@ncukondo/reference-manager 0.25.0 → 0.26.0

package/dist/chunks/{index-QTYx5RaF.js → index-BEQ4YIXx.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 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-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 = "0.26.0";
 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-D2HsxXnK.js").then((n) => n.E);
+    const { searchReferences } = await import("./index-of6eJn8N.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-of6eJn8N.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-of6eJn8N.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-of6eJn8N.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-of6eJn8N.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-k67fQbe4.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-PQkbePWV.js");
+    const { listAttachments: listAttachments2 } = await import("./index-k67fQbe4.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-PQkbePWV.js");
+    const { getAttachment: getAttachment2 } = await import("./index-k67fQbe4.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-PQkbePWV.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-k67fQbe4.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-PQkbePWV.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-k67fQbe4.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-PQkbePWV.js");
+    const { openAttachment: openAttachment2 } = await import("./index-k67fQbe4.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-i1Cnmc16.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-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` : "";
@@ -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-i1Cnmc16.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-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");
@@ -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-i1Cnmc16.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10683,7 +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-Qpgt9cbN.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)
@@ -31561,7 +31628,8 @@ 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 +31639,7 @@ 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 +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-D2HsxXnK.js").then((n) => n.x);
+    const { removeReference } = await import("./index-of6eJn8N.js").then((n) => n.x);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -32086,7 +32155,7 @@ 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-i1Cnmc16.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32311,7 +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-CYEise6v.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();
@@ -32330,7 +32399,7 @@ 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-DWdoHTFh.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32733,7 +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-Qpgt9cbN.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)
@@ -33028,7 +33097,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Qpgt9cbN.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)
@@ -33561,7 +33630,7 @@ 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-of6eJn8N.js").then((n) => n.w);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -33642,7 +33711,9 @@ 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());
   });
 }
@@ -33845,4 +33916,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-QTYx5RaF.js.map
+//# sourceMappingURL=index-BEQ4YIXx.js.map