@ncukondo/reference-manager 0.22.2 → 0.22.3

package/dist/chunks/{index-DxjW_BKA.js → index-CYp8N4gu.js}

@@ -1,13 +1,13 @@
-import { Command } from "commander";
+import { Command, Option } from "commander";
 import { i as isEqual, M as MANAGED_CUSTOM_FIELDS, w as writeFileAtomic, L as Library, h as CslItemSchema, p as pickDefined, a as sortOrderSchema, z as paginationOptionsSchema, F as FileWatcher, b as sortFieldSchema, y as searchSortFieldSchema } from "./file-watcher-Dyns9dxx.js";
 import * as fs from "node:fs";
 import { promises, readFileSync, existsSync, mkdirSync, writeFileSync } from "node:fs";
 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, B as BUILTIN_STYLES, r as getFulltextAttachmentTypes, s as startServerWithFileWatcher } from "./index-DFhoO9RA.js";
+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-CNr_FIip.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-BZgpKsTG.js";
+import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-CJB3-kI5.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 = "0.22.2";
+const version$1 = "0.22.3";
 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-DFhoO9RA.js").then((n) => n.z);
+    const { searchReferences } = await import("./index-CNr_FIip.js").then((n) => n.z);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-DFhoO9RA.js").then((n) => n.y);
+    const { listReferences } = await import("./index-CNr_FIip.js").then((n) => n.y);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-DFhoO9RA.js").then((n) => n.x);
+    const { citeReferences } = await import("./index-CNr_FIip.js").then((n) => n.x);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -921,32 +921,32 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-DFhoO9RA.js").then((n) => n.w);
+    const { addReferences } = await import("./index-CNr_FIip.js").then((n) => n.w);
     return addReferences(inputs, this.library, options ?? {});
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-CXZ_Trjb.js");
+    const { addAttachment: addAttachment2 } = await import("./index-4607sQqe.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-CXZ_Trjb.js");
+    const { listAttachments: listAttachments2 } = await import("./index-4607sQqe.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-CXZ_Trjb.js");
+    const { getAttachment: getAttachment2 } = await import("./index-4607sQqe.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-CXZ_Trjb.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-4607sQqe.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-CXZ_Trjb.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-4607sQqe.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-CXZ_Trjb.js");
+    const { openAttachment: openAttachment2 } = await import("./index-4607sQqe.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1790,7 +1790,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Cpq_Q4f6.js");
+  const { selectReferencesOrExit } = await import("./reference-select-dvLqdttM.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2338,8 +2338,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-B7NyGOm6.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-CQIqnmWS.js");
+  const { runCiteFlow } = await import("./index-DjQiOVp_.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-BpKQvCBz.js");
   const { search } = await import("./file-watcher-Dyns9dxx.js").then((n) => n.B);
   const { tokenize } = await import("./file-watcher-Dyns9dxx.js").then((n) => n.A);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
@@ -2423,6 +2423,7 @@ const ENV_OVERRIDE_MAP = {
   REFERENCE_MANAGER_CLI_DEFAULT_LIMIT: "cli.default_limit",
   REFERENCE_MANAGER_MCP_DEFAULT_LIMIT: "mcp.default_limit",
   REFERENCE_MANAGER_CLIPBOARD_AUTO_COPY: "cli.tui.clipboard_auto_copy",
+  REFERENCE_MANAGER_FULLTEXT_PREFERRED_TYPE: "fulltext.preferred_type",
   PUBMED_EMAIL: "pubmed.email",
   PUBMED_API_KEY: "pubmed.api_key",
   UNPAYWALL_EMAIL: "fulltext.sources.unpaywall_email",
@@ -2496,6 +2497,13 @@ const CONFIG_KEY_REGISTRY = [
     type: "string[]",
     description: "Fulltext source priority order"
   },
+  {
+    key: "fulltext.preferred_type",
+    type: "enum",
+    description: "Preferred fulltext type for open/get",
+    enumValues: ["pdf", "markdown"],
+    optional: true
+  },
   {
     key: "fulltext.auto_fetch_on_add",
     type: "boolean",
@@ -6919,7 +6927,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Cpq_Q4f6.js");
+  const { selectReferencesOrExit } = await import("./reference-select-dvLqdttM.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10247,23 +10255,25 @@ async function fulltextDetach(library, options) {
 function buildFilePath(attachmentsDirectory, directory, filename) {
   return join(attachmentsDirectory, directory, filename);
 }
-function determineTypeToOpen(attachments) {
+function determineTypeToOpen(attachments, preferredType) {
   const files = findFulltextFiles(attachments);
   if (files.length === 0) return void 0;
-  const pdfFile = files.find((f) => f.filename.endsWith(".pdf"));
-  if (pdfFile) return "pdf";
-  const mdFile = files.find((f) => f.filename.endsWith(".md"));
-  if (mdFile) return "markdown";
+  const hasPdf = files.some((f) => f.filename.endsWith(".pdf"));
+  const hasMd = files.some((f) => f.filename.endsWith(".md"));
+  if (preferredType === "markdown" && hasMd) return "markdown";
+  if (preferredType === "pdf" && hasPdf) return "pdf";
+  if (hasPdf) return "pdf";
+  if (hasMd) return "markdown";
   return void 0;
 }
 async function fulltextOpen(library, options) {
-  const { identifier, type: type2, idType = "id", fulltextDirectory } = options;
+  const { identifier, type: type2, preferredType, idType = "id", fulltextDirectory } = options;
   const item = await library.find(identifier, { idType });
   if (!item) {
     return { success: false, error: `Reference not found: ${identifier}` };
   }
   const attachments = item.custom?.attachments;
-  const typeToOpen = type2 ?? determineTypeToOpen(attachments);
+  const typeToOpen = type2 ?? determineTypeToOpen(attachments, preferredType);
   if (!typeToOpen) {
     return { success: false, error: `No fulltext attached to reference: ${identifier}` };
   }
@@ -10309,6 +10319,7 @@ async function executeFulltextGet(options, context) {
   const operationOptions = {
     identifier: options.identifier,
     type: options.type,
+    preferredType: options.preferredType,
     stdout: options.stdout,
     idType: options.idType,
     fulltextDirectory: options.fulltextDirectory
@@ -10329,6 +10340,7 @@ async function executeFulltextOpen(options, context) {
   const operationOptions = {
     identifier: options.identifier,
     type: options.type,
+    preferredType: options.preferredType,
     idType: options.idType,
     fulltextDirectory: options.fulltextDirectory
   };
@@ -10456,7 +10468,7 @@ function getFulltextExitCode(result) {
 }
 async function executeInteractiveSelect$1(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Cpq_Q4f6.js");
+  const { selectReferencesOrExit } = await import("./reference-select-dvLqdttM.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -10552,13 +10564,15 @@ async function handleFulltextGetAction(identifierArg, options, globalOpts) {
       }
       identifier = stdinId;
     }
+    const preferValue = options.prefer ?? config2.fulltext.preferredType;
     const getOptions = {
       identifier,
       fulltextDirectory: config2.attachments.directory,
       ...options.pdf && { type: "pdf" },
       ...options.markdown && { type: "markdown" },
       ...options.stdout && { stdout: options.stdout },
-      ...options.uuid && { idType: "uuid" }
+      ...options.uuid && { idType: "uuid" },
+      ...preferValue && { preferredType: preferValue }
     };
     const result = await executeFulltextGet(getOptions, context);
     outputFulltextGetResult(result, Boolean(options.stdout));
@@ -10629,12 +10643,14 @@ async function handleFulltextOpenAction(identifierArg, options, globalOpts) {
       }
       identifier = stdinId;
     }
+    const preferValue = options.prefer ?? config2.fulltext.preferredType;
     const openOptions = {
       identifier,
       fulltextDirectory: config2.attachments.directory,
       ...options.pdf && { type: "pdf" },
       ...options.markdown && { type: "markdown" },
-      ...options.uuid && { idType: "uuid" }
+      ...options.uuid && { idType: "uuid" },
+      ...preferValue && { preferredType: preferValue }
     };
     const result = await executeFulltextOpen(openOptions, context);
     const output = formatFulltextOpenOutput(result);
@@ -31377,9 +31393,11 @@ function registerFulltextGetTool(server, getLibraryOperations, getConfig) {
     async (args) => {
       const libraryOps = getLibraryOperations();
       const config2 = getConfig();
+      const preferredType = config2.fulltext?.preferredType;
       const pathResult = await fulltextGet(libraryOps, {
         identifier: args.id,
-        fulltextDirectory: config2.attachments.directory
+        fulltextDirectory: config2.attachments.directory,
+        ...preferredType && { preferredType }
       });
       if (!pathResult.success) {
         return {
@@ -31750,7 +31768,7 @@ 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-DFhoO9RA.js").then((n) => n.v);
+    const { removeReference } = await import("./index-CNr_FIip.js").then((n) => n.v);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -31805,7 +31823,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Cpq_Q4f6.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-dvLqdttM.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32030,7 +32048,7 @@ 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-B7NyGOm6.js");
+  const { runSearchFlow } = await import("./index-DjQiOVp_.js");
   const { search } = await import("./file-watcher-Dyns9dxx.js").then((n) => n.B);
   const { tokenize } = await import("./file-watcher-Dyns9dxx.js").then((n) => n.A);
   checkTTY();
@@ -32049,7 +32067,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-R-QKMCZJ.js");
+    const { isSideEffectAction } = await import("./action-menu-CKMhb5fv.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32065,7 +32083,7 @@ 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-BZgpKsTG.js").then((n) => n.j);
+      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-CJB3-kI5.js").then((n) => n.j);
       const item = items2[0];
       if (!item) return;
       const url$1 = resolveDefaultUrl2(item);
@@ -32452,7 +32470,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Cpq_Q4f6.js");
+  const { selectReferencesOrExit } = await import("./reference-select-dvLqdttM.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32747,7 +32765,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Cpq_Q4f6.js");
+  const { selectReferencesOrExit } = await import("./reference-select-dvLqdttM.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33250,7 +33268,7 @@ function shouldAutoFetch(cliFlag, configEnabled) {
   return configEnabled;
 }
 async function performAutoFetch(addedItems, context, config2) {
-  const { fulltextFetch: fulltextFetch2 } = await import("./index-DFhoO9RA.js").then((n) => n.u);
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-CNr_FIip.js").then((n) => n.u);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -33471,13 +33489,17 @@ function registerFulltextCommand(program) {
   fulltextCmd.command("attach").description("Attach a full-text file to a reference").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").argument("[file-path]", "Path to the file to attach").option("--pdf [path]", "Attach as PDF (path optional if provided as argument)").option("--markdown [path]", "Attach as Markdown (path optional if provided as argument)").option("--move", "Move file instead of copy").option("-f, --force", "Overwrite existing attachment").option("--uuid", "Interpret identifier as UUID").action(async (identifier, filePath, options) => {
     await handleFulltextAttachAction(identifier, filePath, options, program.opts());
   });
-  fulltextCmd.command("get").description("Get full-text file path or content").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--pdf", "Get PDF file only").option("--markdown", "Get Markdown file only").option("--stdout", "Output file content to stdout").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
+  fulltextCmd.command("get").description("Get full-text file path or content").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--pdf", "Get PDF file only").option("--markdown", "Get Markdown file only").addOption(
+    new Option("--prefer <type>", "Preferred fulltext type").choices(["pdf", "markdown"])
+  ).option("--stdout", "Output file content to stdout").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
     await handleFulltextGetAction(identifier, options, program.opts());
   });
   fulltextCmd.command("detach").description("Detach full-text file from a reference").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--pdf", "Detach PDF only").option("--markdown", "Detach Markdown only").option("--remove-files", "Also delete the file from disk").option("-f, --force", "Skip confirmation for file removal").option("--uuid", "Interpret identifier as UUID").action(async (identifier, options) => {
     await handleFulltextDetachAction(identifier, options, program.opts());
   });
-  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) => {
+  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").addOption(
+    new Option("--prefer <type>", "Preferred fulltext type").choices(["pdf", "markdown"])
+  ).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) => {
@@ -33525,4 +33547,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-DxjW_BKA.js.map
+//# sourceMappingURL=index-CYp8N4gu.js.map