id\",\n  });\n  await library.save();\n  return { applied: true, message: `Added tag \"${tag}\"` };\n}\n\nasync function applyNoteAction(\n  library: ILibrary,\n  item: CslItem,\n  prefix: string,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const noteText = buildNoteText(prefix, finding);\n  const note = appendNote(item.note, noteText);\n  await library.update(item.id, { note } as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Added note: ${noteText}` };\n}\n\nasync function applyUpdateFromPublished(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const newDoi = finding.details?.newDoi;\n  if (!newDoi) {\n    return { applied: false, message: \"No published DOI available in finding details\" };\n  }\n  const { fetchDoi } = await import(\"../import/fetcher.js\");\n  const fetchResult = await fetchDoi(newDoi);\n  if (!fetchResult.success) {\n    return {\n      applied: false,\n      message: `Failed to fetch metadata for ${newDoi}: ${fetchResult.error}`,\n    };\n  }\n  const { id: _id, custom: _custom, ...metadata } = fetchResult.item;\n  await library.update(item.id, metadata as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Updated metadata from ${newDoi}` };\n}\n\nasync function applyUpdateAllFields(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  let fetchedItem: CslItem;\n\n  if (item.DOI) {\n    const { fetchDoi } = await import(\"../import/fetcher.js\");\n    const fetchResult = await fetchDoi(item.DOI);\n    if (!fetchResult.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for DOI ${item.DOI}: ${fetchResult.error}`,\n      };\n    }\n    fetchedItem = fetchResult.item;\n  } else if (item.PMID) {\n    const { fetchPmids } = await import(\"../import/fetcher.js\");\n    const results = await fetchPmids([item.PMID], {});\n    const result = results[0];\n    if (!result || !result.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for PMID ${item.PMID}: ${result?.error ?? \"unknown error\"}`,\n      };\n    }\n    fetchedItem = result.item;\n  } else {\n    return { applied: false, message: \"No DOI or PMID available for metadata update\" };\n  }\n\n  const updatedFields = finding.details?.updatedFields ?? 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API.\n    case \"update_selected_fields\":\n      return { applied: false, message: \"Field selection not available in CLI mode\" };\n\n    case \"skip\":\n      return { applied: true, message: \"Skipped\" };\n\n    default:\n      return { applied: false, message: `Unknown action: ${actionType}` };\n  }\n}\n","import { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { restoreStdinAfterInk } from \"../interactive/alternate-screen.js\";\nimport { Select } from \"../interactive/components/index.js\";\nimport type { SelectOption } from \"../interactive/components/index.js\";\nimport { type FixActionType, applyFixAction, getFixActionsForFinding } from \"./fix-actions.js\";\nimport type { CheckFinding, CheckResult } from \"./types.js\";\n\nexport interface FixInteractionResult {\n  totalFindings: number;\n  applied: number;\n  skipped: number;\n  removed: string[];\n}\n\nfunction selectFixAction(\n  message: string,\n  options: SelectOption<FixActionType>[]\n): Promise<FixActionType | null> {\n  return new Promise<FixActionType | null>((resolve) => {\n    let selected: FixActionType | null = null;\n\n    const { waitUntilExit } = render(\n      createElement(Select<FixActionType>, {\n        options,\n        message,\n        onSelect: (value: FixActionType) => {\n          selected = value;\n        },\n        onCancel: () => {\n          selected = null;\n        },\n      })\n    );\n\n    waitUntilExit()\n      .then(() => {\n        restoreStdinAfterInk();\n        resolve(selected);\n      })\n      .catch(() => {\n        restoreStdinAfterInk();\n        resolve(null);\n      });\n  });\n}\n\nfunction getStatusLabel(type: string): string {\n  switch (type) {\n    case \"retracted\":\n      return \"RETRACTED\";\n    case \"concern\":\n      return \"CONCERN\";\n    case \"version_changed\":\n      return \"VERSION\";\n    case \"metadata_mismatch\":\n      return \"MISMATCH\";\n    case \"metadata_outdated\":\n      return \"OUTDATED\";\n    default:\n      return \"WARNING\";\n  }\n}\n\nfunction buildSelectOptions(finding: CheckFinding): SelectOption<FixActionType>[] {\n  return getFixActionsForFinding(finding).map((a) => ({\n    label: a.label,\n    value: a.type,\n  }));\n}\n\nasync function processFinding(\n  result: FixInteractionResult,\n  library: ILibrary,\n  item: CslItem,\n  resultId: string,\n  finding: CheckFinding\n): Promise<void> {\n  result.totalFindings++;\n  const options = buildSelectOptions(finding);\n  if (options.length === 0) return;\n\n  const label = getStatusLabel(finding.type);\n  const message = `[${label}] ${resultId}: ${finding.message}`;\n  const selectedAction = await selectFixAction(message, options);\n\n  if (selectedAction === null) {\n    result.skipped++;\n    return;\n  }\n\n  const actionResult = await applyFixAction(library, item, finding, selectedAction);\n\n  if (!actionResult.applied) {\n    process.stderr.write(`  Error: ${actionResult.message}\\n`);\n    return;\n  }\n\n  process.stderr.write(`  ${actionResult.message}\\n`);\n  if (selectedAction === \"skip\") {\n    result.skipped++;\n  } else {\n    result.applied++;\n    if (actionResult.removed) {\n      result.removed.push(resultId);\n    }\n  }\n}\n\nexport async function runFixInteraction(\n  results: CheckResult[],\n  library: ILibrary,\n  findItem: (id: string) => CslItem | undefined\n): Promise<FixInteractionResult> {\n  const interactionResult: FixInteractionResult = {\n    totalFindings: 0,\n    applied: 0,\n    skipped: 0,\n    removed: [],\n  };\n\n  const warningResults = results.filter((r) => r.status === \"warning\");\n\n  for (const checkResult of warningResults) {\n    const item = findItem(checkResult.id);\n    if (!item) continue;\n\n    for (const finding of checkResult.findings) {\n      await processFinding(interactionResult, library, item, 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package/dist/chunks/{index-JA964gjc.js → index-BEQ4YIXx.js}

@@ -5,9 +5,9 @@ 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, g as generateFilename, b as findFulltextFiles, c as findFulltextFile, h as extensionToFormat, j as fulltextAttach, k as fulltextGet, l as fulltextDiscover, m as fulltextFetch, o as fulltextConvert, q as getExtension, r as getDefaultExportFromCjs, B as BUILTIN_STYLES, s as getFulltextAttachmentTypes, t as startServerWithFileWatcher } from "./index-DWAtvFtp.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 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-of6eJn8N.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-CV71qNY2.js";
+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";
 import process$1, { stdin, stdout } from "node:process";
 import * as readline from "node:readline";
@@ -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 = "0.24.1";
+const version$1 = "0.26.0";
 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-DWAtvFtp.js").then((n) => n.A);
+    const { searchReferences } = await import("./index-of6eJn8N.js").then((n) => n.E);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-DWAtvFtp.js").then((n) => n.z);
+    const { listReferences } = await import("./index-of6eJn8N.js").then((n) => n.D);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-DWAtvFtp.js").then((n) => n.y);
+    const { citeReferences } = await import("./index-of6eJn8N.js").then((n) => n.C);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -921,32 +921,36 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-DWAtvFtp.js").then((n) => n.x);
+    const { addReferences } = await import("./index-of6eJn8N.js").then((n) => n.z);
     return addReferences(inputs, this.library, options ?? {});
   }
+  async check(options) {
+    const { checkReferences } = await import("./index-of6eJn8N.js").then((n) => n.A);
+    return checkReferences(this.library, options);
+  }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-zafRwZEZ.js");
+    const { addAttachment: addAttachment2 } = await import("./index-k67fQbe4.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-zafRwZEZ.js");
+    const { listAttachments: listAttachments2 } = await import("./index-k67fQbe4.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-zafRwZEZ.js");
+    const { getAttachment: getAttachment2 } = await import("./index-k67fQbe4.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-zafRwZEZ.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-k67fQbe4.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-zafRwZEZ.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-k67fQbe4.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-zafRwZEZ.js");
+    const { openAttachment: openAttachment2 } = await import("./index-k67fQbe4.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1084,6 +1088,18 @@ class ServerClient {
     }
     return await response.json();
   }
+  async check(options) {
+    const url2 = `${this.baseUrl}/api/check`;
+    const response = await fetch(url2, {
+      method: "POST",
+      headers: { "Content-Type": "application/json" },
+      body: JSON.stringify(options)
+    });
+    if (!response.ok) {
+      throw new Error(await response.text());
+    }
+    return await response.json();
+  }
   /**
    * Generate citations for references.
    * @param options - Cite options including identifiers and formatting
@@ -1790,7 +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-Bbl-roAS.js");
+  const { selectReferencesOrExit } = await import("./reference-select-i1Cnmc16.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2281,6 +2297,259 @@ const attach = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProper
   runInteractiveMode,
   syncNewFilesWithRolePrompt
 }, Symbol.toStringTag, { value: "Module" }));
+function buildCheckOptions(options, appConfig) {
+  const opOptions = {};
+  if (options.all) {
+    opOptions.all = true;
+  } else if (options.search) {
+    opOptions.searchQuery = options.search;
+  } else if (options.identifiers.length > 0) {
+    opOptions.identifiers = options.identifiers;
+  }
+  if (options.uuid) {
+    opOptions.idType = "uuid";
+  }
+  if (options.days !== void 0) {
+    opOptions.skipDays = options.days;
+  }
+  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;
+    if (appConfig.pubmed.apiKey) pubmed.apiKey = appConfig.pubmed.apiKey;
+    opOptions.config = {
+      ...appConfig.email ? { email: appConfig.email } : {},
+      pubmed
+    };
+  }
+  return opOptions;
+}
+async function executeCheck(options, context, appConfig) {
+  return context.library.check(buildCheckOptions(options, appConfig));
+}
+function getStatusLabel(result) {
+  if (result.status === "skipped") return "[SKIPPED]";
+  if (result.status === "ok") return "[OK]";
+  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_mismatch":
+      return "[MISMATCH]";
+    case "metadata_outdated":
+      return "[OUTDATED]";
+    default:
+      return "[WARNING]";
+  }
+}
+function formatFieldDiff(diff) {
+  const local = diff.local ?? "(none)";
+  const remote = diff.remote ?? "(none)";
+  return `  ${diff.field}: "${local}" → "${remote}"`;
+}
+function formatFindingDetails(finding, refId) {
+  const lines = [];
+  if (finding.details?.fieldDiffs && finding.details.fieldDiffs.length > 0) {
+    for (const diff of finding.details.fieldDiffs) {
+      lines.push(formatFieldDiff(diff));
+    }
+  }
+  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} ${r.id}`);
+    for (const finding of r.findings) {
+      lines.push(...formatFindingDetails(finding, r.id));
+    }
+    lines.push("");
+  }
+  const { summary } = result;
+  const parts = [`${summary.total} checked`];
+  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(", ")}`);
+  return lines.join("\n");
+}
+function formatCheckJsonOutput(result, options) {
+  if (!options?.full || !options.items) {
+    return result;
+  }
+  const results = result.results.map((r) => {
+    const item = options.items?.get(r.id);
+    return item ? { ...r, item } : r;
+  });
+  return { ...result, results };
+}
+async function handleCheckAction(identifiers, options, globalOpts) {
+  const outputFormat = options.output ?? "text";
+  if (options.fix && !isTTY()) {
+    outputCheckError(new Error("--fix requires an interactive terminal (TTY)"), outputFormat);
+    setExitCode(ExitCode.ERROR);
+    return;
+  }
+  try {
+    const config2 = await loadConfigWithOverrides({ ...globalOpts, ...options });
+    const context = await createExecutionContext(config2, Library.load);
+    const ids = await resolveIdentifiers$1(identifiers, options, context, config2);
+    if (ids === null) return;
+    const result = await executeCheck({ ...options, identifiers: ids }, context, config2);
+    const needAllRefs = options.full && outputFormat === "json" || options.fix;
+    const allRefs = needAllRefs ? await context.library.getAll() : void 0;
+    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-DNXbmlPr.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` : "";
+      process.stderr.write(
+        `
+Fix summary: ${fixResult.applied} applied, ${fixResult.skipped} skipped${removedSuffix}
+`
+      );
+    }
+    setExitCode(ExitCode.SUCCESS);
+  } catch (error) {
+    outputCheckError(error, outputFormat);
+    setExitCode(ExitCode.ERROR);
+  }
+}
+function buildJsonOptionsFromRefs(options, outputFormat, result, allRefs) {
+  if (!options.full || outputFormat !== "json" || !allRefs) return void 0;
+  const items2 = /* @__PURE__ */ new Map();
+  for (const r of result.results) {
+    const item = allRefs.find((ref2) => ref2.id === r.id);
+    if (item) items2.set(r.id, item);
+  }
+  return { full: true, items: items2 };
+}
+async function resolveIdentifiers$1(identifiers, options, context, config2) {
+  if (identifiers.length > 0 || options.all || options.search) {
+    return identifiers;
+  }
+  if (isTTY()) {
+    const ids = await selectReferencesInteractively(context, config2);
+    if (ids.length === 0) {
+      setExitCode(ExitCode.SUCCESS);
+      return null;
+    }
+    return ids;
+  }
+  const stdinIds = await readIdentifiersFromStdin();
+  if (stdinIds.length === 0) {
+    process.stderr.write(
+      "Error: No identifiers provided. Provide IDs, use --all, --search, or run interactively.\n"
+    );
+    setExitCode(ExitCode.ERROR);
+    return null;
+  }
+  return stdinIds;
+}
+function outputCheckResult(result, format2, jsonOptions) {
+  if (format2 === "json") {
+    process.stdout.write(`${JSON.stringify(formatCheckJsonOutput(result, jsonOptions))}
+`);
+  } else {
+    process.stderr.write(`${formatCheckTextOutput(result)}
+`);
+  }
+}
+function outputCheckError(error, format2) {
+  const message = error instanceof Error ? error.message : String(error);
+  if (format2 === "json") {
+    process.stdout.write(`${JSON.stringify({ error: message })}
+`);
+  } else {
+    process.stderr.write(`Error: ${message}
+`);
+  }
+}
+async function selectReferencesInteractively(context, config2) {
+  const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
+  const { selectReferenceItemsOrExit } = await import("./reference-select-i1Cnmc16.js");
+  const allReferences = await context.library.getAll();
+  if (allReferences.length === 0) {
+    process.stderr.write("No references in library.\n");
+    return [];
+  }
+  const selectedItems = await withAlternateScreen2(
+    () => selectReferenceItemsOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
+  );
+  return selectedItems.map((item) => item.id);
+}
 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`);
@@ -2338,8 +2607,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-C36Us_zC.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-BeAktUts.js");
+  const { runCiteFlow } = await import("./index-tdmbNN9b.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-COnY01qb.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");
@@ -2419,6 +2688,7 @@ async function handleCiteAction(identifiers, options, globalOpts) {
 }
 const ENV_OVERRIDE_MAP = {
   REFERENCE_MANAGER_LIBRARY: "library",
+  EMAIL: "email",
   REFERENCE_MANAGER_ATTACHMENTS_DIR: "attachments.directory",
   REFERENCE_MANAGER_CLI_DEFAULT_LIMIT: "cli.default_limit",
   REFERENCE_MANAGER_MCP_DEFAULT_LIMIT: "mcp.default_limit",
@@ -2454,6 +2724,7 @@ const CONFIG_KEY_REGISTRY = [
     description: "Log level",
     enumValues: ["silent", "info", "debug"]
   },
+  { key: "email", type: "string", description: "Fallback email for API services", optional: true },
   // backup section
   { key: "backup.max_generations", type: "integer", description: "Maximum backup generations" },
   { key: "backup.max_age_days", type: "integer", description: "Maximum backup age in days" },
@@ -6938,7 +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-Bbl-roAS.js");
+  const { selectReferencesOrExit } = await import("./reference-select-i1Cnmc16.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10479,7 +10750,7 @@ function getFulltextExitCode(result) {
 }
 async function executeInteractiveSelect$1(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Bbl-roAS.js");
+  const { selectReferencesOrExit } = await import("./reference-select-i1Cnmc16.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -31328,6 +31599,55 @@ function registerAddTool(server, getLibraryOperations) {
     }
   );
 }
+function formatCheckResult(result) {
+  const lines = [];
+  for (const r of result.results) {
+    if (r.status === "ok") {
+      lines.push(`[OK] ${r.id}`);
+    } else if (r.status === "skipped") {
+      lines.push(`[SKIPPED] ${r.id}`);
+    } else {
+      for (const f of r.findings) {
+        lines.push(`[${f.type.toUpperCase()}] ${r.id}: ${f.message}`);
+      }
+    }
+  }
+  const { summary } = result;
+  lines.push(
+    `
+Summary: ${summary.total} checked, ${summary.ok} ok, ${summary.warnings} warnings, ${summary.skipped} skipped`
+  );
+  return lines.join("\n");
+}
+function registerCheckTool(server, getLibraryOperations) {
+  server.registerTool(
+    "check",
+    {
+      description: "Check references for retractions, expressions of concern, and version changes by querying Crossref and PubMed APIs.",
+      inputSchema: {
+        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)"),
+        metadata: z.boolean().optional().describe("Compare metadata against remote sources (default: true)")
+      }
+    },
+    async (args) => {
+      const libraryOps = getLibraryOperations();
+      const options = {};
+      if (args.ids?.length) options.identifiers = args.ids;
+      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 {
+        content: [{ type: "text", text }]
+      };
+    }
+  );
+}
 function registerCiteTool(server, getLibraryOperations) {
   server.registerTool(
     "cite",
@@ -31718,6 +32038,7 @@ function registerAllTools(server, getLibraryOperations, getConfig) {
   registerSearchTool(server, getLibraryOperations, getConfig);
   registerListTool(server, getLibraryOperations, getConfig);
   registerCiteTool(server, getLibraryOperations);
+  registerCheckTool(server, getLibraryOperations);
   registerAddTool(server, getLibraryOperations);
   registerRemoveTool(server, getLibraryOperations);
   registerFulltextAttachTool(server, getLibraryOperations, getConfig);
@@ -31779,7 +32100,7 @@ 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-DWAtvFtp.js").then((n) => n.w);
+    const { removeReference } = await import("./index-of6eJn8N.js").then((n) => n.x);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -31834,7 +32155,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Bbl-roAS.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-i1Cnmc16.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32059,7 +32380,7 @@ 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-C36Us_zC.js");
+  const { runSearchFlow } = await import("./index-tdmbNN9b.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();
@@ -32078,7 +32399,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-BCgv1m3v.js");
+    const { isSideEffectAction } = await import("./action-menu-DWdoHTFh.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32094,7 +32415,7 @@ 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-CV71qNY2.js").then((n) => n.j);
+      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-B-fte1uv.js").then((n) => n.j);
       const item = items2[0];
       if (!item) return;
       const url$1 = resolveDefaultUrl2(item);
@@ -32481,7 +32802,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Bbl-roAS.js");
+  const { selectReferencesOrExit } = await import("./reference-select-i1Cnmc16.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32776,7 +33097,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Bbl-roAS.js");
+  const { selectReferencesOrExit } = await import("./reference-select-i1Cnmc16.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33147,6 +33468,7 @@ function createProgram() {
   registerRemoveCommand(program);
   registerUpdateCommand(program);
   registerEditCommand(program);
+  registerCheckCommand(program);
   registerCiteCommand(program);
   registerServerCommand(program);
   registerFulltextCommand(program);
@@ -33308,7 +33630,7 @@ function shouldAutoFetch(cliFlag, configEnabled) {
   return configEnabled;
 }
 async function performAutoFetch(addedItems, context, config2) {
-  const { fulltextFetch: fulltextFetch2 } = await import("./index-DWAtvFtp.js").then((n) => n.v);
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-of6eJn8N.js").then((n) => n.w);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -33388,6 +33710,13 @@ function registerEditCommand(program) {
     await handleEditAction(identifiers, options, program.opts());
   });
 }
+function registerCheckCommand(program) {
+  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());
+  });
+}
 function registerCiteCommand(program) {
   program.command("cite").description("Generate formatted citations for references").argument(
     "[id-or-uuid...]",
@@ -33587,4 +33916,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-JA964gjc.js.map
+//# sourceMappingURL=index-BEQ4YIXx.js.map