@ncukondo/reference-manager 0.29.6 → 0.30.0

package/dist/chunks/{index-Czz9ZhIH.js → index-C7BVI2qL.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, b as generateFilename, c as findFulltextFiles, h as findFulltextFile, j as extensionToFormat, k as fulltextAttach, l as fulltextDiscover, m as fulltextFetch, o as fulltextConvert, q as fulltextGet, r as getExtension, s as getDefaultExportFromCjs, B as BUILTIN_STYLES, t as getFulltextAttachmentTypes, u as startServerWithFileWatcher } from "./index-6Aild0Uk.js";
+import { n as normalizePathForOutput, d as deleteDirectoryIfEmpty, p as parseFilename, i as isReservedRole, e as ensureDirectory, a as addAttachment, R as RESERVED_ROLES, b as generateFilename, c as findFulltextFiles, h as findFulltextFile, j as extensionToFormat, k as fulltextAttach, l as fulltextDiscover, m as fulltextFetch, o as fulltextConvert, q as fulltextGet, r as getExtension, s as getDefaultExportFromCjs, B as BUILTIN_STYLES, t as getFulltextAttachmentTypes, u as startServerWithFileWatcher } from "./index-DoOmAYKd.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-B6sytmQd.js";
+import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-6TuXzBbw.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 = "0.29.6";
+const version$1 = "0.30.0";
 const description$1 = "A local reference management tool using CSL-JSON as the single source of truth";
 const packageJson = {
   name,
@@ -901,15 +901,15 @@ class OperationsLibrary {
   }
   // High-level operations
   async search(options) {
-    const { searchReferences } = await import("./index-6Aild0Uk.js").then((n) => n.E);
+    const { searchReferences } = await import("./index-DoOmAYKd.js").then((n) => n.E);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-6Aild0Uk.js").then((n) => n.D);
+    const { listReferences } = await import("./index-DoOmAYKd.js").then((n) => n.D);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-6Aild0Uk.js").then((n) => n.C);
+    const { citeReferences } = await import("./index-DoOmAYKd.js").then((n) => n.C);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -920,36 +920,36 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-6Aild0Uk.js").then((n) => n.z);
+    const { addReferences } = await import("./index-DoOmAYKd.js").then((n) => n.z);
     return addReferences(inputs, this.library, options ?? {});
   }
   async check(options) {
-    const { checkReferences } = await import("./index-6Aild0Uk.js").then((n) => n.A);
+    const { checkReferences } = await import("./index-DoOmAYKd.js").then((n) => n.A);
     return checkReferences(this.library, options);
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-CGV9-f_j.js");
+    const { addAttachment: addAttachment2 } = await import("./index-4KRTx7Fg.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-CGV9-f_j.js");
+    const { listAttachments: listAttachments2 } = await import("./index-4KRTx7Fg.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-CGV9-f_j.js");
+    const { getAttachment: getAttachment2 } = await import("./index-4KRTx7Fg.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-CGV9-f_j.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-4KRTx7Fg.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-CGV9-f_j.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-4KRTx7Fg.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-CGV9-f_j.js");
+    const { openAttachment: openAttachment2 } = await import("./index-4KRTx7Fg.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1814,7 +1814,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
+  const { selectReferencesOrExit } = await import("./reference-select-CES2SpzK.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2479,7 +2479,7 @@ 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-B6FGIOz8.js");
+      const { runFixInteraction } = await import("./fix-interaction-CIstlQZN.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` : "";
@@ -2547,7 +2547,7 @@ function outputCheckError(error, format2) {
 }
 async function selectReferencesInteractively(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Hc3wU8jL.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-CES2SpzK.js");
   const allReferences = await context.library.getAll();
   if (allReferences.length === 0) {
     process.stderr.write("No references in library.\n");
@@ -2615,8 +2615,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-KAr1YWtM.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-CcRnu0nC.js");
+  const { runCiteFlow } = await import("./index-AvQ2XqcY.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-DrECo2bW.js");
   const { search } = await import("./file-watcher-CWHg1yol.js").then((n) => n.B);
   const { tokenize } = await import("./file-watcher-CWHg1yol.js").then((n) => n.A);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
@@ -7217,7 +7217,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
+  const { selectReferencesOrExit } = await import("./reference-select-CES2SpzK.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10659,7 +10659,10 @@ async function executeFulltextConvert(options, context) {
   const operationOptions = {
     identifier: options.identifier,
     idType: options.idType,
-    fulltextDirectory: options.fulltextDirectory
+    fulltextDirectory: options.fulltextDirectory,
+    from: options.from,
+    converter: options.converter,
+    fulltextConfig: options.fulltextConfig
   };
   return fulltextConvert(context.library, operationOptions);
 }
@@ -10770,16 +10773,27 @@ function formatFetchErrorOutput(result) {
 }
 function formatFulltextConvertOutput(result) {
   if (!result.success) {
-    return `Error: ${result.error}`;
+    const lines = [`Error: ${result.error}`];
+    if (result.stderr) {
+      const stderrLines = result.stderr.trim().split("\n").slice(-5);
+      lines.push("", "  stderr (last lines):");
+      for (const line of stderrLines) {
+        lines.push(`    ${line}`);
+      }
+    }
+    if (result.hints) {
+      lines.push("", result.hints);
+    }
+    return lines.join("\n");
   }
-  return `Converted PMC XML to Markdown: ${result.filename}`;
+  return `Converted to Markdown: ${result.filename}`;
 }
 function getFulltextExitCode(result) {
   return result.success ? 0 : 1;
 }
 async function executeInteractiveSelect$1(context, config2, multiSelect = false) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
+  const { selectReferencesOrExit } = await import("./reference-select-CES2SpzK.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect }, config2.cli.tui)
@@ -11158,7 +11172,11 @@ async function handleFulltextConvertAction(identifierArg, options, globalOpts) {
     const convertOptions = {
       identifier,
       fulltextDirectory: config2.attachments.directory,
-      ...options.uuid && { idType: "uuid" }
+      ...options.uuid && { idType: "uuid" },
+      ...options.from && { from: options.from },
+      ...options.converter && { converter: options.converter },
+      ...options.force && { force: options.force },
+      fulltextConfig: config2.fulltext
     };
     const result = await executeFulltextConvert(convertOptions, context);
     const output = formatFulltextConvertOutput(result);
@@ -32015,9 +32033,11 @@ function registerFulltextConvertTool(server, getLibraryOperations, getConfig) {
   server.registerTool(
     "fulltext_convert",
     {
-      description: "Convert an attached PMC JATS XML file to Markdown for a reference.",
+      description: "Convert an attached fulltext file (PMC JATS XML or PDF) to Markdown for a reference. Auto-detects format (XML preferred over PDF). Use 'from' to force a specific format.",
       inputSchema: {
-        id: z.string().describe("Reference ID")
+        id: z.string().describe("Reference ID"),
+        from: z.enum(["xml", "pdf"]).optional().describe("Input format: xml, pdf (default: auto-detect)"),
+        converter: z.string().optional().describe("PDF converter: auto, marker, docling, mineru, pymupdf, or custom name")
       }
     },
     async (args) => {
@@ -32025,11 +32045,18 @@ function registerFulltextConvertTool(server, getLibraryOperations, getConfig) {
       const config2 = getConfig();
       const result = await fulltextConvert(libraryOps, {
         identifier: args.id,
-        fulltextDirectory: config2.attachments.directory
+        fulltextDirectory: config2.attachments.directory,
+        from: args.from,
+        converter: args.converter,
+        fulltextConfig: config2.fulltext
       });
       if (!result.success) {
+        const errorParts = [result.error ?? "Unknown error"];
+        if (result.hints) {
+          errorParts.push(result.hints);
+        }
         return {
-          content: [{ type: "text", text: result.error ?? "Unknown error" }],
+          content: [{ type: "text", text: errorParts.join("\n\n") }],
           isError: true
         };
       }
@@ -32037,7 +32064,7 @@ function registerFulltextConvertTool(server, getLibraryOperations, getConfig) {
         content: [
           {
             type: "text",
-            text: `Converted PMC XML to Markdown for '${args.id}': ${result.filename}`
+            text: `Converted to Markdown for '${args.id}': ${result.filename}`
           }
         ]
       };
@@ -32234,7 +32261,7 @@ 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-6Aild0Uk.js").then((n) => n.x);
+    const { removeReference } = await import("./index-DoOmAYKd.js").then((n) => n.x);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -32289,7 +32316,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Hc3wU8jL.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-CES2SpzK.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32514,7 +32541,7 @@ 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-KAr1YWtM.js");
+  const { runSearchFlow } = await import("./index-AvQ2XqcY.js");
   const { search } = await import("./file-watcher-CWHg1yol.js").then((n) => n.B);
   const { tokenize } = await import("./file-watcher-CWHg1yol.js").then((n) => n.A);
   checkTTY();
@@ -32533,7 +32560,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-C4nIA-Sl.js");
+    const { isSideEffectAction } = await import("./action-menu-DwHspdjM.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32549,7 +32576,7 @@ 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-B6sytmQd.js").then((n) => n.j);
+      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-6TuXzBbw.js").then((n) => n.j);
       const item = items2[0];
       if (!item) return;
       const url$1 = resolveDefaultUrl2(item);
@@ -32944,7 +32971,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
+  const { selectReferencesOrExit } = await import("./reference-select-CES2SpzK.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33239,7 +33266,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Hc3wU8jL.js");
+  const { selectReferencesOrExit } = await import("./reference-select-CES2SpzK.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33796,7 +33823,7 @@ function shouldAutoFetch(cliFlag, configEnabled) {
   return configEnabled;
 }
 async function performAutoFetch(addedItems, context, config2) {
-  const { fulltextFetch: fulltextFetch2 } = await import("./index-6Aild0Uk.js").then((n) => n.w);
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-DoOmAYKd.js").then((n) => n.w);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -34049,7 +34076,10 @@ function registerFulltextCommand(program) {
   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) => {
+  fulltextCmd.command("convert").description("Convert attached fulltext (XML or PDF) to Markdown").argument("[identifier]", "Citation key or UUID (interactive selection if omitted)").option("--uuid", "Interpret identifier as UUID").option("--from <format>", "Input format: xml, pdf (default: auto-detect)").option(
+    "--converter <name>",
+    "PDF converter: auto, marker, docling, mineru, pymupdf, or custom name"
+  ).option("--force", "Overwrite existing markdown attachment").action(async (identifier, options) => {
     await handleFulltextConvertAction(identifier, options, program.opts());
   });
 }
@@ -34088,4 +34118,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-Czz9ZhIH.js.map
+//# sourceMappingURL=index-C7BVI2qL.js.map