@ncukondo/search-hub 0.23.0 → 0.24.0

package/dist/cli/suggestions/rules.js

@@ -1,7 +1,7 @@
 import { generateReviewNextSteps, computeBatchContinuation } from "../commands/review/next-steps.js";
 const queryInitRule = (ctx) => {
   if (ctx.command !== "query init") return null;
-  const file = ctx.outputFile ?? "queries/query.yaml";
+  const file = ctx.outputFile ?? ".search-hub/queries/query.yaml";
   return {
     next: [
       { command: `$EDITOR ${file}`, description: "Edit your query" },

package/dist/cli/suggestions/rules.js.map

@@ -1 +1 @@
-{"version":3,"file":"rules.js","sources":["../../../src/cli/suggestions/rules.ts"],"sourcesContent":["import type { SuggestionContext, SuggestionResult, SuggestionRule } from './types.js';\nimport { computeBatchContinuation, generateReviewNextSteps } from '../commands/review/next-steps.js';\n\n// Phase 1: Query Preparation rules\n\nconst queryInitRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'query init') return null;\n  const file = ctx.outputFile ?? 'queries/query.yaml';\n  return {\n    next: [\n      { command: `$EDITOR ${file}`, description: 'Edit your query' },\n      { command: `search-hub query validate ${file}`, description: 'Validate query' },\n      { command: `search-hub search ${file} --count-only`, description: 'Check hit counts' },\n    ],\n    seeAlso: [],\n  };\n};\n\nconst queryValidateRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'query validate') return null;\n  const file = ctx.queryFile ?? '<query-file>';\n\n  if (ctx.validationSuccess === false) {\n    const next = [{ command: `$EDITOR ${file}`, description: 'Fix errors and re-validate' }];\n\n    if (ctx.hasSchemaLink === false) {\n      return {\n        next,\n        or: {\n          label: 'Or create a new query from the template',\n          items: [{ command: 'search-hub query init \"<title>\"', description: '' }],\n        },\n        seeAlso: [],\n      };\n    }\n\n    return { next, seeAlso: [] };\n  }\n\n  const next = [\n    { command: `search-hub search ${file} --dry-run`, description: 'Check DB translations' },\n    { command: `search-hub search ${file} --preview`, description: 'Preview hit counts + sample titles' },\n  ];\n\n  if (ctx.hasSchemaLink === false) {\n    return {\n      tip: 'Tip: Start from a template to get $schema support and usage examples:\\n'\n         + '     search-hub query init \"<title>\"',\n      next,\n      seeAlso: [],\n    };\n  }\n\n  return { next, seeAlso: [] };\n};\n\nconst queryTranslateRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'query translate') return null;\n  const file = ctx.queryFile ?? '<query-file>';\n  return {\n    next: [\n      { command: `search-hub search ${file} --preview`, description: 'Preview hit counts + sample titles' },\n      { command: `search-hub search ${file}`, description: 'Execute search' },\n    ],\n    seeAlso: [],\n  };\n};\n\n// Phase 2: Search Execution rules\n\n/**\n * Build search completion suggestions based on session status.\n * Shared by search, search --query, and resume commands.\n */\nfunction searchCompletionSuggestion(ctx: SuggestionContext): SuggestionResult | null {\n  const sid = ctx.sessionId ?? '<session-id>';\n\n  switch (ctx.sessionStatus) {\n    case 'completed': {\n      const seeAlso: SuggestionResult['seeAlso'] = [];\n      if (ctx.previousSessionId) {\n        seeAlso.push({\n          command: `search-hub diff ${ctx.previousSessionId} ${sid}`,\n          description: 'Compare with previous',\n        });\n      } else if (ctx.sessionCount !== undefined && ctx.sessionCount > 1) {\n        seeAlso.push({\n          command: `search-hub diff <other-session> ${sid}`,\n          description: 'Compare with another query version',\n        });\n      }\n      return {\n        next: [{ command: `search-hub results ${sid}`, description: 'View results' }],\n        seeAlso,\n      };\n    }\n    case 'partial':\n      return {\n        next: [{ command: `search-hub resume ${sid}`, description: 'Retry failed databases' }],\n        seeAlso: [],\n      };\n    case 'failed':\n      return {\n        next: [\n          { command: `search-hub resume ${sid} --retry-failed`, description: 'Retry all databases' },\n          { command: `search-hub status ${sid}`, description: 'View error details' },\n        ],\n        seeAlso: [],\n      };\n    default:\n      return null;\n  }\n}\n\nconst searchDryRunRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'search --dry-run') return null;\n  const file = ctx.queryFile ?? '<query-file>';\n  return {\n    next: [\n      { command: `search-hub search ${file} --preview`, description: 'Preview hit counts + sample titles' },\n      { command: `search-hub search ${file}`, description: 'Execute search' },\n    ],\n    seeAlso: [],\n  };\n};\n\nconst searchPreviewRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'search --preview') return null;\n  const file = ctx.queryFile ?? '<query-file>';\n  return {\n    next: [\n      { command: `search-hub query assess ${file} --verdict <verdict>`, description: 'Record assessment' },\n      { command: `search-hub search ${file}`, description: 'Execute full search' },\n    ],\n    seeAlso: [],\n  };\n};\n\nconst searchCountOnlyRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'search --count-only') return null;\n  const file = ctx.queryFile ?? '<query-file>';\n  return {\n    next: [\n      { command: `$EDITOR ${file}`, description: 'Edit query to refine' },\n      { command: `search-hub search ${file} --count-only`, description: 'Re-check counts' },\n      { command: `search-hub query assess ${file} --verdict refine`, description: 'Record assessment' },\n    ],\n    seeAlso: [\n      { command: `search-hub search ${file}`, description: 'Execute full search' },\n    ],\n  };\n};\n\nconst searchDirectQueryRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'search --query') return null;\n  const base = searchCompletionSuggestion(ctx);\n  if (base === null) return null;\n  return {\n    next: base.next,\n    seeAlso: [\n      ...base.seeAlso,\n      { command: 'search-hub query init \"<title>\"', description: 'Save as YAML for reproducibility' },\n    ],\n  };\n};\n\nconst searchRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'search') return null;\n  return searchCompletionSuggestion(ctx);\n};\n\nconst resumeRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'resume') return null;\n  return searchCompletionSuggestion(ctx);\n};\n\n// Phase 3: Result Analysis rules\n\nconst statusRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'status') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n\n  switch (ctx.sessionStatus) {\n    case 'completed':\n      return {\n        next: [{ command: `search-hub results ${sid}`, description: 'View results' }],\n        seeAlso: [],\n      };\n    case 'partial':\n      return {\n        next: [{ command: `search-hub resume ${sid}`, description: 'Resume search' }],\n        seeAlso: [],\n      };\n    case 'failed':\n      return {\n        next: [{ command: `search-hub resume ${sid} --retry-failed`, description: 'Retry all databases' }],\n        seeAlso: [],\n      };\n    default:\n      return null;\n  }\n};\n\n/**\n * Suggestion for results/summary commands - conditional based on reviews.yaml existence.\n */\nfunction resultReviewSuggestion(ctx: SuggestionContext): SuggestionResult {\n  const sid = ctx.sessionId ?? '<session-id>';\n  if (ctx.hasReviews === true) {\n    return {\n      next: [{ command: `search-hub review status --session ${sid}`, description: 'Check review progress' }],\n      seeAlso: [],\n    };\n  }\n  return {\n    next: [{ command: `search-hub review init --session ${sid}`, description: 'Start systematic review' }],\n    seeAlso: [],\n  };\n}\n\nconst resultsRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'results') return null;\n  return resultReviewSuggestion(ctx);\n};\n\nconst summaryRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'summary') return null;\n  return resultReviewSuggestion(ctx);\n};\n\nconst diffRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'diff') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  const seeAlso: SuggestionResult['seeAlso'] = [];\n\n  // Suggest merge when both sessions have unique articles\n  if (ctx.diffAddedCount !== undefined && ctx.diffAddedCount > 0 &&\n      ctx.diffRemovedCount !== undefined && ctx.diffRemovedCount > 0) {\n    const sid1 = ctx.diffSession1Id ?? '<session-id-1>';\n    seeAlso.push({\n      command: `search-hub merge ${sid1} ${sid}`,\n      description: 'Combine results from both sessions',\n    });\n  }\n\n  seeAlso.push({ command: `search-hub results ${sid}`, description: 'View detailed results' });\n\n  return { next: [], seeAlso };\n};\n\nconst mergeRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'merge') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  return {\n    next: [\n      { command: `search-hub results ${sid}`, description: 'View merged results' },\n      { command: `search-hub summary ${sid}`, description: 'View merge statistics' },\n    ],\n    seeAlso: [],\n  };\n};\n\nconst relatedRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'related') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  return {\n    next: [\n      { command: `search-hub results ${sid}`, description: 'View related articles' },\n      { command: `search-hub review init ${sid}`, description: 'Screen related articles' },\n      { command: `search-hub export ${sid}`, description: 'Export results' },\n    ],\n    seeAlso: [],\n  };\n};\n\n// Phase 4: Review Workflow rules\n\nconst reviewInitRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'review init') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  return {\n    next: [\n      {\n        command: `search-hub review extract --session ${sid} --basis title --name title-screening`,\n        description: 'Start title screening',\n      },\n    ],\n    seeAlso: [],\n  };\n};\n\nconst reviewStatusRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'review status') return null;\n  const rs = ctx.reviewStatus;\n  if (!rs) return null;\n\n  return generateReviewNextSteps({\n    sessionId: ctx.sessionId ?? '<session-id>',\n    statusResult: rs,\n    ...(rs.mode && { mode: rs.mode }),\n  });\n};\n\nconst reviewListRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'review list') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  return {\n    next: [],\n    seeAlso: [\n      {\n        command: `search-hub review extract --session ${sid} --name <name>`,\n        description: 'Extract subset for review',\n      },\n    ],\n  };\n};\n\nconst reviewExtractRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'review extract') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  const name = ctx.extractName ?? '<name>';\n  const result: SuggestionResult = {\n    next: [\n      {\n        command: `search-hub review merge --session ${sid} --name ${name}`,\n        description: 'Merge review results',\n      },\n    ],\n    seeAlso: [],\n  };\n\n  // Batch continuation: suggest next batch if --limit was used with remaining articles\n  if (\n    ctx.extractLimit !== undefined &&\n    ctx.extractedCount !== undefined &&\n    ctx.totalMatching !== undefined\n  ) {\n    const batch = computeBatchContinuation({\n      sessionId: sid,\n      extractName: name !== '<name>' ? name : undefined,\n      extractedCount: ctx.extractedCount,\n      totalMatching: ctx.totalMatching,\n      limit: ctx.extractLimit,\n      offset: ctx.extractOffset,\n    });\n    if (batch) result.seeAlso.push(batch);\n  }\n\n  return result;\n};\n\nconst reviewMergeRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'review merge') return null;\n  const rs = ctx.reviewStatus;\n  if (!rs) {\n    // Fallback: suggest status check when reviewStatus not available\n    const sid = ctx.sessionId ?? '<session-id>';\n    return {\n      next: [\n        {\n          command: `search-hub review status --session ${sid}`,\n          description: 'Check progress',\n        },\n      ],\n      seeAlso: [],\n    };\n  }\n\n  return generateReviewNextSteps({\n    sessionId: ctx.sessionId ?? '<session-id>',\n    statusResult: rs,\n    ...(rs.mode && { mode: rs.mode }),\n  });\n};\n\nconst reviewFinalizeRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'review finalize') return null;\n  const rs = ctx.reviewStatus;\n  if (!rs) return null;\n\n  return generateReviewNextSteps({\n    sessionId: ctx.sessionId ?? '<session-id>',\n    statusResult: rs,\n    ...(rs.mode && { mode: rs.mode }),\n  });\n};\n\nconst reviewExportRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'review export') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  return {\n    next: [],\n    seeAlso: [\n      {\n        command: `search-hub register ${sid} --reviewed`,\n        description: 'Register with reference-manager',\n      },\n    ],\n  };\n};\n\n// Phase 5: Registration & Export rules\n\nconst exportRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'export') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  if (ctx.hasReviews === false) {\n    return {\n      next: [],\n      seeAlso: [\n        {\n          command: `search-hub review init --session ${sid}`,\n          description: 'Start review workflow',\n        },\n      ],\n    };\n  }\n  return { next: [], seeAlso: [] };\n};\n\nconst registerRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'register') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  if (ctx.hasReviews === false) {\n    return {\n      next: [],\n      seeAlso: [\n        {\n          command: `search-hub review init --session ${sid}`,\n          description: 'Start systematic review',\n        },\n      ],\n    };\n  }\n  // Terminal state: no suggestions\n  return null;\n};\n\nconst queryAssessRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'query assess') return null;\n  const file = ctx.queryFile ?? '<query-file>';\n  return {\n    next: [\n      { command: `search-hub query log ${file}`, description: 'View iteration history' },\n    ],\n    seeAlso: [\n      { command: `$EDITOR ${file}`, description: 'Edit query and re-run count' },\n    ],\n  };\n};\n\nconst notesRule: SuggestionRule = (ctx) => {\n  if (ctx.command !== 'notes add' && ctx.command !== 'notes assess') return null;\n  const sid = ctx.sessionId ?? '<session-id>';\n  return {\n    next: [],\n    seeAlso: [{ command: `search-hub notes list ${sid}`, description: 'View notes' }],\n  };\n};\n\n/**\n * All suggestion rules in evaluation order.\n */\nconst rules: SuggestionRule[] = [\n  // Phase 1\n  queryInitRule,\n  queryValidateRule,\n  queryTranslateRule,\n  // Phase 2\n  searchDryRunRule,\n  searchPreviewRule,\n  searchCountOnlyRule,\n  searchDirectQueryRule,\n  searchRule,\n  resumeRule,\n  // Phase 3\n  statusRule,\n  resultsRule,\n  summaryRule,\n  diffRule,\n  mergeRule,\n  relatedRule,\n  // Phase 4\n  reviewInitRule,\n  reviewStatusRule,\n  reviewListRule,\n  reviewExtractRule,\n  reviewMergeRule,\n  reviewFinalizeRule,\n  reviewExportRule,\n  // Query iteration\n  queryAssessRule,\n  // Phase 5\n  exportRule,\n  registerRule,\n  notesRule,\n];\n\n/**\n * Evaluate suggestion rules for the given context.\n * Returns the first matching rule's result, or null if no rules match.\n */\nexport function getSuggestion(ctx: SuggestionContext): SuggestionResult | null {\n  for (const rule of rules) {\n    const result = rule(ctx);\n    if (result !== null) return result;\n  }\n  return 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package/dist/cli/utils/argv.d.ts

@@ -0,0 +1,34 @@
+import { Command } from 'commander';
+/**
+ * Extract the subcommand name from argv (best-effort).
+ *
+ * Skips global options that take a value so things like `--config upgrade`
+ * are not misread as the `upgrade` subcommand. The set of value-taking
+ * options is derived from the Commander program itself, so it stays in sync
+ * with the option definitions.
+ */
+export declare function extractCommandName(argv: string[], program: Command): string;
+/**
+ * Best-effort detection of `--no-update-check` in argv, without relying on
+ * Commander having parsed yet (the async check starts before parseAsync).
+ */
+export declare function hasNoUpdateCheckFlag(argv: string[]): boolean;
+/**
+ * Best-effort detection of the global `--quiet` flag in argv, without relying
+ * on Commander having parsed yet (the async check starts before parseAsync).
+ * `--quiet` promises "suppress all output except errors", which includes the
+ * update notice.
+ */
+export declare function hasQuietFlag(argv: string[]): boolean;
+/**
+ * Rewrite `search-hub upgrade --version <tag>` to `--version=<tag>`.
+ *
+ * The program has `.version(VERSION)` which registers a no-arg `--version`
+ * flag at the root. Commander's parser consumes the root `--version` before
+ * subcommand options, so the space-separated form is caught by the root
+ * (prints + exits) instead of reaching `upgrade`'s `--version <tag>`. The
+ * `=` form binds the value to the subcommand's option and sidesteps the
+ * root flag.
+ */
+export declare function rewriteUpgradeVersionFlag(argv: string[], program: Command): string[];
+//# sourceMappingURL=argv.d.ts.map

package/dist/cli/utils/argv.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"argv.d.ts","sourceRoot":"","sources":["../../../src/cli/utils/argv.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiBzC;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,OAAO,GAAG,MAAM,CAkB3E;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAK5D;AAED;;;;;GAKG;AACH,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAKpD;AAED;;;;;;;;;GASG;AACH,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,OAAO,GAAG,MAAM,EAAE,CAiBpF"}

package/dist/cli/utils/argv.js

@@ -0,0 +1,63 @@
+function collectValueTakingFlags(program) {
+  const flags = /* @__PURE__ */ new Set();
+  for (const opt of program.options) {
+    if (!opt.required && !opt.optional) continue;
+    if (opt.long) flags.add(opt.long);
+    if (opt.short) flags.add(opt.short);
+  }
+  return flags;
+}
+function extractCommandName(argv, program) {
+  const valueTakingFlags = collectValueTakingFlags(program);
+  let skipNext = false;
+  for (let i = 2; i < argv.length; i++) {
+    const token = argv[i];
+    if (!token) continue;
+    if (skipNext) {
+      skipNext = false;
+      continue;
+    }
+    if (token.startsWith("-")) {
+      if (!token.includes("=") && valueTakingFlags.has(token)) skipNext = true;
+      continue;
+    }
+    return token;
+  }
+  return "";
+}
+function hasNoUpdateCheckFlag(argv) {
+  for (let i = 2; i < argv.length; i++) {
+    if (argv[i] === "--no-update-check") return true;
+  }
+  return false;
+}
+function hasQuietFlag(argv) {
+  for (let i = 2; i < argv.length; i++) {
+    if (argv[i] === "--quiet") return true;
+  }
+  return false;
+}
+function rewriteUpgradeVersionFlag(argv, program) {
+  if (extractCommandName(argv, program) !== "upgrade") return argv;
+  const out = [];
+  for (let i = 0; i < argv.length; i++) {
+    const token = argv[i];
+    if (token === "--version" && i + 1 < argv.length) {
+      const next = argv[i + 1];
+      if (next !== void 0 && !next.startsWith("-")) {
+        out.push(`--version=${next}`);
+        i++;
+        continue;
+      }
+    }
+    if (token !== void 0) out.push(token);
+  }
+  return out;
+}
+export {
+  extractCommandName,
+  hasNoUpdateCheckFlag,
+  hasQuietFlag,
+  rewriteUpgradeVersionFlag
+};
+//# sourceMappingURL=argv.js.map

package/dist/cli/utils/argv.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"argv.js","sources":["../../../src/cli/utils/argv.ts"],"sourcesContent":["/**\n * Argv helpers for the update-check notifier and the `upgrade` command.\n *\n * These run before Commander parses argv (the async update check starts\n * before command dispatch), so they are best-effort token scanners.\n */\nimport type { Command } from 'commander';\n\n/**\n * Collect flags (both `--long` and `-s`) for global options that take a value.\n * Used by {@link extractCommandName} so the subcommand parser can skip the\n * value after options like `--config <path>`.\n */\nfunction collectValueTakingFlags(program: Command): Set<string> {\n  const flags = new Set<string>();\n  for (const opt of program.options) {\n    if (!opt.required && !opt.optional) continue;\n    if (opt.long) flags.add(opt.long);\n    if (opt.short) flags.add(opt.short);\n  }\n  return flags;\n}\n\n/**\n * Extract the subcommand name from argv (best-effort).\n *\n * Skips global options that take a value so things like `--config upgrade`\n * are not misread as the `upgrade` subcommand. The set of value-taking\n * options is derived from the Commander program itself, so it stays in sync\n * with the option definitions.\n */\nexport function extractCommandName(argv: string[], program: Command): string {\n  const valueTakingFlags = collectValueTakingFlags(program);\n  let skipNext = false;\n  for (let i = 2; i < argv.length; i++) {\n    const token = argv[i];\n    if (!token) continue;\n    if (skipNext) {\n      skipNext = false;\n      continue;\n    }\n    if (token.startsWith('-')) {\n      // `--opt=value` bundles its value, no skip needed.\n      if (!token.includes('=') && valueTakingFlags.has(token)) skipNext = true;\n      continue;\n    }\n    return token;\n  }\n  return '';\n}\n\n/**\n * Best-effort detection of `--no-update-check` in argv, without relying on\n * Commander having parsed yet (the async check starts before parseAsync).\n */\nexport function hasNoUpdateCheckFlag(argv: string[]): boolean {\n  for (let i = 2; i < argv.length; i++) {\n    if (argv[i] === '--no-update-check') return true;\n  }\n  return false;\n}\n\n/**\n * Best-effort detection of the global `--quiet` flag in argv, without relying\n * on Commander having parsed yet (the async check starts before parseAsync).\n * `--quiet` promises \"suppress all output except errors\", which includes the\n * update notice.\n */\nexport function hasQuietFlag(argv: string[]): boolean {\n  for (let i = 2; i < argv.length; i++) {\n    if (argv[i] === '--quiet') return true;\n  }\n  return false;\n}\n\n/**\n * Rewrite `search-hub upgrade --version <tag>` to `--version=<tag>`.\n *\n * The program has `.version(VERSION)` which registers a no-arg `--version`\n * flag at the root. Commander's parser consumes the root `--version` before\n * subcommand options, so the space-separated form is caught by the root\n * (prints + exits) instead of reaching `upgrade`'s `--version <tag>`. The\n * `=` form binds the value to the subcommand's option and sidesteps the\n * root flag.\n */\nexport function rewriteUpgradeVersionFlag(argv: string[], program: Command): string[] {\n  if (extractCommandName(argv, program) !== 'upgrade') return argv;\n\n  const out: string[] = [];\n  for (let i = 0; i < argv.length; i++) {\n    const token = argv[i];\n    if (token === '--version' && i + 1 < argv.length) {\n      const next = argv[i + 1];\n      if (next !== undefined && !next.startsWith('-')) {\n        out.push(`--version=${next}`);\n        i++;\n        continue;\n      }\n    }\n    if (token !== undefined) out.push(token);\n  }\n  return out;\n}\n"],"names":[],"mappings":"AAaA,SAAS,wBAAwB,SAA+B;AAC9D,QAAM,4BAAY,IAAA;AAClB,aAAW,OAAO,QAAQ,SAAS;AACjC,QAAI,CAAC,IAAI,YAAY,CAAC,IAAI,SAAU;AACpC,QAAI,IAAI,KAAM,OAAM,IAAI,IAAI,IAAI;AAChC,QAAI,IAAI,MAAO,OAAM,IAAI,IAAI,KAAK;AAAA,EACpC;AACA,SAAO;AACT;AAUO,SAAS,mBAAmB,MAAgB,SAA0B;AAC3E,QAAM,mBAAmB,wBAAwB,OAAO;AACxD,MAAI,WAAW;AACf,WAAS,IAAI,GAAG,IAAI,KAAK,QAAQ,KAAK;AACpC,UAAM,QAAQ,KAAK,CAAC;AACpB,QAAI,CAAC,MAAO;AACZ,QAAI,UAAU;AACZ,iBAAW;AACX;AAAA,IACF;AACA,QAAI,MAAM,WAAW,GAAG,GAAG;AAEzB,UAAI,CAAC,MAAM,SAAS,GAAG,KAAK,iBAAiB,IAAI,KAAK,EAAG,YAAW;AACpE;AAAA,IACF;AACA,WAAO;AAAA,EACT;AACA,SAAO;AACT;AAMO,SAAS,qBAAqB,MAAyB;AAC5D,WAAS,IAAI,GAAG,IAAI,KAAK,QAAQ,KAAK;AACpC,QAAI,KAAK,CAAC,MAAM,oBAAqB,QAAO;AAAA,EAC9C;AACA,SAAO;AACT;AAQO,SAAS,aAAa,MAAyB;AACpD,WAAS,IAAI,GAAG,IAAI,KAAK,QAAQ,KAAK;AACpC,QAAI,KAAK,CAAC,MAAM,UAAW,QAAO;AAAA,EACpC;AACA,SAAO;AACT;AAYO,SAAS,0BAA0B,MAAgB,SAA4B;AACpF,MAAI,mBAAmB,MAAM,OAAO,MAAM,UAAW,QAAO;AAE5D,QAAM,MAAgB,CAAA;AACtB,WAAS,IAAI,GAAG,IAAI,KAAK,QAAQ,KAAK;AACpC,UAAM,QAAQ,KAAK,CAAC;AACpB,QAAI,UAAU,eAAe,IAAI,IAAI,KAAK,QAAQ;AAChD,YAAM,OAAO,KAAK,IAAI,CAAC;AACvB,UAAI,SAAS,UAAa,CAAC,KAAK,WAAW,GAAG,GAAG;AAC/C,YAAI,KAAK,aAAa,IAAI,EAAE;AAC5B;AACA;AAAA,MACF;AAAA,IACF;AACA,QAAI,UAAU,OAAW,KAAI,KAAK,KAAK;AAAA,EACzC;AACA,SAAO;AACT;"}

package/dist/config/index.d.ts

@@ -6,5 +6,5 @@
 export { loadConfig, saveConfig, type LoadConfigOptions, type SaveConfigOptions } from './loader';
 export { ConfigSchema, type Config, type ProviderConfig } from './schema';
 export { getDefaultConfig, DEFAULT_CONFIG } from './defaults';
-export { getProjectDir, getLocalConfigPath, getLocalSessionsDir, getLocalQueriesDir, isInsideProject, } from './paths';
+export { getProjectDir, getLocalConfigPath, getLocalSessionsDir, getQueriesDir, isInsideProject, } from './paths';
 //# sourceMappingURL=index.d.ts.map

package/dist/config/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/config/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,iBAAiB,EAAE,KAAK,iBAAiB,EAAE,MAAM,UAAU,CAAC;AAClG,OAAO,EAAE,YAAY,EAAE,KAAK,MAAM,EAAE,KAAK,cAAc,EAAE,MAAM,UAAU,CAAC;AAC1E,OAAO,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAC9D,OAAO,EACL,aAAa,EACb,kBAAkB,EAClB,mBAAmB,EACnB,kBAAkB,EAClB,eAAe,GAChB,MAAM,SAAS,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/config/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,iBAAiB,EAAE,KAAK,iBAAiB,EAAE,MAAM,UAAU,CAAC;AAClG,OAAO,EAAE,YAAY,EAAE,KAAK,MAAM,EAAE,KAAK,cAAc,EAAE,MAAM,UAAU,CAAC;AAC1E,OAAO,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAC9D,OAAO,EACL,aAAa,EACb,kBAAkB,EAClB,mBAAmB,EACnB,aAAa,EACb,eAAe,GAChB,MAAM,SAAS,CAAC"}

package/dist/config/paths.d.ts

@@ -36,7 +36,7 @@ export declare function getLocalSessionsDir(baseDir?: string): string;
 /**
  * Get the local queries directory (.search-hub/queries/).
  */
-export declare function getLocalQueriesDir(baseDir?: string): string;
+export declare function getQueriesDir(baseDir?: string): string;
 /**
  * Check if the given directory (default: cwd) contains a .search-hub/ project directory.
  */

package/dist/config/paths.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"paths.d.ts","sourceRoot":"","sources":["../../src/config/paths.ts"],"names":[],"mappings":"AAWA;;;;;GAKG;AACH,wBAAgB,YAAY,IAAI,MAAM,CAErC;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,IAAI,MAAM,CAEnC;AAED;;GAEG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,CAE7C;AAED;;GAEG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,CAE9C;AAKD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAEtD;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAE5D;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED;;GAEG;AACH,wBAAsB,eAAe,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAOxE"}
+{"version":3,"file":"paths.d.ts","sourceRoot":"","sources":["../../src/config/paths.ts"],"names":[],"mappings":"AAWA;;;;;GAKG;AACH,wBAAgB,YAAY,IAAI,MAAM,CAErC;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,IAAI,MAAM,CAEnC;AAED;;GAEG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,CAE7C;AAED;;GAEG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,CAE9C;AAKD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAEtD;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAE5D;AAED;;GAEG;AACH,wBAAgB,aAAa,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAEtD;AAED;;GAEG;AACH,wBAAsB,eAAe,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAOxE"}

package/dist/config/paths.js

@@ -5,6 +5,9 @@ const paths = envPaths("search-hub", { suffix: "" });
 function getConfigDir() {
   return paths.config;
 }
+function getDataDir() {
+  return paths.data;
+}
 function getDefaultConfigPath() {
   return join(paths.config, "config.toml");
 }
@@ -21,7 +24,7 @@ function getLocalConfigPath(baseDir) {
 function getLocalSessionsDir(baseDir) {
   return join(getProjectDir(baseDir), "sessions");
 }
-function getLocalQueriesDir(baseDir) {
+function getQueriesDir(baseDir) {
   return join(getProjectDir(baseDir), "queries");
 }
 async function isInsideProject(baseDir) {
@@ -34,12 +37,13 @@ async function isInsideProject(baseDir) {
 }
 export {
   getConfigDir,
+  getDataDir,
   getDefaultConfigPath,
   getDefaultSessionsDir,
   getLocalConfigPath,
-  getLocalQueriesDir,
   getLocalSessionsDir,
   getProjectDir,
+  getQueriesDir,
   isInsideProject
 };
 //# sourceMappingURL=paths.js.map

package/dist/config/paths.js.map

@@ -1 +1 @@
-{"version":3,"file":"paths.js","sources":["../../src/config/paths.ts"],"sourcesContent":["/**\n * Platform-specific paths using XDG Base Directory spec on Linux,\n * ~/Library on macOS, and AppData on Windows.\n */\nimport envPaths from 'env-paths';\nimport { join } from 'node:path';\nimport { stat } from 'node:fs/promises';\n\n// Use empty suffix to get clean 'search-hub' directory names\nconst paths = envPaths('search-hub', { suffix: '' });\n\n/**\n * Get the config directory for search-hub.\n * - Linux: ~/.config/search-hub\n * - macOS: ~/Library/Preferences/search-hub\n * - Windows: %APPDATA%\\search-hub\\Config\n */\nexport function getConfigDir(): string {\n  return paths.config;\n}\n\n/**\n * Get the data directory for search-hub.\n * - Linux: ~/.local/share/search-hub\n * - macOS: ~/Library/Application Support/search-hub\n * - Windows: %LOCALAPPDATA%\\search-hub\\Data\n */\nexport function getDataDir(): string {\n  return paths.data;\n}\n\n/**\n * Get the default config file path.\n */\nexport function getDefaultConfigPath(): string {\n  return join(paths.config, 'config.toml');\n}\n\n/**\n * Get the default sessions directory.\n */\nexport function getDefaultSessionsDir(): string {\n  return join(paths.data, 'sessions');\n}\n\n/** Name of the project-local directory. */\nconst PROJECT_DIR_NAME = '.search-hub';\n\n/**\n * Get the project directory path (.search-hub/) relative to a base directory.\n * Defaults to cwd.\n */\nexport function getProjectDir(baseDir?: string): string {\n  return join(baseDir ?? process.cwd(), PROJECT_DIR_NAME);\n}\n\n/**\n * Get the local config file path (.search-hub/config.toml).\n */\nexport function getLocalConfigPath(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'config.toml');\n}\n\n/**\n * Get the local sessions directory (.search-hub/sessions/).\n */\nexport function getLocalSessionsDir(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'sessions');\n}\n\n/**\n * Get the local queries directory (.search-hub/queries/).\n */\nexport function getLocalQueriesDir(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'queries');\n}\n\n/**\n * Check if the given directory (default: cwd) contains a .search-hub/ project directory.\n */\nexport async function isInsideProject(baseDir?: string): Promise<boolean> {\n  try {\n    const stats = await stat(getProjectDir(baseDir));\n    return stats.isDirectory();\n  } catch {\n    return false;\n  }\n}\n"],"names":[],"mappings":";;;AASA,MAAM,QAAQ,SAAS,cAAc,EAAE,QAAQ,IAAI;AAQ5C,SAAS,eAAuB;AACrC,SAAO,MAAM;AACf;AAeO,SAAS,uBAA+B;AAC7C,SAAO,KAAK,MAAM,QAAQ,aAAa;AACzC;AAKO,SAAS,wBAAgC;AAC9C,SAAO,KAAK,MAAM,MAAM,UAAU;AACpC;AAGA,MAAM,mBAAmB;AAMlB,SAAS,cAAc,SAA0B;AACtD,SAAO,KAAK,WAAW,QAAQ,IAAA,GAAO,gBAAgB;AACxD;AAKO,SAAS,mBAAmB,SAA0B;AAC3D,SAAO,KAAK,cAAc,OAAO,GAAG,aAAa;AACnD;AAKO,SAAS,oBAAoB,SAA0B;AAC5D,SAAO,KAAK,cAAc,OAAO,GAAG,UAAU;AAChD;AAKO,SAAS,mBAAmB,SAA0B;AAC3D,SAAO,KAAK,cAAc,OAAO,GAAG,SAAS;AAC/C;AAKA,eAAsB,gBAAgB,SAAoC;AACxE,MAAI;AACF,UAAM,QAAQ,MAAM,KAAK,cAAc,OAAO,CAAC;AAC/C,WAAO,MAAM,YAAA;AAAA,EACf,QAAQ;AACN,WAAO;AAAA,EACT;AACF;"}
+{"version":3,"file":"paths.js","sources":["../../src/config/paths.ts"],"sourcesContent":["/**\n * Platform-specific paths using XDG Base Directory spec on Linux,\n * ~/Library on macOS, and AppData on Windows.\n */\nimport envPaths from 'env-paths';\nimport { join } from 'node:path';\nimport { stat } from 'node:fs/promises';\n\n// Use empty suffix to get clean 'search-hub' directory names\nconst paths = envPaths('search-hub', { suffix: '' });\n\n/**\n * Get the config directory for search-hub.\n * - Linux: ~/.config/search-hub\n * - macOS: ~/Library/Preferences/search-hub\n * - Windows: %APPDATA%\\search-hub\\Config\n */\nexport function getConfigDir(): string {\n  return paths.config;\n}\n\n/**\n * Get the data directory for search-hub.\n * - Linux: ~/.local/share/search-hub\n * - macOS: ~/Library/Application Support/search-hub\n * - Windows: %LOCALAPPDATA%\\search-hub\\Data\n */\nexport function getDataDir(): string {\n  return paths.data;\n}\n\n/**\n * Get the default config file path.\n */\nexport function getDefaultConfigPath(): string {\n  return join(paths.config, 'config.toml');\n}\n\n/**\n * Get the default sessions directory.\n */\nexport function getDefaultSessionsDir(): string {\n  return join(paths.data, 'sessions');\n}\n\n/** Name of the project-local directory. */\nconst PROJECT_DIR_NAME = '.search-hub';\n\n/**\n * Get the project directory path (.search-hub/) relative to a base directory.\n * Defaults to cwd.\n */\nexport function getProjectDir(baseDir?: string): string {\n  return join(baseDir ?? process.cwd(), PROJECT_DIR_NAME);\n}\n\n/**\n * Get the local config file path (.search-hub/config.toml).\n */\nexport function getLocalConfigPath(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'config.toml');\n}\n\n/**\n * Get the local sessions directory (.search-hub/sessions/).\n */\nexport function getLocalSessionsDir(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'sessions');\n}\n\n/**\n * Get the local queries directory (.search-hub/queries/).\n */\nexport function getQueriesDir(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'queries');\n}\n\n/**\n * Check if the given directory (default: cwd) contains a .search-hub/ project directory.\n */\nexport async function isInsideProject(baseDir?: string): Promise<boolean> {\n  try {\n    const stats = await stat(getProjectDir(baseDir));\n    return stats.isDirectory();\n  } catch {\n    return false;\n  }\n}\n"],"names":[],"mappings":";;;AASA,MAAM,QAAQ,SAAS,cAAc,EAAE,QAAQ,IAAI;AAQ5C,SAAS,eAAuB;AACrC,SAAO,MAAM;AACf;AAQO,SAAS,aAAqB;AACnC,SAAO,MAAM;AACf;AAKO,SAAS,uBAA+B;AAC7C,SAAO,KAAK,MAAM,QAAQ,aAAa;AACzC;AAKO,SAAS,wBAAgC;AAC9C,SAAO,KAAK,MAAM,MAAM,UAAU;AACpC;AAGA,MAAM,mBAAmB;AAMlB,SAAS,cAAc,SAA0B;AACtD,SAAO,KAAK,WAAW,QAAQ,IAAA,GAAO,gBAAgB;AACxD;AAKO,SAAS,mBAAmB,SAA0B;AAC3D,SAAO,KAAK,cAAc,OAAO,GAAG,aAAa;AACnD;AAKO,SAAS,oBAAoB,SAA0B;AAC5D,SAAO,KAAK,cAAc,OAAO,GAAG,UAAU;AAChD;AAKO,SAAS,cAAc,SAA0B;AACtD,SAAO,KAAK,cAAc,OAAO,GAAG,SAAS;AAC/C;AAKA,eAAsB,gBAAgB,SAAoC;AACxE,MAAI;AACF,UAAM,QAAQ,MAAM,KAAK,cAAc,OAAO,CAAC;AAC/C,WAAO,MAAM,YAAA;AAAA,EACf,QAAQ;AACN,WAAO;AAAA,EACT;AACF;"}

package/dist/index.js

@@ -6,7 +6,7 @@ import { extractControlledVocabTerms, validateControlledVocab } from "./query/vo
 import { loadConfig, saveConfig } from "./config/loader.js";
 import { ConfigSchema } from "./config/schema.js";
 import { DEFAULT_CONFIG, getDefaultConfig } from "./config/defaults.js";
-import { getLocalConfigPath, getLocalQueriesDir, getLocalSessionsDir, getProjectDir, isInsideProject } from "./config/paths.js";
+import { getLocalConfigPath, getLocalSessionsDir, getProjectDir, getQueriesDir, isInsideProject } from "./config/paths.js";
 import { createSession, generateSessionId, getResumableProviders, listSessions, loadSession, sanitizeName, saveSession, sessionExists, updateDatabaseStatus, updateSessionStatus } from "./session/manager.js";
 import { SessionLogger } from "./session/logger.js";
 import { createProviderError, isAuthError, isProviderError, isRateLimitError } from "./providers/base/types.js";
@@ -35,9 +35,9 @@ export {
   generateSessionId,
   getDefaultConfig,
   getLocalConfigPath,
-  getLocalQueriesDir,
   getLocalSessionsDir,
   getProjectDir,
+  getQueriesDir,
   getResumableProviders,
   globalRegistry,
   isAuthError,

package/dist/integration/csl-json.d.ts

@@ -10,6 +10,7 @@ export interface CslJsonItem {
     }>;
     DOI?: string;
     PMID?: string;
+    URL?: string;
     abstract?: string;
     issued?: {
         'date-parts': number[][];
@@ -18,6 +19,15 @@ export interface CslJsonItem {
     volume?: string;
     issue?: string;
     page?: string;
+    /**
+     * Alternative identifiers. Key names match what reference-manager reads:
+     * its duplicate detector and fulltext discovery use `custom.arxiv_id`.
+     */
+    custom?: {
+        arxiv_id?: string;
+        eric_id?: string;
+        scopus_id?: string;
+    };
 }
 /**
  * Generate a human-readable CSL ID from an article (author-year format).

package/dist/integration/csl-json.d.ts.map

@@ -1 +1 @@
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package/dist/integration/csl-json.js

@@ -27,6 +27,18 @@ function articleToCslJson(article, id) {
   };
   if (article.doi) item.DOI = article.doi;
   if (article.pmid) item.PMID = article.pmid;
+  const custom = {};
+  if (article.arxivId) custom.arxiv_id = article.arxivId;
+  if (article.ericId) custom.eric_id = article.ericId;
+  if (article.scopusId) custom.scopus_id = article.scopusId;
+  if (Object.keys(custom).length > 0) item.custom = custom;
+  if (!article.doi) {
+    if (article.arxivId) {
+      item.URL = `https://arxiv.org/abs/${article.arxivId}`;
+    } else if (article.ericId) {
+      item.URL = `https://eric.ed.gov/?id=${article.ericId}`;
+    }
+  }
   if (article.abstract) item.abstract = article.abstract;
   const dateParts = parseDateParts(article.publicationDate);
   if (dateParts) item.issued = { "date-parts": dateParts };

package/dist/integration/csl-json.js.map

@@ -1 +1 @@
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article.authors[0]!.family.toLowerCase()\n      : 'anon';\n\n  const yearPart = extractYear(article.publicationDate);\n\n  return `${authorPart}-${yearPart}`;\n}\n\n/**\n * Extract year from a publication date string.\n * Handles formats: \"2024-01-15\", \"2024-01\", \"2024\"\n */\nfunction extractYear(date: string | undefined): string {\n  if (!date) return 'nd';\n  const match = date.match(/^(\\d{4})/);\n  return match ? match[1]! : 'nd';\n}\n\n/**\n * Parse a publication date string into CSL date-parts format.\n *\n * - `\"2024-01-15\"` → `[[2024, 1, 15]]`\n * - `\"2024-01\"` → `[[2024, 1]]`\n * - `\"2024\"` → `[[2024]]`\n * - `undefined` or `\"\"` → `undefined`\n */\nexport function parseDateParts(\n  date: string | undefined\n): number[][] | undefined {\n  if (!date) return undefined;\n\n  const parts = date.split('-').map(Number);\n  if (parts.length === 0 || Number.isNaN(parts[0])) return undefined;\n\n  return [parts];\n}\n\n/**\n * Convert a single Article to a CSL-JSON item.\n * The `id` parameter must be pre-generated (with duplicate resolution already applied).\n */\nexport function articleToCslJson(article: Article, id: string): CslJsonItem {\n  const item: CslJsonItem = {\n    id,\n    type: 'article-journal',\n    title: article.title,\n    author: article.authors.map((a) => {\n      const entry: { family: string; given?: string } = { family: a.family };\n      if (a.given) entry.given = a.given;\n      return entry;\n    }),\n  };\n\n  if (article.doi) item.DOI = article.doi;\n  if (article.pmid) item.PMID = article.pmid;\n  if (article.abstract) item.abstract = article.abstract;\n\n  const dateParts = parseDateParts(article.publicationDate);\n  if (dateParts) item.issued = { 'date-parts': dateParts };\n\n  if (article.journal) item['container-title'] = article.journal;\n  if (article.volume) item.volume = article.volume;\n  if (article.issue) item.issue = article.issue;\n  if (article.pages) item.page = article.pages;\n\n  return item;\n}\n\n/**\n * Convert an array of Articles to CSL-JSON items with duplicate ID resolution.\n *\n * Duplicates within the batch are resolved by appending suffixes:\n * `smith-2024`, `smith-2024a`, `smith-2024b`, ...\n */\nexport function articlesToCslJson(articles: Article[]): CslJsonItem[] {\n  const idCounts = new Map<string, number>();\n  const result: CslJsonItem[] = [];\n\n  for (const article of articles) {\n    const baseId = generateCslId(article);\n    const count = idCounts.get(baseId) ?? 0;\n    idCounts.set(baseId, count + 1);\n\n    let resolvedId: string;\n    if (count === 0) {\n      resolvedId = baseId;\n    } else {\n      // a=97 in ASCII, so suffix is 'a', 'b', 'c', ...\n      resolvedId = `${baseId}${String.fromCharCode(96 + count)}`;\n    }\n\n    result.push(articleToCslJson(article, resolvedId));\n  }\n\n  return result;\n}\n"],"names":[],"mappings":"AA+BO,SAAS,cAAc,SAA0B;AACtD,QAAM,aACJ,QAAQ,QAAQ,SAAS,IACrB,QAAQ,QAAQ,CAAC,EAAG,OAAO,YAAA,IAC3B;AAEN,QAAM,WAAW,YAAY,QAAQ,eAAe;AAEpD,SAAO,GAAG,UAAU,IAAI,QAAQ;AAClC;AAMA,SAAS,YAAY,MAAkC;AACrD,MAAI,CAAC,KAAM,QAAO;AAClB,QAAM,QAAQ,KAAK,MAAM,UAAU;AACnC,SAAO,QAAQ,MAAM,CAAC,IAAK;AAC7B;AAUO,SAAS,eACd,MACwB;AACxB,MAAI,CAAC,KAAM,QAAO;AAElB,QAAM,QAAQ,KAAK,MAAM,GAAG,EAAE,IAAI,MAAM;AACxC,MAAI,MAAM,WAAW,KAAK,OAAO,MAAM,MAAM,CAAC,CAAC,EAAG,QAAO;AAEzD,SAAO,CAAC,KAAK;AACf;AAMO,SAAS,iBAAiB,SAAkB,IAAyB;AAC1E,QAAM,OAAoB;AAAA,IACxB;AAAA,IACA,MAAM;AAAA,IACN,OAAO,QAAQ;AAAA,IACf,QAAQ,QAAQ,QAAQ,IAAI,CAAC,MAAM;AACjC,YAAM,QAA4C,EAAE,QAAQ,EAAE,OAAA;AAC9D,UAAI,EAAE,MAAO,OAAM,QAAQ,EAAE;AAC7B,aAAO;AAAA,IACT,CAAC;AAAA,EAAA;AAGH,MAAI,QAAQ,IAAK,MAAK,MAAM,QAAQ;AACpC,MAAI,QAAQ,KAAM,MAAK,OAAO,QAAQ;AACtC,MAAI,QAAQ,SAAU,MAAK,WAAW,QAAQ;AAE9C,QAAM,YAAY,eAAe,QAAQ,eAAe;AACxD,MAAI,UAAW,MAAK,SAAS,EAAE,cAAc,UAAA;AAE7C,MAAI,QAAQ,QAAS,MAAK,iBAAiB,IAAI,QAAQ;AACvD,MAAI,QAAQ,OAAQ,MAAK,SAAS,QAAQ;AAC1C,MAAI,QAAQ,MAAO,MAAK,QAAQ,QAAQ;AACxC,MAAI,QAAQ,MAAO,MAAK,OAAO,QAAQ;AAEvC,SAAO;AACT;AAQO,SAAS,kBAAkB,UAAoC;AACpE,QAAM,+BAAe,IAAA;AACrB,QAAM,SAAwB,CAAA;AAE9B,aAAW,WAAW,UAAU;AAC9B,UAAM,SAAS,cAAc,OAAO;AACpC,UAAM,QAAQ,SAAS,IAAI,MAAM,KAAK;AACtC,aAAS,IAAI,QAAQ,QAAQ,CAAC;AAE9B,QAAI;AACJ,QAAI,UAAU,GAAG;AACf,mBAAa;AAAA,IACf,OAAO;AAEL,mBAAa,GAAG,MAAM,GAAG,OAAO,aAAa,KAAK,KAAK,CAAC;AAAA,IAC1D;AAEA,WAAO,KAAK,iBAAiB,SAAS,UAAU,CAAC;AAAA,EACnD;AAEA,SAAO;AACT;"}
+{"version":3,"file":"csl-json.js","sources":["../../src/integration/csl-json.ts"],"sourcesContent":["/**\n * CSL-JSON conversion module.\n * Converts Article objects to CSL-JSON format for bulk import via ref add -i json.\n */\n\nimport type { Article } from '../providers/base/types.js';\n\n/** CSL-JSON item type used for bulk import. */\nexport interface CslJsonItem {\n  id: string;\n  type: string;\n  title: string;\n  author: Array<{ family: string; given?: string }>;\n  DOI?: string;\n  PMID?: string;\n  URL?: string;\n  abstract?: string;\n  issued?: { 'date-parts': number[][] };\n  'container-title'?: string;\n  volume?: string;\n  issue?: string;\n  page?: string;\n  /**\n   * Alternative identifiers. Key names match what reference-manager reads:\n   * its duplicate detector and fulltext discovery use `custom.arxiv_id`.\n   */\n  custom?: {\n    arxiv_id?: string;\n    eric_id?: string;\n    scopus_id?: string;\n  };\n}\n\n/**\n * Generate a human-readable CSL ID from an article (author-year format).\n *\n * Format: `{first-author-family}-{year}`\n * - No author: `anon-{year}`\n * - No year: `{author}-nd`\n * - Duplicate resolution is handled by `articlesToCslJson()` at the batch level.\n */\nexport function generateCslId(article: Article): string {\n  const authorPart =\n    article.authors.length > 0\n      ? article.authors[0]!.family.toLowerCase()\n      : 'anon';\n\n  const yearPart = extractYear(article.publicationDate);\n\n  return `${authorPart}-${yearPart}`;\n}\n\n/**\n * Extract year from a publication date string.\n * Handles formats: \"2024-01-15\", \"2024-01\", \"2024\"\n */\nfunction extractYear(date: string | undefined): string {\n  if (!date) return 'nd';\n  const match = date.match(/^(\\d{4})/);\n  return match ? match[1]! : 'nd';\n}\n\n/**\n * Parse a publication date string into CSL date-parts format.\n *\n * - `\"2024-01-15\"` → `[[2024, 1, 15]]`\n * - `\"2024-01\"` → `[[2024, 1]]`\n * - `\"2024\"` → `[[2024]]`\n * - `undefined` or `\"\"` → `undefined`\n */\nexport function parseDateParts(\n  date: string | undefined\n): number[][] | undefined {\n  if (!date) return undefined;\n\n  const parts = date.split('-').map(Number);\n  if (parts.length === 0 || Number.isNaN(parts[0])) return undefined;\n\n  return [parts];\n}\n\n/**\n * Convert a single Article to a CSL-JSON item.\n * The `id` parameter must be pre-generated (with duplicate resolution already applied).\n */\nexport function articleToCslJson(article: Article, id: string): CslJsonItem {\n  const item: CslJsonItem = {\n    id,\n    type: 'article-journal',\n    title: article.title,\n    author: article.authors.map((a) => {\n      const entry: { family: string; given?: string } = { family: a.family };\n      if (a.given) entry.given = a.given;\n      return entry;\n    }),\n  };\n\n  if (article.doi) item.DOI = article.doi;\n  if (article.pmid) item.PMID = article.pmid;\n\n  const custom: NonNullable<CslJsonItem['custom']> = {};\n  if (article.arxivId) custom.arxiv_id = article.arxivId;\n  if (article.ericId) custom.eric_id = article.ericId;\n  if (article.scopusId) custom.scopus_id = article.scopusId;\n  if (Object.keys(custom).length > 0) item.custom = custom;\n\n  // Without a DOI, give resolvers a landing page for the alternative identifier\n  if (!article.doi) {\n    if (article.arxivId) {\n      item.URL = `https://arxiv.org/abs/${article.arxivId}`;\n    } else if (article.ericId) {\n      item.URL = `https://eric.ed.gov/?id=${article.ericId}`;\n    }\n  }\n\n  if (article.abstract) item.abstract = article.abstract;\n\n  const dateParts = parseDateParts(article.publicationDate);\n  if (dateParts) item.issued = { 'date-parts': dateParts };\n\n  if (article.journal) item['container-title'] = article.journal;\n  if (article.volume) item.volume = article.volume;\n  if (article.issue) item.issue = article.issue;\n  if (article.pages) item.page = article.pages;\n\n  return item;\n}\n\n/**\n * Convert an array of Articles to CSL-JSON items with duplicate ID resolution.\n *\n * Duplicates within the batch are resolved by appending suffixes:\n * `smith-2024`, `smith-2024a`, `smith-2024b`, ...\n */\nexport function articlesToCslJson(articles: Article[]): CslJsonItem[] {\n  const idCounts = new Map<string, number>();\n  const result: CslJsonItem[] = [];\n\n  for (const article of articles) {\n    const baseId = generateCslId(article);\n    const count = idCounts.get(baseId) ?? 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package/dist/integration/register.d.ts.map

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package/dist/integration/register.js

@@ -12,7 +12,7 @@ async function saveRegistrationRecord(sessionDir, record) {
   await fs.writeFile(filePath, JSON.stringify(record, null, 2));
 }
 function hasIdentifier(article) {
-  return !!(article.pmid || article.doi);
+  return !!(article.pmid || article.doi || article.arxivId || article.scopusId || article.ericId);
 }
 async function registerArticles(articles, options) {
   const { sessionId, sessionDir, withAbstracts, noAttachFulltext, onProgress, onAttachProgress } = options;

package/dist/integration/register.js.map

@@ -1 +1 @@
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+{"version":3,"file":"register.js","sources":["../../src/integration/register.ts"],"sourcesContent":["/**\n * Registration logic for reference-manager integration.\n * Uses bulk CSL-JSON import for performance.\n */\n\nimport * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport type { Article } from '../providers/base/types.js';\nimport { RegistrationRecordSchema, type RegistrationRecord } from './types.js';\nimport { refAddBulk } from './ref-cli.js';\nimport { articlesToCslJson } from './csl-json.js';\nimport { attachFulltexts } from './fulltext-attach.js';\n\nconst REGISTRATION_FILE = 'registration.json';\nconst BULK_IMPORT_FILE = '_bulk_import.json';\n\n/**\n * Save registration record to session directory.\n */\nexport async function saveRegistrationRecord(\n  sessionDir: string,\n  record: RegistrationRecord\n): Promise<void> {\n  await fs.mkdir(sessionDir, { recursive: true });\n  const filePath = path.join(sessionDir, REGISTRATION_FILE);\n  await fs.writeFile(filePath, JSON.stringify(record, null, 2));\n}\n\n/**\n * Load registration record from session directory.\n * Returns null if file does not exist.\n * Throws if file exists but is invalid.\n */\nexport async function loadRegistrationRecord(\n  sessionDir: string\n): Promise<RegistrationRecord | null> {\n  const filePath = path.join(sessionDir, REGISTRATION_FILE);\n  try {\n    const content = await fs.readFile(filePath, 'utf-8');\n    const data = JSON.parse(content);\n    return RegistrationRecordSchema.parse(data);\n  } catch (error) {\n    // File not found - return null\n    if (error instanceof Error && 'code' in error && error.code === 'ENOENT') {\n      return null;\n    }\n    // Parse or validation error - re-throw\n    throw error;\n  }\n}\n\n/**\n * Options for registerArticles function.\n */\nexport interface RegisterOptions {\n  sessionId: string;\n  sessionDir: string;\n  withAbstracts?: boolean;\n  /** Skip fulltext attach step */\n  noAttachFulltext?: boolean;\n  onProgress?: (current: number, total: number) => void;\n  onAttachProgress?: (current: number, total: number) => void;\n}\n\n/**\n * Check if an article has an identifier suitable for registration.\n * Any of DOI / PMID / arXiv ID / Scopus ID / ERIC ID qualifies;\n * only articles with none of these are counted as noId and skipped.\n */\nfunction hasIdentifier(article: Article): boolean {\n  return !!(\n    article.pmid ||\n    article.doi ||\n    article.arxivId ||\n    article.scopusId ||\n    article.ericId\n  );\n}\n\n/**\n * Register articles with reference-manager using bulk CSL-JSON import.\n *\n * Flow:\n * 1. 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error.message : 'Unknown error',\n    });\n  } finally {\n    // Clean up temporary file\n    await fs.unlink(tempFilePath).catch(() => {});\n  }\n\n  // Fulltext attach step (after successful import)\n  if (!noAttachFulltext) {\n    const addedRefs = record.added.map((item) => ({\n      id: item.id,\n      source: item.source,\n    }));\n    // Also include duplicates (already in library) — they may need fulltext attachment\n    const dupRefs = record.duplicates.map((item) => ({\n      id: item.existingId,\n      source: item.source,\n    }));\n    const allRefs = [...addedRefs, ...dupRefs];\n\n    if (allRefs.length > 0) {\n      const attachOptions = {\n        sessionDir,\n        libraryPath,\n        addedRefs: allRefs,\n        ...(onAttachProgress ? { onProgress: onAttachProgress } : {}),\n      };\n      const fulltextResult = await attachFulltexts(attachOptions);\n\n      record.fulltext = fulltextResult;\n    }\n  }\n\n  return record;\n}\n"],"names":[],"mappings":";;;;;;AAaA,MAAM,oBAAoB;AAC1B,MAAM,mBAAmB;AAKzB,eAAsB,uBACpB,YACA,QACe;AACf,QAAM,GAAG,MAAM,YAAY,EAAE,WAAW,MAAM;AAC9C,QAAM,WAAW,KAAK,KAAK,YAAY,iBAAiB;AACxD,QAAM,GAAG,UAAU,UAAU,KAAK,UAAU,QAAQ,MAAM,CAAC,CAAC;AAC9D;AA2CA,SAAS,cAAc,SAA2B;AAChD,SAAO,CAAC,EACN,QAAQ,QACR,QAAQ,OACR,QAAQ,WACR,QAAQ,YACR,QAAQ;AAEZ;AAaA,eAAsB,iBACpB,UACA,SAC6B;AAC7B,QAAM,EAAE,WAAW,YAAY,eAAe,kBAAkB,YAAY,qBAAqB;AACjG,QAAM,cAAc,KAAK,KAAK,YAAY,iBAAiB;AAE3D,MAAI,eAAe;AACjB,YAAQ;AAAA,MACN;AAAA,IAAA;AAAA,EAEJ;AAEA,QAAM,SAA6B;AAAA,IACjC;AAAA,IACA,YAAW,oBAAI,KAAA,GAAO,YAAA;AAAA,IACtB,SAAS;AAAA,MACP,OAAO,SAAS;AAAA,MAChB,OAAO;AAAA,MACP,SAAS;AAAA,MACT,QAAQ;AAAA,MACR,MAAM;AAAA,IAAA;AAAA,IAER,OAAO,CAAA;AAAA,IACP,YAAY,CAAA;AAAA,IACZ,QAAQ,CAAA;AAAA,EAAC;AAIX,QAAM,iBAA4B,CAAA;AAClC,aAAW,WAAW,UAAU;AAC9B,QAAI,cAAc,OAAO,GAAG;AAC1B,qBAAe,KAAK,OAAO;AAAA,IAC7B,OAAO;AACL,aAAO,QAAQ;AAAA,IACjB;AAAA,EACF;AAGA,MAAI,YAAY;AACd,eAAW,eAAe,QAAQ,SAAS,MAAM;AAAA,EACnD;AAGA,MAAI,eAAe,WAAW,GAAG;AAC/B,WAAO;AAAA,EACT;AAGA,QAAM,eAAe,kBAAkB,cAAc;AACrD,QAAM,eAAe,KAAK,KAAK,YAAY,gBAAgB;AAE3D,MAAI;AAEF,UAAM,GAAG,UAAU,cAAc,KAAK,UAAU,YAAY,CAAC;AAG7D,UAAM,SAAS,MAAM,WAAW,cAAc,EAAE,aAAa;AAG7D,WAAO,QAAQ,QAAQ,OAAO,QAAQ;AACtC,WAAO,QAAQ,UAAU,OAAO,QAAQ;AACxC,WAAO,QAAQ,SAAS,OAAO,QAAQ;AAGvC,eAAW,QAAQ,OAAO,OAAO;AAC/B,aAAO,MAAM,KAAK;AAAA,QAChB,QAAQ,KAAK;AAAA,QACb,IAAI,KAAK;AAAA,QACT,OAAO,KAAK;AAAA,MAAA,CACb;AAAA,IACH;AAGA,eAAW,QAAQ,OAAO,SAAS;AACjC,aAAO,WAAW,KAAK;AAAA,QACrB,QAAQ,KAAK;AAAA,QACb,YAAY,KAAK;AAAA,QACjB,eAAe,KAAK;AAAA,MAAA,CACrB;AAAA,IACH;AAGA,eAAW,QAAQ,OAAO,QAAQ;AAChC,aAAO,OAAO,KAAK;AAAA,QACjB,QAAQ,KAAK;AAAA,QACb,QAAQ,KAAK;AAAA,QACb,OAAO,KAAK;AAAA,MAAA,CACb;AAAA,IACH;AAAA,EACF,SAAS,OAAO;AAEd,WAAO,QAAQ,SAAS,eAAe;AACvC,WAAO,OAAO,KAAK;AAAA,MACjB,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,OAAO,iBAAiB,QAAQ,MAAM,UAAU;AAAA,IAAA,CACjD;AAAA,EACH,UAAA;AAEE,UAAM,GAAG,OAAO,YAAY,EAAE,MAAM,MAAM;AAAA,IAAC,CAAC;AAAA,EAC9C;AAGA,MAAI,CAAC,kBAAkB;AACrB,UAAM,YAAY,OAAO,MAAM,IAAI,CAAC,UAAU;AAAA,MAC5C,IAAI,KAAK;AAAA,MACT,QAAQ,KAAK;AAAA,IAAA,EACb;AAEF,UAAM,UAAU,OAAO,WAAW,IAAI,CAAC,UAAU;AAAA,MAC/C,IAAI,KAAK;AAAA,MACT,QAAQ,KAAK;AAAA,IAAA,EACb;AACF,UAAM,UAAU,CAAC,GAAG,WAAW,GAAG,OAAO;AAEzC,QAAI,QAAQ,SAAS,GAAG;AACtB,YAAM,gBAAgB;AAAA,QACpB;AAAA,QACA;AAAA,QACA,WAAW;AAAA,QACX,GAAI,mBAAmB,EAAE,YAAY,qBAAqB,CAAA;AAAA,MAAC;AAE7D,YAAM,iBAAiB,MAAM,gBAAgB,aAAa;AAE1D,aAAO,WAAW;AAAA,IACpB;AAAA,EACF;AAEA,SAAO;AACT;"}

package/dist/node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js

@@ -724,6 +724,29 @@ function parseSection(secChildren, level) {
   }
   return { title, level, content, subsections };
 }
+function flushBlockBuffer(buffer, sections) {
+  const content = parseBlockContent(buffer);
+  if (content.length > 0) {
+    sections.push({ title: "", level: 2, content, subsections: [] });
+  }
+}
+function parseMixedBodyChildren(children, sections) {
+  let blockBuffer = [];
+  for (const child of children) {
+    if (getTagName(child) === "sec") {
+      if (blockBuffer.length > 0) {
+        flushBlockBuffer(blockBuffer, sections);
+        blockBuffer = [];
+      }
+      sections.push(parseSection(getChildren(child), 2));
+    } else {
+      blockBuffer.push(child);
+    }
+  }
+  if (blockBuffer.length > 0) {
+    flushBlockBuffer(blockBuffer, sections);
+  }
+}
 function parseJatsBody(xml) {
   const parsed = parser.parse(xml);
   const article = findArticle(parsed);
@@ -735,14 +758,9 @@ function parseJatsBody(xml) {
   const sections = [];
   const secs = findChildren(body.children, "sec");
   if (secs.length > 0) {
-    for (const sec of secs) {
-      sections.push(parseSection(sec.children, 2));
-    }
+    parseMixedBodyChildren(body.children, sections);
   } else {
-    const content = parseBlockContent(body.children);
-    if (content.length > 0) {
-      sections.push({ title: "", level: 2, content, subsections: [] });
-    }
+    flushBlockBuffer(body.children, sections);
   }
   return sections;
 }