@ncukondo/reference-manager 0.31.0 → 0.33.0

package/dist/chunks/{index-DCBYzNj-.js → index-PkCQJBdt.js}

@@ -1,13 +1,14 @@
 import { Command, Option } from "commander";
-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 packageJson, u as getFulltextAttachmentTypes, v as startServerWithFileWatcher, w as BUILTIN_CONVERTER_NAMES, x as BUILTIN_CONVERTER_INFO } from "./index-CS8S6gE4.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 packageJson, u as getFulltextAttachmentTypes, v as startServerWithFileWatcher, w as BUILTIN_CONVERTER_NAMES, x as BUILTIN_CONVERTER_INFO } from "./index-a52FHX03.js";
 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-CWHg1yol.js";
 import * as fs from "node:fs";
-import { promises, readFileSync, existsSync, mkdirSync, writeFileSync } from "node:fs";
+import { promises, readFileSync, existsSync, mkdirSync, writeFileSync, lstatSync, unlinkSync, rmSync, symlinkSync } from "node:fs";
 import * as os from "node:os";
+import { homedir } from "node:os";
 import * as path from "node:path";
-import path__default, { join, basename, dirname } from "node:path";
+import path__default, { join, basename, dirname, relative } from "node:path";
 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-BG2eomDC.js";
+import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-CMu82BI5.js";
 import { spawn, spawnSync } from "node:child_process";
 import process$1, { stdin, stdout } from "node:process";
 import * as readline from "node:readline";
@@ -163,6 +164,9 @@ function formatAddJsonOutput(result, options) {
       output.idChanged = true;
       output.originalId = item.originalId;
     }
+    if (item.warnings && item.warnings.length > 0) {
+      output.warnings = item.warnings;
+    }
     if (full) {
       const cslItem = items2.get(item.id);
       if (cslItem) {
@@ -348,12 +352,30 @@ async function executeAdd(options, context) {
   if (stdinContent !== void 0) {
     importOptions.stdinContent = stdinContent;
   }
+  if (options.urlConfig !== void 0) {
+    importOptions.urlConfig = options.urlConfig;
+  }
+  if (options.archiveFormat !== void 0) {
+    importOptions.archiveFormat = options.archiveFormat;
+  }
+  if (options.noArchive !== void 0) {
+    importOptions.noArchive = options.noArchive;
+  }
+  if (options.attachmentsDirectory !== void 0) {
+    importOptions.attachmentsDirectory = options.attachmentsDirectory;
+  }
   return context.library.import(inputs, importOptions);
 }
 function formatAddedItem(item) {
   const idPart = item.idChanged ? `${item.id} (was: ${item.originalId})` : item.id;
   const title2 = item.title ?? "(no title)";
-  return `  - ${idPart}: "${title2}"`;
+  const lines = [`  - ${idPart}: "${title2}"`];
+  if (item.warnings && item.warnings.length > 0) {
+    for (const warning of item.warnings) {
+      lines.push(`    Warning: ${warning}`);
+    }
+  }
+  return lines.join("\n");
 }
 function formatFailedItem(item, verbose) {
   let error = item.error;
@@ -893,15 +915,15 @@ class OperationsLibrary {
   }
   // High-level operations
   async search(options) {
-    const { searchReferences } = await import("./index-CS8S6gE4.js").then((n) => n.H);
+    const { searchReferences } = await import("./index-a52FHX03.js").then((n) => n.H);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-CS8S6gE4.js").then((n) => n.G);
+    const { listReferences } = await import("./index-a52FHX03.js").then((n) => n.G);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-CS8S6gE4.js").then((n) => n.F);
+    const { citeReferences } = await import("./index-a52FHX03.js").then((n) => n.F);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -912,36 +934,36 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-CS8S6gE4.js").then((n) => n.D);
+    const { addReferences } = await import("./index-a52FHX03.js").then((n) => n.D);
     return addReferences(inputs, this.library, options ?? {});
   }
   async check(options) {
-    const { checkReferences } = await import("./index-CS8S6gE4.js").then((n) => n.E);
+    const { checkReferences } = await import("./index-a52FHX03.js").then((n) => n.E);
     return checkReferences(this.library, options);
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-Cqss7VR_.js");
+    const { addAttachment: addAttachment2 } = await import("./index-DpZ-Ma7M.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-Cqss7VR_.js");
+    const { listAttachments: listAttachments2 } = await import("./index-DpZ-Ma7M.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-Cqss7VR_.js");
+    const { getAttachment: getAttachment2 } = await import("./index-DpZ-Ma7M.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-Cqss7VR_.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-DpZ-Ma7M.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-Cqss7VR_.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-DpZ-Ma7M.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-Cqss7VR_.js");
+    const { openAttachment: openAttachment2 } = await import("./index-DpZ-Ma7M.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1806,7 +1828,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$3(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-aEB3-5rp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2471,7 +2493,7 @@ 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-h15RI_Ae.js");
+      const { runFixInteraction } = await import("./fix-interaction-D_zhtL9k.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` : "";
@@ -2539,7 +2561,7 @@ function outputCheckError(error, format2) {
 }
 async function selectReferencesInteractively(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-aEB3-5rp.js");
   const allReferences = await context.library.getAll();
   if (allReferences.length === 0) {
     process.stderr.write("No references in library.\n");
@@ -2607,8 +2629,8 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-BG3Ef4Pd.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-D8beMum_.js");
+  const { runCiteFlow } = await import("./index-DMShdNwY.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-CQ4BBBZJ.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");
@@ -2823,6 +2845,15 @@ const CONFIG_KEY_REGISTRY = [
   },
   // attachments section
   { key: "attachments.directory", type: "string", description: "Attachments storage directory" },
+  // url section
+  {
+    key: "url.archive_format",
+    type: "enum",
+    description: "Default archive format for URL import",
+    enumValues: ["mhtml", "html"]
+  },
+  { key: "url.browser_path", type: "string", description: "Browser executable path" },
+  { key: "url.timeout", type: "integer", description: "Navigation timeout (seconds)" },
   // cli section
   {
     key: "cli.default_limit",
@@ -7291,7 +7322,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-aEB3-5rp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10867,7 +10898,7 @@ function getFulltextExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2, multiSelect = false) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-aEB3-5rp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect }, config2.cli.tui)
@@ -11290,6 +11321,79 @@ const fulltext = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProp
   handleFulltextGetAction,
   handleFulltextOpenAction
 }, Symbol.toStringTag, { value: "Module" }));
+const skillMd = '---\nname: ref\ndescription: Manage academic references in CSL-JSON format. Add papers by DOI/PMID/ISBN/arXiv, search and list references, generate citations, manage full-text PDFs, and check for retractions.\nallowed-tools:\n  - Bash\n  - Read\n  - Write\n  - Edit\n  - Glob\n  - Grep\n---\n\n# ref — Reference Manager\n\nA CLI tool for managing academic references using CSL-JSON as the single source of truth.\n\n## Quick Reference\n\n| Task | Command |\n|------|---------|\n| Add by DOI | `ref add 10.1234/example` |\n| Add by PMID | `ref add 12345678` |\n| Add by ISBN | `ref add 978-0-123456-78-9` |\n| Add by arXiv | `ref add 2301.12345` |\n| Add from BibTeX | `ref add references.bib` |\n| Add from RIS | `ref add references.ris` |\n| Search | `ref search "query"` |\n| List all | `ref list` |\n| Show details | `ref show <id>` |\n| Generate citation | `ref cite <id>` |\n| Export | `ref export <id> --output bibtex` |\n| Attach full-text | `ref fulltext attach <id> paper.pdf` |\n| Fetch full-text | `ref fulltext fetch <id>` |\n| Check retractions | `ref check <id>` |\n| Remove | `ref remove <id>` |\n| Update fields | `ref update <id> --set "title=New Title"` |\n| Configure | `ref config set <key> <value>` |\n\n## Search Syntax\n\n- Simple text: `ref search "machine learning"`\n- By author: `ref search "author:Smith"`\n- By year: `ref search "year:2024"`\n- By type: `ref search "type:article-journal"`\n- By tag: `ref search "tag:review"`\n- Combined: `ref search "author:Smith year:2024"`\n- Case-sensitive: prefix with `C/` (e.g., `ref search "C/RNA"`)\n\n## Output Formats\n\nMost commands support `--output` or `--json` flags:\n\n- `--json` — JSON output for programmatic use\n- `--output bibtex` — BibTeX format\n- `--output yaml` — YAML format\n\n## Full Help\n\nRun `ref --help` for all commands and options.\nRun `ref <command> --help` for command-specific help.\n';
+const fulltextMd = '---\nname: ref/fulltext\ndescription: Guide for managing full-text PDFs and Markdown files. Covers fetching, attaching, converting, and organizing full-text content.\n---\n\n# Full-Text Management\n\nGuide for working with full-text files (PDFs and Markdown) using `ref`.\n\n## Attach Files\n\n```bash\n# Attach a PDF\nref fulltext attach <id> paper.pdf\n\n# Attach Markdown\nref fulltext attach <id> paper.md\n```\n\n## Fetch Open Access\n\n```bash\n# Auto-discover and download OA full text\nref fulltext fetch <id>\n\n# Fetch with auto-attach on add\nref add 10.1234/example --fetch-fulltext\n```\n\n## Convert Formats\n\n```bash\n# Convert PDF to Markdown (requires external converter)\nref fulltext convert <id>\n\n# Supported converters: marker, docling, mineru, pymupdf\n# Configure custom converter:\nref config set fulltext.pdfConverter.command "marker"\nref config set fulltext.pdfConverter.args "{input} --output {output_dir}"\n```\n\n## Retrieve Full Text\n\n```bash\n# Get file path\nref fulltext get <id>\n\n# Get Markdown content to stdout\nref fulltext get <id> --stdout\n\n# Prefer specific format\nref fulltext get <id> --markdown\nref fulltext get <id> --pdf\n\n# Open in default system viewer\nref fulltext open <id>\n```\n\n## Check Availability\n\n```bash\n# Discover OA sources without downloading\nref fulltext discover <id>\n```\n\n## Detach\n\n```bash\n# Remove full-text association (file remains on disk)\nref fulltext detach <id>\n```\n\n## Tips\n\n- Use `ref fulltext get <id> --stdout` to pipe content to other tools\n- Full-text files are stored in the attachments directory (see `ref config get attachments.directory`)\n- Use `ref show <id>` to see full-text status alongside metadata\n- Markdown is preferred for AI-readable content; use `ref fulltext convert` after attaching PDF\n';
+const manuscriptWritingMd = "---\nname: ref/manuscript-writing\ndescription: Workflow for managing references while writing academic manuscripts. Covers citation generation, bibliography export, and reference verification.\n---\n\n# Manuscript Writing Workflow\n\nGuide for managing references during academic manuscript writing with `ref`.\n\n## 1. Find and Cite\n\n```bash\n# Search your library\nref search \"Smith 2024\"\n\n# Generate an inline citation\nref cite <id>\n\n# Generate citation in specific style\nref cite <id> --style apa\nref cite <id> --style vancouver\n\n# Get Pandoc/LaTeX citation key\nref cite <id> --key\n```\n\n## 2. Build Bibliography\n\n```bash\n# Export all cited references as BibTeX\nref export <id1> <id2> <id3> --output bibtex > references.bib\n\n# Export by search query\nref search \"tag:cited\" --output bibtex > references.bib\n\n# Export all references\nref export --all --output bibtex > library.bib\n```\n\n## 3. Add New References During Writing\n\n```bash\n# Quick add by DOI from a paper you're reading\nref add 10.1234/example\n\n# Add from clipboard BibTeX (pipe from stdin)\necho '<bibtex>' | ref add -\n\n# Add and immediately get citation key\nref add 10.1234/example --json | jq -r '.added[0].id'\n```\n\n## 4. Verify Before Submission\n\n```bash\n# Check all cited references for retractions\nref check <id1> <id2> <id3>\n\n# Verify metadata accuracy\nref check <id> --metadata\n\n# Show full details for final review\nref show <id>\n```\n\n## 5. Full-Text Management\n\n```bash\n# Attach supplementary files\nref fulltext attach <id> paper.pdf\nref fulltext attach <id> supplement.pdf\n\n# Get full-text path for reading\nref fulltext get <id>\n\n# Open in default viewer\nref fulltext open <id>\n```\n\n## Tips\n\n- Use `ref cite <id> --key` to get `@AuthorYear` keys for Pandoc\n- Use `ref show <id> --output yaml` for quick metadata overview\n- Use `ref url <id>` to get DOI/PubMed URLs for linking\n- Tag references with `ref update <id> --set \"tags=cited\"` to track what's in the manuscript\n";
+const systematicReviewMd = '---\nname: ref/systematic-review\ndescription: Workflow for conducting systematic literature reviews using reference-manager. Covers search strategy, screening, and evidence synthesis.\n---\n\n# Systematic Review Workflow\n\nGuide for conducting systematic literature reviews with `ref`.\n\n## 1. Build Search Set\n\nAdd references from multiple sources:\n\n```bash\n# From DOIs (e.g., exported from database search)\nref add 10.1234/study1 10.1234/study2 10.1234/study3\n\n# From BibTeX exported by PubMed/Scopus/Web of Science\nref add pubmed-results.bib\nref add scopus-results.ris\n\n# By PMID list\nref add 12345678 23456789 34567890\n```\n\n## 2. Tag and Organize\n\nUse tags to track screening stages:\n\n```bash\n# Tag references for screening\nref update <id> --set "tags=screening"\n\n# After title/abstract screening\nref update <id> --set "tags=included"\nref update <id> --set "tags=excluded"\n\n# After full-text review\nref update <id> --set "tags=final-included"\n```\n\n## 3. Full-Text Collection\n\n```bash\n# Auto-fetch open access full texts\nref fulltext fetch <id>\n\n# Attach manually obtained PDFs\nref fulltext attach <id> path/to/paper.pdf\n\n# Convert PDF to Markdown for text analysis\nref fulltext convert <id>\n```\n\n## 4. Quality Check\n\n```bash\n# Check for retractions or corrections\nref check <id>\n\n# Verify metadata against upstream sources\nref check <id> --metadata\n```\n\n## 5. Export for Analysis\n\n```bash\n# Export included studies as BibTeX\nref search "tag:final-included" --output bibtex > included.bib\n\n# Export as JSON for custom analysis\nref search "tag:final-included" --json > included.json\n```\n\n## Tips\n\n- Use `ref list --sort date-desc` to review chronologically\n- Use `ref search "tag:screening"` to find unprocessed references\n- Use `ref show <id>` to inspect full metadata before decisions\n- Duplicates are auto-detected on `ref add` — review skip messages\n';
+const SKILL_FILES = [
+  ["SKILL.md", skillMd],
+  ["references/systematic-review.md", systematicReviewMd],
+  ["references/manuscript-writing.md", manuscriptWritingMd],
+  ["references/fulltext.md", fulltextMd]
+];
+async function writeSkills(options) {
+  const { targetDir, force = false, user = false } = options;
+  const baseDir = user ? homedir() : targetDir;
+  const agentsDir = join(baseDir, ".agents", "skills", "ref");
+  const claudeDir = join(baseDir, ".claude", "skills");
+  const claudeLink = join(claudeDir, "ref");
+  const written = [];
+  const skipped = [];
+  mkdirSync(join(agentsDir, "references"), { recursive: true });
+  for (const [relativePath, content] of SKILL_FILES) {
+    const filePath = join(agentsDir, relativePath);
+    if (existsSync(filePath) && !force) {
+      skipped.push(relativePath);
+      continue;
+    }
+    writeFileSync(filePath, content, "utf-8");
+    written.push(relativePath);
+  }
+  let linkCreated = false;
+  mkdirSync(claudeDir, { recursive: true });
+  if (force && existsSync(claudeLink)) {
+    const stat2 = lstatSync(claudeLink);
+    if (stat2.isSymbolicLink()) {
+      unlinkSync(claudeLink);
+    } else if (stat2.isDirectory()) {
+      rmSync(claudeLink, { recursive: true, force: true });
+    }
+  }
+  if (!existsSync(claudeLink)) {
+    const linkTarget = relative(claudeDir, agentsDir);
+    symlinkSync(linkTarget, claudeLink, "junction");
+    linkCreated = true;
+  }
+  return { written, skipped, linkCreated };
+}
+async function executeInstallSkills(options) {
+  return writeSkills({
+    targetDir: process.cwd(),
+    force: options.force,
+    ...options.user != null && { user: options.user }
+  });
+}
+function formatInstallSkillsOutput(result) {
+  const lines = [];
+  if (result.written.length === 0 && result.skipped.length > 0) {
+    lines.push("Skills already up-to-date. Use --force to overwrite.");
+    lines.push(`  ${result.skipped.length} files skipped`);
+    return lines.join("\n");
+  }
+  if (result.written.length > 0) {
+    lines.push(`Installed ${result.written.length} skill files to .agents/skills/ref/`);
+    for (const file of result.written) {
+      lines.push(`  + ${file}`);
+    }
+  }
+  if (result.skipped.length > 0) {
+    lines.push(`  ${result.skipped.length} files skipped (already exist)`);
+  }
+  if (result.linkCreated) {
+    lines.push("Created symlink: .claude/skills/ref -> .agents/skills/ref");
+  }
+  return lines.join("\n");
+}
 function buildResourceIndicators(item) {
   const labels = [];
   const attachments = item.custom?.attachments;
@@ -26836,49 +26940,49 @@ function requireFastUri() {
     schemelessOptions.skipEscape = true;
     return serialize2(resolved, schemelessOptions);
   }
-  function resolveComponent(base, relative, options, skipNormalization) {
+  function resolveComponent(base, relative2, options, skipNormalization) {
     const target = {};
     if (!skipNormalization) {
       base = parse2(serialize2(base, options), options);
-      relative = parse2(serialize2(relative, options), options);
+      relative2 = parse2(serialize2(relative2, options), options);
     }
     options = options || {};
-    if (!options.tolerant && relative.scheme) {
-      target.scheme = relative.scheme;
-      target.userinfo = relative.userinfo;
-      target.host = relative.host;
-      target.port = relative.port;
-      target.path = removeDotSegments(relative.path || "");
-      target.query = relative.query;
+    if (!options.tolerant && relative2.scheme) {
+      target.scheme = relative2.scheme;
+      target.userinfo = relative2.userinfo;
+      target.host = relative2.host;
+      target.port = relative2.port;
+      target.path = removeDotSegments(relative2.path || "");
+      target.query = relative2.query;
     } else {
-      if (relative.userinfo !== void 0 || relative.host !== void 0 || relative.port !== void 0) {
-        target.userinfo = relative.userinfo;
-        target.host = relative.host;
-        target.port = relative.port;
-        target.path = removeDotSegments(relative.path || "");
-        target.query = relative.query;
+      if (relative2.userinfo !== void 0 || relative2.host !== void 0 || relative2.port !== void 0) {
+        target.userinfo = relative2.userinfo;
+        target.host = relative2.host;
+        target.port = relative2.port;
+        target.path = removeDotSegments(relative2.path || "");
+        target.query = relative2.query;
       } else {
-        if (!relative.path) {
+        if (!relative2.path) {
           target.path = base.path;
-          if (relative.query !== void 0) {
-            target.query = relative.query;
+          if (relative2.query !== void 0) {
+            target.query = relative2.query;
           } else {
             target.query = base.query;
           }
         } else {
-          if (relative.path[0] === "/") {
-            target.path = removeDotSegments(relative.path);
+          if (relative2.path[0] === "/") {
+            target.path = removeDotSegments(relative2.path);
           } else {
             if ((base.userinfo !== void 0 || base.host !== void 0 || base.port !== void 0) && !base.path) {
-              target.path = "/" + relative.path;
+              target.path = "/" + relative2.path;
             } else if (!base.path) {
-              target.path = relative.path;
+              target.path = relative2.path;
             } else {
-              target.path = base.path.slice(0, base.path.lastIndexOf("/") + 1) + relative.path;
+              target.path = base.path.slice(0, base.path.lastIndexOf("/") + 1) + relative2.path;
             }
             target.path = removeDotSegments(target.path);
           }
-          target.query = relative.query;
+          target.query = relative2.query;
         }
         target.userinfo = base.userinfo;
         target.host = base.host;
@@ -26886,7 +26990,7 @@ function requireFastUri() {
       }
       target.scheme = base.scheme;
     }
-    target.fragment = relative.fragment;
+    target.fragment = relative2.fragment;
     return target;
   }
   function equal2(uriA, uriB, options) {
@@ -32451,7 +32555,7 @@ 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-CS8S6gE4.js").then((n) => n.A);
+    const { removeReference } = await import("./index-a52FHX03.js").then((n) => n.A);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -32506,7 +32610,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-aEB3-5rp.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32731,7 +32835,7 @@ 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-BG3Ef4Pd.js");
+  const { runSearchFlow } = await import("./index-DMShdNwY.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();
@@ -32750,7 +32854,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-D5s90TfM.js");
+    const { isSideEffectAction } = await import("./action-menu-i1v02Qig.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32766,7 +32870,7 @@ 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-BG2eomDC.js").then((n) => n.j);
+      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-CMu82BI5.js").then((n) => n.j);
       const item = items2[0];
       if (!item) return;
       const url$1 = resolveDefaultUrl2(item);
@@ -33048,7 +33152,7 @@ function formatShowOutput(item, options, attachmentsDirectory) {
 }
 async function executeInteractiveSelect$1(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-aEB3-5rp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33297,7 +33401,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-aEB3-5rp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33592,7 +33696,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-CNWexQGu.js");
+  const { selectReferencesOrExit } = await import("./reference-select-aEB3-5rp.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -34040,6 +34144,7 @@ function createProgram() {
   registerAttachCommand(program);
   registerMcpCommand(program);
   registerUrlCommand(program);
+  registerInstallCommand(program);
   registerConfigCommand(program);
   registerCompletionCommand(program);
   return program;
@@ -34180,6 +34285,14 @@ function buildAddOptions(inputs, options, config2, stdinContent) {
   if (Object.keys(pubmedConfig).length > 0) {
     addOptions.pubmedConfig = pubmedConfig;
   }
+  addOptions.urlConfig = config2.url;
+  if (options.archiveFormat !== void 0) {
+    addOptions.archiveFormat = options.archiveFormat;
+  }
+  if (options.archive === false) {
+    addOptions.noArchive = true;
+  }
+  addOptions.attachmentsDirectory = config2.attachments.directory;
   return addOptions;
 }
 async function outputAddResultJson(result, context, full) {
@@ -34204,7 +34317,7 @@ function shouldAutoFetch(cliFlag, configEnabled) {
   return configEnabled;
 }
 async function performAutoFetch(addedItems, context, config2) {
-  const { fulltextFetch: fulltextFetch2 } = await import("./index-CS8S6gE4.js").then((n) => n.z);
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-a52FHX03.js").then((n) => n.z);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -34266,7 +34379,12 @@ function registerAddCommand(program) {
     "-i, --input <format>",
     "Input format: json|bibtex|ris|pmid|doi|isbn|arxiv|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) => {
+  ).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)").addOption(
+    new Option("--archive-format <format>", "Archive format for URL import").choices([
+      "mhtml",
+      "html"
+    ])
+  ).option("--no-archive", "Skip archive creation for URL import").action(async (inputs, options) => {
     await handleAddAction(inputs, options, program);
   });
 }
@@ -34470,6 +34588,25 @@ function registerUrlCommand(program) {
     await handleUrlAction(identifiers.length > 0 ? identifiers : void 0, options, globalOpts);
   });
 }
+function registerInstallCommand(program) {
+  const installCmd = program.command("install").description("Install tools and integrations");
+  installCmd.command("skills").description("Install Agent Skills (SKILL.md) for AI coding agents").option("-f, --force", "Overwrite existing files").option("-u, --user", "Install to user-level directory (~/.agents/skills/)").action(async (options) => {
+    try {
+      const result = await executeInstallSkills({
+        force: options.force ?? false,
+        ...options.user != null && { user: options.user }
+      });
+      const output = formatInstallSkillsOutput(result);
+      process.stdout.write(`${output}
+`);
+      setExitCode(ExitCode.SUCCESS);
+    } catch (error) {
+      process.stderr.write(`Error: ${error instanceof Error ? error.message : String(error)}
+`);
+      setExitCode(ExitCode.INTERNAL_ERROR);
+    }
+  });
+}
 async function main(argv) {
   const program = createProgram();
   if (process.env.COMP_LINE) {
@@ -34499,4 +34636,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-DCBYzNj-.js.map
+//# sourceMappingURL=index-PkCQJBdt.js.map