@ncukondo/reference-manager 0.20.0 → 0.22.0

package/dist/chunks/{index-Cno7_aWr.js → index-DOvEusHb.js}

@@ -1,14 +1,13 @@
 import { Command } from "commander";
 import { i as isEqual, M as MANAGED_CUSTOM_FIELDS, L as Library, g as CslItemSchema, p as pickDefined, a as sortOrderSchema, x as paginationOptionsSchema, F as FileWatcher, b as sortFieldSchema, v as searchSortFieldSchema } from "./file-watcher-CrsNHUpz.js";
 import * as fs from "node:fs";
-import { promises, readFileSync, existsSync, writeFileSync, mkdirSync, mkdtempSync } from "node:fs";
+import { promises, readFileSync, existsSync, writeFileSync, mkdirSync } from "node:fs";
 import * as os from "node:os";
-import { tmpdir } from "node:os";
 import * as path from "node:path";
-import path__default, { extname, join, basename, dirname } from "node:path";
-import { g as getExtension, i as isValidFulltextFiles, a as isReservedRole, R as RESERVED_ROLES, 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-DrZawbND.js";
-import fs__default, { stat, rename, copyFile, readFile, unlink, readdir, mkdir, rm } from "node:fs/promises";
-import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-BtW20O32.js";
+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, B as BUILTIN_STYLES, r as getFulltextAttachmentTypes, s as startServerWithFileWatcher } from "./index-BK3hTiKR.js";
+import { readFile, unlink, stat, readdir, rename, mkdir } from "node:fs/promises";
+import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-BHvcats5.js";
 import { spawn, spawnSync } from "node:child_process";
 import process$1, { stdin, stdout } from "node:process";
 import * as readline from "node:readline";
@@ -20,7 +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 = "0.20.0";
+const version$1 = "0.22.0";
 const description$1 = "A local reference management tool using CSL-JSON as the single source of truth";
 const packageJson = {
   name,
@@ -414,216 +413,28 @@ function getExitCode(result) {
   }
   return 0;
 }
-function slugifyLabel(label) {
-  return label.toLowerCase().replace(/[^a-z0-9]+/g, "-").replace(/-+/g, "-").replace(/^-|-$/g, "");
-}
-function generateFilename(role, ext, label) {
-  if (label) {
-    const slug = slugifyLabel(label);
-    return `${role}-${slug}.${ext}`;
-  }
-  return `${role}.${ext}`;
-}
-function parseFilename(filename) {
-  if (!filename) {
-    return null;
-  }
-  const ext = path__default.extname(filename);
-  const extWithoutDot = ext.startsWith(".") ? ext.slice(1) : ext;
-  const basename2 = ext ? filename.slice(0, -ext.length) : filename;
-  const firstHyphenIndex = basename2.indexOf("-");
-  if (firstHyphenIndex === -1) {
-    return {
-      role: basename2,
-      ext: extWithoutDot
-    };
-  }
-  const role = basename2.slice(0, firstHyphenIndex);
-  const label = basename2.slice(firstHyphenIndex + 1);
-  if (label) {
-    return {
-      role,
-      ext: extWithoutDot,
-      label
-    };
-  }
-  return {
-    role,
-    ext: extWithoutDot
-  };
-}
-function normalizePathForOutput(p) {
-  return p.replace(/\\/g, "/");
-}
-function extractUuidPrefix(uuid2) {
-  const normalized = uuid2.replace(/-/g, "");
-  return normalized.slice(0, 8);
-}
-function generateDirectoryName(ref2) {
-  const uuid2 = ref2.custom?.uuid;
-  if (!uuid2) {
-    throw new Error("Reference must have custom.uuid");
-  }
-  const uuidPrefix = extractUuidPrefix(uuid2);
-  const pmid = ref2.PMID?.trim();
-  if (pmid) {
-    return `${ref2.id}-PMID${pmid}-${uuidPrefix}`;
-  }
-  return `${ref2.id}-${uuidPrefix}`;
-}
-function getDirectoryPath(ref2, baseDir) {
-  const existingDir = ref2.custom?.attachments?.directory;
-  if (existingDir) {
-    return normalizePathForOutput(path__default.join(baseDir, existingDir));
-  }
-  const dirName = generateDirectoryName(ref2);
-  return normalizePathForOutput(path__default.join(baseDir, dirName));
-}
-async function ensureDirectory(ref2, baseDir) {
-  const dirPath = getDirectoryPath(ref2, baseDir);
-  try {
-    await fs__default.mkdir(dirPath, { recursive: true });
-  } catch (error) {
-    if (error.code !== "EEXIST") {
-      throw error;
-    }
-  }
-  return dirPath;
-}
-async function deleteDirectoryIfEmpty(dirPath) {
-  try {
-    const files = await fs__default.readdir(dirPath);
-    if (files.length === 0) {
-      await fs__default.rmdir(dirPath);
-    }
-  } catch (error) {
-    if (error.code !== "ENOENT") {
-      throw error;
-    }
-  }
-}
-async function checkSourceFile(filePath) {
-  try {
-    await stat(filePath);
-    return null;
-  } catch {
-    return `Source file not found: ${filePath}`;
-  }
-}
-function validateFulltextConstraint(existingFiles, newFile) {
-  if (newFile.role !== "fulltext") {
-    return null;
-  }
-  const newExt = getExtension(newFile.filename);
-  const existingFulltexts = existingFiles.filter((f) => f.role === "fulltext");
-  for (const existing of existingFulltexts) {
-    const existingExt = getExtension(existing.filename);
-    if (existingExt === newExt) {
-      return `A fulltext ${newExt.toUpperCase()} already exists. Use --force to overwrite.`;
-    }
-  }
-  const testFiles = [...existingFiles, newFile];
-  if (!isValidFulltextFiles(testFiles)) {
-    return "fulltext role allows max 2 files (1 PDF + 1 Markdown)";
-  }
-  return null;
-}
-function findExistingFile(files, filename) {
-  return files.find((f) => f.filename === filename);
-}
-async function copyOrMoveFile(sourcePath, destPath, move) {
-  try {
-    if (move) {
-      await rename(sourcePath, destPath);
-    } else {
-      await copyFile(sourcePath, destPath);
-    }
-    return null;
-  } catch (error) {
-    return `Failed to ${move ? "move" : "copy"} file: ${error instanceof Error ? error.message : String(error)}`;
-  }
-}
-async function updateAttachmentMetadata$1(library, item, updatedAttachments) {
-  await library.update(item.id, {
-    custom: {
-      ...item.custom,
-      attachments: updatedAttachments
-    }
-  });
-}
-function buildUpdatedFiles$1(existingFiles, newFile, existingFile) {
-  if (existingFile) {
-    return existingFiles.map((f) => f.filename === newFile.filename ? newFile : f);
-  }
-  return [...existingFiles, newFile];
-}
-async function addAttachment(library, options) {
-  const {
-    identifier,
-    filePath,
-    role,
-    label,
-    move = false,
-    force = false,
-    idType = "id",
-    attachmentsDirectory
-  } = options;
-  const item = await library.find(identifier, { idType });
-  if (!item) {
-    return { success: false, error: `Reference '${identifier}' not found` };
-  }
-  const uuid2 = item.custom?.uuid;
-  if (!uuid2) {
-    return { success: false, error: "Reference has no UUID. Cannot create attachment directory." };
-  }
-  const sourceError = await checkSourceFile(filePath);
-  if (sourceError) {
-    return { success: false, error: sourceError };
+async function autoFetchFulltext(addedItems, context, options) {
+  if (addedItems.length === 0) {
+    return [];
   }
-  const ext = extname(filePath).slice(1).toLowerCase();
-  const filename = generateFilename(role, ext, label);
-  const existingAttachments = item.custom?.attachments;
-  const existingFiles = existingAttachments?.files ?? [];
-  const newFile = {
-    filename,
-    role,
-    ...label && { label }
-  };
-  const existingFile = findExistingFile(existingFiles, filename);
-  if (!existingFile || !force) {
-    const constraintError = validateFulltextConstraint(existingFiles, newFile);
-    if (constraintError) {
-      return { success: false, error: constraintError };
+  const results = [];
+  for (const item of addedItems) {
+    try {
+      const result = await options.fulltextFetchFn(context.library, {
+        identifier: item.id,
+        idType: "id",
+        fulltextConfig: options.fulltextConfig,
+        fulltextDirectory: options.fulltextDirectory
+      });
+      results.push(result);
+    } catch (error) {
+      results.push({
+        success: false,
+        error: error instanceof Error ? error.message : String(error)
+      });
     }
   }
-  if (existingFile && !force) {
-    return {
-      success: false,
-      existingFile: filename,
-      requiresConfirmation: true
-    };
-  }
-  const ref2 = item;
-  const dirPath = await ensureDirectory(ref2, attachmentsDirectory);
-  const dirName = existingAttachments?.directory ?? generateDirectoryName(ref2);
-  const destPath = join(dirPath, filename);
-  const copyError = await copyOrMoveFile(filePath, destPath, move);
-  if (copyError) {
-    return { success: false, error: copyError };
-  }
-  const updatedFiles = buildUpdatedFiles$1(existingFiles, newFile, existingFile);
-  const updatedAttachments = {
-    directory: dirName,
-    files: updatedFiles
-  };
-  await updateAttachmentMetadata$1(library, item, updatedAttachments);
-  await library.save();
-  return {
-    success: true,
-    filename,
-    directory: dirName,
-    overwritten: !!existingFile
-  };
+  return results;
 }
 async function listAttachments(library, options) {
   const { identifier, idType = "id", role } = options;
@@ -1093,15 +904,15 @@ class OperationsLibrary {
   }
   // High-level operations
   async search(options) {
-    const { searchReferences } = await import("./index-DrZawbND.js").then((n) => n.n);
+    const { searchReferences } = await import("./index-BK3hTiKR.js").then((n) => n.z);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-DrZawbND.js").then((n) => n.m);
+    const { listReferences } = await import("./index-BK3hTiKR.js").then((n) => n.y);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-DrZawbND.js").then((n) => n.l);
+    const { citeReferences } = await import("./index-BK3hTiKR.js").then((n) => n.x);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -1112,32 +923,32 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-DrZawbND.js").then((n) => n.k);
+    const { addReferences } = await import("./index-BK3hTiKR.js").then((n) => n.w);
     return addReferences(inputs, this.library, options ?? {});
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-BR5tlrNU.js");
+    const { addAttachment: addAttachment2 } = await import("./index-D7eiOplw.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-BR5tlrNU.js");
+    const { listAttachments: listAttachments2 } = await import("./index-D7eiOplw.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-BR5tlrNU.js");
+    const { getAttachment: getAttachment2 } = await import("./index-D7eiOplw.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-BR5tlrNU.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-D7eiOplw.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-BR5tlrNU.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-D7eiOplw.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-BR5tlrNU.js");
+    const { openAttachment: openAttachment2 } = await import("./index-D7eiOplw.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1981,7 +1792,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-DrINWBuP.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DTqhevya.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2529,8 +2340,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-D--7n1SB.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-DxcSWBSF.js");
+  const { runCiteFlow } = await import("./index-BvIfOciH.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-CXclvgJO.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");
@@ -2615,7 +2426,9 @@ const ENV_OVERRIDE_MAP = {
   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"
+  PUBMED_API_KEY: "pubmed.api_key",
+  UNPAYWALL_EMAIL: "fulltext.sources.unpaywall_email",
+  CORE_API_KEY: "fulltext.sources.core_api_key"
 };
 const KEY_TO_ENV_MAP = Object.fromEntries(
   Object.entries(ENV_OVERRIDE_MAP).map(([envVar, configKey]) => [configKey, envVar])
@@ -2679,6 +2492,29 @@ const CONFIG_KEY_REGISTRY = [
   // 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 },
+  // fulltext section
+  {
+    key: "fulltext.prefer_sources",
+    type: "string[]",
+    description: "Fulltext source priority order"
+  },
+  {
+    key: "fulltext.auto_fetch_on_add",
+    type: "boolean",
+    description: "Auto-fetch fulltext when adding references"
+  },
+  {
+    key: "fulltext.sources.unpaywall_email",
+    type: "string",
+    description: "Email for Unpaywall API",
+    optional: true
+  },
+  {
+    key: "fulltext.sources.core_api_key",
+    type: "string",
+    description: "API key for CORE",
+    optional: true
+  },
   // attachments section
   { key: "attachments.directory", type: "string", description: "Attachments storage directory" },
   // cli section
@@ -6478,7 +6314,7 @@ function writeBlockMapping(state, level, object2, compact) {
   state.tag = _tag;
   state.dump = _result || "{}";
 }
-function detectType$1(state, object2, explicit) {
+function detectType(state, object2, explicit) {
   var _result, typeList, index, length, type2, style;
   typeList = explicit ? state.explicitTypes : state.implicitTypes;
   for (index = 0, length = typeList.length; index < length; index += 1) {
@@ -6512,8 +6348,8 @@ function detectType$1(state, object2, explicit) {
 function writeNode(state, level, object2, block, compact, iskey, isblockseq) {
   state.tag = null;
   state.dump = object2;
-  if (!detectType$1(state, object2, false)) {
-    detectType$1(state, object2, true);
+  if (!detectType(state, object2, false)) {
+    detectType(state, object2, true);
   }
   var type2 = _toString.call(state.dump);
   var inblock = block;
@@ -7087,7 +6923,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-DrINWBuP.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DTqhevya.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10346,188 +10182,6 @@ function formatExportOutput(result, options) {
 function getExportExitCode(result) {
   return result.notFound.length > 0 ? 1 : 0;
 }
-function detectType(filePath) {
-  const ext = extname(filePath).toLowerCase();
-  if (ext === ".pdf") return "pdf";
-  if (ext === ".md" || ext === ".markdown") return "markdown";
-  return void 0;
-}
-function resolveFileType(explicitType, filePath, stdinContent) {
-  let fileType = explicitType;
-  if (!fileType && filePath) {
-    fileType = detectType(filePath);
-  }
-  if (stdinContent && !fileType) {
-    return {
-      error: "File type must be specified with --pdf or --markdown when reading from stdin."
-    };
-  }
-  if (!fileType) {
-    return { error: "Cannot detect file type. Use --pdf or --markdown to specify the type." };
-  }
-  return fileType;
-}
-function prepareStdinSource(stdinContent, fileType) {
-  try {
-    const tempDir = mkdtempSync(join(tmpdir(), "refmgr-"));
-    const ext = formatToExtension(fileType);
-    const sourcePath = join(tempDir, `stdin.${ext}`);
-    writeFileSync(sourcePath, stdinContent);
-    return { sourcePath, tempDir };
-  } catch (error) {
-    return {
-      error: `Failed to write stdin content: ${error instanceof Error ? error.message : String(error)}`
-    };
-  }
-}
-async function cleanupTempDir(tempDir) {
-  if (tempDir) {
-    await rm(tempDir, { recursive: true, force: true }).catch(() => {
-    });
-  }
-}
-function prepareSourcePath(filePath, stdinContent, fileType) {
-  if (stdinContent) {
-    return prepareStdinSource(stdinContent, fileType);
-  }
-  if (!filePath) {
-    return { error: "No file path or stdin content provided." };
-  }
-  return { sourcePath: filePath };
-}
-function convertResult(result, fileType) {
-  if (result.success) {
-    return {
-      success: true,
-      filename: result.filename,
-      type: fileType,
-      overwritten: result.overwritten
-    };
-  }
-  if (result.requiresConfirmation) {
-    return {
-      success: false,
-      existingFile: result.existingFile,
-      requiresConfirmation: true
-    };
-  }
-  return {
-    success: false,
-    error: result.error
-  };
-}
-async function fulltextAttach(library, options) {
-  const {
-    identifier,
-    filePath,
-    type: explicitType,
-    move,
-    force,
-    idType = "id",
-    fulltextDirectory,
-    stdinContent
-  } = options;
-  const fileTypeResult = resolveFileType(explicitType, filePath, stdinContent);
-  if (typeof fileTypeResult === "object" && "error" in fileTypeResult) {
-    const item = await library.find(identifier, { idType });
-    if (!item) {
-      return { success: false, error: `Reference '${identifier}' not found` };
-    }
-    return { success: false, error: fileTypeResult.error };
-  }
-  const fileType = fileTypeResult;
-  const sourceResult = prepareSourcePath(filePath, stdinContent, fileType);
-  if ("error" in sourceResult) {
-    const item = await library.find(identifier, { idType });
-    if (!item) {
-      return { success: false, error: `Reference '${identifier}' not found` };
-    }
-    return { success: false, error: sourceResult.error };
-  }
-  const { sourcePath, tempDir } = sourceResult;
-  try {
-    const result = await addAttachment(library, {
-      identifier,
-      filePath: sourcePath,
-      role: FULLTEXT_ROLE,
-      move: move ?? false,
-      force: force ?? false,
-      idType,
-      attachmentsDirectory: fulltextDirectory
-    });
-    await cleanupTempDir(tempDir);
-    return convertResult(result, fileType);
-  } catch (error) {
-    await cleanupTempDir(tempDir);
-    throw error;
-  }
-}
-function buildFilePath$1(attachmentsDirectory, directory, filename) {
-  return normalizePathForOutput(join(attachmentsDirectory, directory, filename));
-}
-async function getFileContent(filePath) {
-  const content = await readFile(filePath);
-  return { success: true, content };
-}
-async function handleStdoutMode(attachments, type2, identifier, fulltextDirectory) {
-  const file = findFulltextFile(attachments, type2);
-  if (!file || !attachments?.directory) {
-    return { success: false, error: `No ${type2} fulltext attached to '${identifier}'` };
-  }
-  const filePath = buildFilePath$1(fulltextDirectory, attachments.directory, file.filename);
-  try {
-    return await getFileContent(filePath);
-  } catch {
-    return { success: false, error: `No ${type2} fulltext attached to '${identifier}'` };
-  }
-}
-function getSingleTypePath(attachments, type2, identifier, fulltextDirectory) {
-  const file = findFulltextFile(attachments, type2);
-  if (!file || !attachments?.directory) {
-    return { success: false, error: `No ${type2} fulltext attached to '${identifier}'` };
-  }
-  const filePath = buildFilePath$1(fulltextDirectory, attachments.directory, file.filename);
-  const paths = {};
-  paths[type2] = filePath;
-  return { success: true, paths };
-}
-function getAllFulltextPaths(attachments, fulltextFiles, fulltextDirectory, identifier) {
-  const paths = {};
-  for (const file of fulltextFiles) {
-    const ext = file.filename.split(".").pop() || "";
-    const format2 = extensionToFormat(ext);
-    if (format2) {
-      const filePath = buildFilePath$1(fulltextDirectory, attachments.directory, file.filename);
-      paths[format2] = filePath;
-    }
-  }
-  if (Object.keys(paths).length === 0) {
-    return { success: false, error: `No fulltext attached to '${identifier}'` };
-  }
-  return { success: true, paths };
-}
-async function fulltextGet(library, options) {
-  const { identifier, type: type2, stdout: stdout2, idType = "id", fulltextDirectory } = options;
-  const item = await library.find(identifier, { idType });
-  if (!item) {
-    return { success: false, error: `Reference '${identifier}' not found` };
-  }
-  const attachments = item.custom?.attachments;
-  if (stdout2 && type2) {
-    return handleStdoutMode(attachments, type2, identifier, fulltextDirectory);
-  }
-  const fulltextFiles = findFulltextFiles(attachments);
-  if (fulltextFiles.length === 0) {
-    return { success: false, error: `No fulltext attached to '${identifier}'` };
-  }
-  if (type2) {
-    return getSingleTypePath(attachments, type2, identifier, fulltextDirectory);
-  }
-  if (!attachments) {
-    return { success: false, error: `No fulltext attached to '${identifier}'` };
-  }
-  return getAllFulltextPaths(attachments, fulltextFiles, fulltextDirectory, identifier);
-}
 function getFilesToDetach(attachments, type2) {
   if (type2) {
     const file = findFulltextFile(attachments, type2);
@@ -10684,6 +10338,33 @@ async function executeFulltextOpen(options, context) {
   };
   return fulltextOpen(context.library, operationOptions);
 }
+async function executeFulltextDiscover(options, context, config2) {
+  const operationOptions = {
+    identifier: options.identifier,
+    idType: options.idType,
+    fulltextConfig: config2.fulltext
+  };
+  return fulltextDiscover(context.library, operationOptions);
+}
+async function executeFulltextFetch(options, context, config2) {
+  const operationOptions = {
+    identifier: options.identifier,
+    idType: options.idType,
+    fulltextConfig: config2.fulltext,
+    fulltextDirectory: options.fulltextDirectory,
+    source: options.source,
+    force: options.force
+  };
+  return fulltextFetch(context.library, operationOptions);
+}
+async function executeFulltextConvert(options, context) {
+  const operationOptions = {
+    identifier: options.identifier,
+    idType: options.idType,
+    fulltextDirectory: options.fulltextDirectory
+  };
+  return fulltextConvert(context.library, operationOptions);
+}
 function formatFulltextAttachOutput(result) {
   if (result.requiresConfirmation) {
     return `File already attached: ${result.existingFile}
@@ -10736,12 +10417,50 @@ function formatFulltextOpenOutput(result) {
   }
   return `Opened ${result.openedType}: ${result.openedPath}`;
 }
+function formatFulltextDiscoverOutput(result, identifier) {
+  if (!result.success) {
+    return `Error: ${result.error}`;
+  }
+  if (!result.locations || result.locations.length === 0) {
+    return `No OA sources found for ${identifier}`;
+  }
+  const lines = [`OA sources for ${identifier}:`];
+  for (const loc of result.locations) {
+    const license = loc.license ? ` (${loc.license})` : "";
+    lines.push(`  ${loc.source}: ${loc.url}${license}`);
+  }
+  if (result.errors && result.errors.length > 0) {
+    for (const err of result.errors) {
+      lines.push(`  Warning: ${err.source}: ${err.error}`);
+    }
+  }
+  return lines.join("\n");
+}
+function formatFulltextFetchOutput(result) {
+  if (!result.success) {
+    return `Error: ${result.error}`;
+  }
+  const lines = [];
+  if (result.source) {
+    lines.push(`Source: ${result.source}`);
+  }
+  for (const file of result.attachedFiles ?? []) {
+    lines.push(`Attached ${file}: fulltext.${file === "markdown" ? "md" : file}`);
+  }
+  return lines.join("\n");
+}
+function formatFulltextConvertOutput(result) {
+  if (!result.success) {
+    return `Error: ${result.error}`;
+  }
+  return `Converted PMC XML to Markdown: ${result.filename}`;
+}
 function getFulltextExitCode(result) {
   return result.success ? 0 : 1;
 }
 async function executeInteractiveSelect$1(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-DrINWBuP.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DTqhevya.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -10932,22 +10651,167 @@ async function handleFulltextOpenAction(identifierArg, options, globalOpts) {
     setExitCode(ExitCode.INTERNAL_ERROR);
   }
 }
+async function handleFulltextDiscoverAction(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$1(context, config2);
+    } else {
+      const stdinId = await readIdentifierFromStdin();
+      if (!stdinId) {
+        process.stderr.write(
+          "Error: No identifier provided. Provide an ID, pipe one via stdin, or run interactively in a TTY.\n"
+        );
+        setExitCode(ExitCode.ERROR);
+        return;
+      }
+      identifier = stdinId;
+    }
+    const discoverOptions = {
+      identifier,
+      ...options.uuid && { idType: "uuid" }
+    };
+    const result = await executeFulltextDiscover(discoverOptions, context, config2);
+    const output = formatFulltextDiscoverOutput(result, identifier);
+    if (result.success) {
+      process.stdout.write(`${output}
+`);
+    } else {
+      process.stderr.write(`${output}
+`);
+    }
+    setExitCode(getFulltextExitCode(result));
+  } catch (error) {
+    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}
+`);
+    setExitCode(ExitCode.INTERNAL_ERROR);
+  }
+}
+async function handleFulltextFetchAction(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;
+    }
+    process.stderr.write(`Fetching fulltext for ${identifier}...
+`);
+    const fetchOptions = {
+      identifier,
+      fulltextDirectory: config2.attachments.directory,
+      ...options.source && { source: options.source },
+      ...options.force && { force: options.force },
+      ...options.uuid && { idType: "uuid" }
+    };
+    const result = await executeFulltextFetch(fetchOptions, context, config2);
+    const output = formatFulltextFetchOutput(result);
+    process.stderr.write(`${output}
+`);
+    setExitCode(getFulltextExitCode(result));
+  } catch (error) {
+    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}
+`);
+    setExitCode(ExitCode.INTERNAL_ERROR);
+  }
+}
+async function handleFulltextConvertAction(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$1(context, config2);
+    } else {
+      const stdinId = await readIdentifierFromStdin();
+      if (!stdinId) {
+        process.stderr.write(
+          "Error: No identifier provided. Provide an ID, pipe one via stdin, or run interactively in a TTY.\n"
+        );
+        setExitCode(ExitCode.ERROR);
+        return;
+      }
+      identifier = stdinId;
+    }
+    const convertOptions = {
+      identifier,
+      fulltextDirectory: config2.attachments.directory,
+      ...options.uuid && { idType: "uuid" }
+    };
+    const result = await executeFulltextConvert(convertOptions, context);
+    const output = formatFulltextConvertOutput(result);
+    process.stderr.write(`${output}
+`);
+    setExitCode(getFulltextExitCode(result));
+  } catch (error) {
+    process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}
+`);
+    setExitCode(ExitCode.INTERNAL_ERROR);
+  }
+}
 const fulltext = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
   __proto__: null,
   executeFulltextAttach,
+  executeFulltextConvert,
   executeFulltextDetach,
+  executeFulltextDiscover,
+  executeFulltextFetch,
   executeFulltextGet,
   executeFulltextOpen,
   formatFulltextAttachOutput,
+  formatFulltextConvertOutput,
   formatFulltextDetachOutput,
+  formatFulltextDiscoverOutput,
+  formatFulltextFetchOutput,
   formatFulltextGetOutput,
   formatFulltextOpenOutput,
   getFulltextExitCode,
   handleFulltextAttachAction,
+  handleFulltextConvertAction,
   handleFulltextDetachAction,
+  handleFulltextDiscoverAction,
+  handleFulltextFetchAction,
   handleFulltextGetAction,
   handleFulltextOpenAction
 }, Symbol.toStringTag, { value: "Module" }));
+function buildResourceIndicators(item) {
+  const icons = [];
+  const attachments = item.custom?.attachments;
+  const fulltextFiles = findFulltextFiles(attachments);
+  const hasFulltextPdf = fulltextFiles.some(
+    (f) => extensionToFormat(getExtension(f.filename)) === "pdf"
+  );
+  if (hasFulltextPdf) icons.push("📄");
+  const hasFulltextMd = fulltextFiles.some(
+    (f) => extensionToFormat(getExtension(f.filename)) === "markdown"
+  );
+  if (hasFulltextMd) icons.push("📝");
+  const allFiles = attachments?.files ?? [];
+  const hasOtherAttachments = allFiles.length > fulltextFiles.length;
+  if (hasOtherAttachments) icons.push("📎");
+  if (item.URL) icons.push("🔗");
+  const tags = item.custom?.tags;
+  if (Array.isArray(tags) && tags.length > 0) icons.push("🏷");
+  return icons.join("");
+}
 function formatAuthor(author) {
   const family = author.family || "";
   const givenInitial = author.given ? `${author.given.charAt(0)}.` : "";
@@ -10980,6 +10844,10 @@ function formatSingleReference(item) {
   }
   const uuid2 = item.custom?.uuid || "(no uuid)";
   lines.push(`  UUID: ${uuid2}`);
+  const indicators = buildResourceIndicators(item);
+  if (indicators) {
+    lines.push(`  ${indicators}`);
+  }
   return lines.join("\n");
 }
 function formatPretty(items2) {
@@ -31588,6 +31456,115 @@ function registerFulltextDetachTool(server, getLibraryOperations, getConfig) {
     }
   );
 }
+function registerFulltextDiscoverTool(server, getLibraryOperations, getConfig) {
+  server.registerTool(
+    "fulltext_discover",
+    {
+      description: "Check Open Access (OA) availability for a reference. Returns available sources and URLs.",
+      inputSchema: {
+        id: z.string().describe("Reference ID")
+      }
+    },
+    async (args) => {
+      const libraryOps = getLibraryOperations();
+      const config2 = getConfig();
+      const result = await fulltextDiscover(libraryOps, {
+        identifier: args.id,
+        fulltextConfig: config2.fulltext
+      });
+      if (!result.success) {
+        return {
+          content: [{ type: "text", text: result.error ?? "Unknown error" }],
+          isError: true
+        };
+      }
+      if (!result.locations || result.locations.length === 0) {
+        return {
+          content: [{ type: "text", text: `No OA sources found for '${args.id}'` }]
+        };
+      }
+      const lines = [`OA sources for '${args.id}' (status: ${result.oaStatus}):`];
+      for (const loc of result.locations) {
+        lines.push(`  ${loc.source}: ${loc.url} (${loc.urlType})`);
+      }
+      return {
+        content: [{ type: "text", text: lines.join("\n") }]
+      };
+    }
+  );
+}
+function registerFulltextFetchTool(server, getLibraryOperations, getConfig) {
+  server.registerTool(
+    "fulltext_fetch",
+    {
+      description: "Download and attach Open Access full-text for a reference. Automatically discovers OA sources, downloads PDF/XML, converts PMC XML to Markdown, and attaches files.",
+      inputSchema: {
+        id: z.string().describe("Reference ID"),
+        source: z.enum(["pmc", "arxiv", "unpaywall", "core"]).optional().describe("Preferred source (optional)"),
+        force: z.boolean().optional().describe("Force overwrite existing attachment")
+      }
+    },
+    async (args) => {
+      const libraryOps = getLibraryOperations();
+      const config2 = getConfig();
+      const result = await fulltextFetch(libraryOps, {
+        identifier: args.id,
+        fulltextConfig: config2.fulltext,
+        fulltextDirectory: config2.attachments.directory,
+        source: args.source,
+        force: args.force
+      });
+      if (!result.success) {
+        return {
+          content: [{ type: "text", text: result.error ?? "Unknown error" }],
+          isError: true
+        };
+      }
+      const files = result.attachedFiles?.join(", ") ?? "none";
+      return {
+        content: [
+          {
+            type: "text",
+            text: `Fetched fulltext for '${args.id}' from ${result.source}: ${files}`
+          }
+        ]
+      };
+    }
+  );
+}
+function registerFulltextConvertTool(server, getLibraryOperations, getConfig) {
+  server.registerTool(
+    "fulltext_convert",
+    {
+      description: "Convert an attached PMC JATS XML file to Markdown for a reference.",
+      inputSchema: {
+        id: z.string().describe("Reference ID")
+      }
+    },
+    async (args) => {
+      const libraryOps = getLibraryOperations();
+      const config2 = getConfig();
+      const result = await fulltextConvert(libraryOps, {
+        identifier: args.id,
+        fulltextDirectory: config2.attachments.directory
+      });
+      if (!result.success) {
+        return {
+          content: [{ type: "text", text: result.error ?? "Unknown error" }],
+          isError: true
+        };
+      }
+      return {
+        content: [
+          {
+            type: "text",
+            text: `Converted PMC XML to Markdown for '${args.id}': ${result.filename}`
+          }
+        ]
+      };
+    }
+  );
+}
 function registerListTool(server, getLibraryOperations, getConfig) {
   server.registerTool(
     "list",
@@ -31721,6 +31698,9 @@ function registerAllTools(server, getLibraryOperations, getConfig) {
   registerFulltextAttachTool(server, getLibraryOperations, getConfig);
   registerFulltextGetTool(server, getLibraryOperations, getConfig);
   registerFulltextDetachTool(server, getLibraryOperations, getConfig);
+  registerFulltextDiscoverTool(server, getLibraryOperations, getConfig);
+  registerFulltextFetchTool(server, getLibraryOperations, getConfig);
+  registerFulltextConvertTool(server, getLibraryOperations, getConfig);
 }
 async function createMcpServer(options) {
   const serverInfo = {
@@ -31774,7 +31754,7 @@ 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-DrZawbND.js").then((n) => n.r);
+    const { removeReference } = await import("./index-BK3hTiKR.js").then((n) => n.v);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -31829,7 +31809,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-DrINWBuP.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-DTqhevya.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32054,7 +32034,7 @@ 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-D--7n1SB.js");
+  const { runSearchFlow } = await import("./index-BvIfOciH.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();
@@ -32073,7 +32053,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-Brg5Lmz7.js");
+    const { isSideEffectAction } = await import("./action-menu-B1DCdkkp.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32089,7 +32069,7 @@ 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-BtW20O32.js").then((n) => n.j);
+      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-BHvcats5.js").then((n) => n.j);
       const item = items2[0];
       if (!item) return;
       const url$1 = resolveDefaultUrl2(item);
@@ -32476,7 +32456,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-DrINWBuP.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DTqhevya.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32771,7 +32751,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-DrINWBuP.js");
+  const { selectReferencesOrExit } = await import("./reference-select-DTqhevya.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33267,6 +33247,35 @@ async function outputAddResultJson(result, context, full) {
   process.stdout.write(`${JSON.stringify(jsonOutput2)}
 `);
 }
+function shouldAutoFetch(cliFlag, configEnabled) {
+  if (cliFlag !== void 0) {
+    return cliFlag;
+  }
+  return configEnabled;
+}
+async function performAutoFetch(addedItems, context, config2) {
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-BK3hTiKR.js").then((n) => n.u);
+  const fetchResults = await autoFetchFulltext(addedItems, context, {
+    fulltextConfig: config2.fulltext,
+    fulltextDirectory: config2.attachments.directory,
+    fulltextFetchFn: fulltextFetch2
+  });
+  for (const [i, fetchResult] of fetchResults.entries()) {
+    const addedItem = addedItems[i];
+    if (!addedItem) continue;
+    if (fetchResult.success) {
+      process.stderr.write(
+        `Fulltext for ${addedItem.id}: ${formatFulltextFetchOutput(fetchResult)}
+`
+      );
+    } else {
+      process.stderr.write(
+        `Fulltext for ${addedItem.id}: ${fetchResult.error ?? "unknown error"}
+`
+      );
+    }
+  }
+}
 async function handleAddAction(inputs, options, program) {
   const outputFormat = options.output ?? "text";
   try {
@@ -33286,6 +33295,9 @@ async function handleAddAction(inputs, options, program) {
       process.stderr.write(`${output}
 `);
     }
+    if (result.added.length > 0 && shouldAutoFetch(options.fetchFulltext, config2.fulltext.autoFetchOnAdd)) {
+      await performAutoFetch(result.added, context, config2);
+    }
     setExitCode(getExitCode(result));
   } catch (error) {
     const message = error instanceof Error ? error.message : String(error);
@@ -33300,7 +33312,7 @@ async function handleAddAction(inputs, options, program) {
   }
 }
 function registerAddCommand(program) {
-  program.command("add").description("Add new reference(s) to the library").argument("[input...]", "File paths or identifiers (PMID/DOI/ISBN), or use stdin").option("-f, --force", "Skip duplicate detection").option("-i, --input <format>", "Input format: json|bibtex|ris|pmid|doi|isbn|auto", "auto").option("--verbose", "Show detailed error information").option("-o, --output <format>", "Output format: json|text", "text").option("--full", "Include full CSL-JSON data in JSON output").action(async (inputs, options) => {
+  program.command("add").description("Add new reference(s) to the library").argument("[input...]", "File paths or identifiers (PMID/DOI/ISBN), or use stdin").option("-f, --force", "Skip duplicate detection").option("-i, --input <format>", "Input format: json|bibtex|ris|pmid|doi|isbn|auto", "auto").option("--verbose", "Show detailed error information").option("-o, --output <format>", "Output format: json|text", "text").option("--full", "Include full CSL-JSON data in JSON output").option("--fetch-fulltext", "Auto-fetch OA fulltext after adding").option("--no-fetch-fulltext", "Disable auto-fetch fulltext (overrides config)").action(async (inputs, options) => {
     await handleAddAction(inputs, options, program);
   });
 }
@@ -33472,6 +33484,15 @@ function registerFulltextCommand(program) {
   fulltextCmd.command("open").description("Open full-text file with system default application").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--pdf", "Open PDF file").option("--markdown", "Open Markdown file").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
     await handleFulltextOpenAction(identifier, options, program.opts());
   });
+  fulltextCmd.command("discover").description("Check OA (Open Access) availability for a reference").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
+    await handleFulltextDiscoverAction(identifier, options, program.opts());
+  });
+  fulltextCmd.command("fetch").description("Download OA full text and auto-attach to a reference").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--source <source>", "Preferred source: pmc, arxiv, unpaywall, core").option("-f, --force", "Overwrite existing fulltext attachment").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
+    await handleFulltextFetchAction(identifier, options, program.opts());
+  });
+  fulltextCmd.command("convert").description("Convert attached PMC XML to Markdown").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
+    await handleFulltextConvertAction(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) => {
@@ -33495,8 +33516,8 @@ async function main(argv) {
 }
 export {
   Select as S,
-  addAttachment as a,
-  stringify as b,
+  stringify as a,
+  buildResourceIndicators as b,
   createProgram as c,
   detachAttachment as d,
   formatBibtex as f,
@@ -33508,4 +33529,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-Cno7_aWr.js.map
+//# sourceMappingURL=index-DOvEusHb.js.map