research-copilot 0.2.16 → 0.2.20

package/app/out/renderer/assets/{line-OzQTpJsh.js → line-D0U74KO0.js}

@@ -1,6 +1,6 @@
 import { a as array } from "./array-DgktLKBx.js";
 import { w as withPath, c as constant } from "./path-Cp2qmpkd.js";
-import { an as curveLinear } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
+import { an as curveLinear } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
 function x(p) {
   return p[0];
 }

package/app/out/renderer/assets/{linear-DO5pdnqi.js → linear-BclyBoiT.js}

@@ -1,4 +1,4 @@
-import { a_ as constant, a$ as interpolateNumber, b0 as color, b1 as interpolateRgb, b2 as interpolateString } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
+import { a_ as constant, a$ as interpolateNumber, b0 as color, b1 as interpolateRgb, b2 as interpolateString } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
 import { i as initRange } from "./init-ZxktEp_H.js";
 function ascending(a, b) {
   return a == null || b == null ? NaN : a < b ? -1 : a > b ? 1 : a >= b ? 0 : NaN;

package/app/out/renderer/assets/{mindmap-definition-8da855dc-D3zWs3h1.js → mindmap-definition-8da855dc-un1bPKBj.js}

@@ -1,6 +1,6 @@
-import { v as log$1, r as getConfig, Z as selectSvgElement, ak as setupGraphViewbox$1, ab as defaultConfig$2, z as sanitizeText$2, aq as isDark, ar as lighten, as as darken, u as select, af as parseFontSize } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { c as commonjsGlobal$1, g as getDefaultExportFromCjs$1 } from "./index-B2UUF9y9.js";
-import { c as createText } from "./createText-1719965b-ciE8YuqI.js";
+import { v as log$1, r as getConfig, Z as selectSvgElement, ak as setupGraphViewbox$1, ab as defaultConfig$2, z as sanitizeText$2, aq as isDark, ar as lighten, as as darken, u as select, af as parseFontSize } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { c as commonjsGlobal$1, g as getDefaultExportFromCjs$1 } from "./index-CUsEKU8Q.js";
+import { c as createText } from "./createText-1719965b-CE_0jsfj.js";
 function _arrayLikeToArray(r, a) {
   (null == a || a > r.length) && (a = r.length);
   for (var e = 0, n = Array(a); e < a; e++) n[e] = r[e];

package/app/out/renderer/assets/{pieDiagram-a8764435-DDoNhSgQ.js → pieDiagram-a8764435-B7KM3duv.js}

@@ -1,9 +1,9 @@
-import { a3 as tau, n as getAccDescription, m as setAccDescription, o as getAccTitle, q as setAccTitle, H as getDiagramTitle, J as setDiagramTitle, v as log$1, r as getConfig$1, aM as cleanAndMerge, Z as selectSvgElement, af as parseFontSize, w as configureSvgSize, z as sanitizeText$2, M as clear$1, ab as defaultConfig$2 } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { a as arc } from "./arc-BAWS3N-F.js";
+import { a3 as tau, n as getAccDescription, m as setAccDescription, o as getAccTitle, q as setAccTitle, H as getDiagramTitle, J as setDiagramTitle, v as log$1, r as getConfig$1, aM as cleanAndMerge, Z as selectSvgElement, af as parseFontSize, w as configureSvgSize, z as sanitizeText$2, M as clear$1, ab as defaultConfig$2 } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { a as arc } from "./arc-CPL9nDFE.js";
 import { o as ordinal } from "./ordinal-DSZU4PqD.js";
 import { a as array } from "./array-DgktLKBx.js";
 import { c as constant } from "./path-Cp2qmpkd.js";
-import "./index-B2UUF9y9.js";
+import "./index-CUsEKU8Q.js";
 import "./init-ZxktEp_H.js";
 function descending(a, b) {
   return b < a ? -1 : b > a ? 1 : b >= a ? 0 : NaN;

package/app/out/renderer/assets/{quadrantDiagram-1e28029f-ZO85SsRM.js → quadrantDiagram-1e28029f-C8i5m3Os.js}

@@ -1,6 +1,6 @@
-import { m as setAccDescription, n as getAccDescription, H as getDiagramTitle, J as setDiagramTitle, o as getAccTitle, q as setAccTitle, r as getConfig, v as log$1, u as select, w as configureSvgSize, M as clear$1, ab as defaultConfig$2, z as sanitizeText$2, ac as getThemeVariables$2 } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { l as linear } from "./linear-DO5pdnqi.js";
-import "./index-B2UUF9y9.js";
+import { m as setAccDescription, n as getAccDescription, H as getDiagramTitle, J as setDiagramTitle, o as getAccTitle, q as setAccTitle, r as getConfig, v as log$1, u as select, w as configureSvgSize, M as clear$1, ab as defaultConfig$2, z as sanitizeText$2, ac as getThemeVariables$2 } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { l as linear } from "./linear-BclyBoiT.js";
+import "./index-CUsEKU8Q.js";
 import "./init-ZxktEp_H.js";
 var parser = function() {
   var o = function(k, v, o2, l) {

package/app/out/renderer/assets/{requirementDiagram-08caed73-C-vKE6g8.js → requirementDiagram-08caed73-FjqENNN5.js}

@@ -1,8 +1,8 @@
-import { n as getAccDescription, m as setAccDescription, o as getAccTitle, q as setAccTitle, r as getConfig, u as select, w as configureSvgSize, M as clear$1, v as log$1, C as common$1 } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { G as Graph } from "./graph-jZhookGR.js";
-import { l as layout } from "./layout-BsbNXXgR.js";
-import { l as line } from "./line-OzQTpJsh.js";
-import "./index-B2UUF9y9.js";
+import { n as getAccDescription, m as setAccDescription, o as getAccTitle, q as setAccTitle, r as getConfig, u as select, w as configureSvgSize, M as clear$1, v as log$1, C as common$1 } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { G as Graph } from "./graph-CZfltE7S.js";
+import { l as layout } from "./layout-5MwFTPs7.js";
+import { l as line } from "./line-D0U74KO0.js";
+import "./index-CUsEKU8Q.js";
 import "./array-DgktLKBx.js";
 import "./path-Cp2qmpkd.js";
 var parser = function() {

package/app/out/renderer/assets/{sankeyDiagram-a04cb91d-Cbqb2K-X.js → sankeyDiagram-a04cb91d-BKV22yuJ.js}

@@ -1,7 +1,7 @@
-import { J as setDiagramTitle, H as getDiagramTitle, m as setAccDescription, n as getAccDescription, q as setAccTitle, o as getAccTitle, r as getConfig, K as defaultConfig, u as select, ak as setupGraphViewbox$1, M as clear$1, C as common$1 } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
+import { J as setDiagramTitle, H as getDiagramTitle, m as setAccDescription, n as getAccDescription, q as setAccTitle, o as getAccTitle, r as getConfig, K as defaultConfig, u as select, ak as setupGraphViewbox$1, M as clear$1, C as common$1 } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
 import { o as ordinal } from "./ordinal-DSZU4PqD.js";
 import { s as schemeTableau10 } from "./Tableau10-BqnYsPR6.js";
-import "./index-B2UUF9y9.js";
+import "./index-CUsEKU8Q.js";
 import "./init-ZxktEp_H.js";
 function max(values, valueof) {
   let max2;

package/app/out/renderer/assets/{sequenceDiagram-c5b8d532-BK4uvpEA.js → sequenceDiagram-c5b8d532-DWO-Z2i3.js}

@@ -1,6 +1,6 @@
-import { n as getAccDescription, m as setAccDescription, q as setAccTitle, J as setDiagramTitle, H as getDiagramTitle, o as getAccTitle, r as getConfig, u as select, v as log$1, A as dist, w as configureSvgSize, x as assignWithDepth$1, C as common$1, z as sanitizeText$2, M as clear$1, O as utils, ad as hasKatex, ae as calculateMathMLDimensions, af as parseFontSize, ag as ZERO_WIDTH_SPACE, ah as renderKatexSanitized, ai as getConfig$1 } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { a as drawBackgroundRect$1, d as drawRect$1, b as getTextObj$1, c as drawEmbeddedImage, e as drawImage, g as getNoteRect$1 } from "./svgDrawCommon-b86b1483-DK4i-dfJ.js";
-import "./index-B2UUF9y9.js";
+import { n as getAccDescription, m as setAccDescription, q as setAccTitle, J as setDiagramTitle, H as getDiagramTitle, o as getAccTitle, r as getConfig, u as select, v as log$1, A as dist, w as configureSvgSize, x as assignWithDepth$1, C as common$1, z as sanitizeText$2, M as clear$1, O as utils, ad as hasKatex, ae as calculateMathMLDimensions, af as parseFontSize, ag as ZERO_WIDTH_SPACE, ah as renderKatexSanitized, ai as getConfig$1 } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { a as drawBackgroundRect$1, d as drawRect$1, b as getTextObj$1, c as drawEmbeddedImage, e as drawImage, g as getNoteRect$1 } from "./svgDrawCommon-b86b1483-BXgThwM_.js";
+import "./index-CUsEKU8Q.js";
 var parser = function() {
   var o = function(k, v, o2, l) {
     for (o2 = o2 || {}, l = k.length; l--; o2[k[l]] = v)

package/app/out/renderer/assets/{stateDiagram-1ecb1508-DXa_YqNi.js → stateDiagram-1ecb1508-BqohgALA.js}

@@ -1,9 +1,9 @@
-import { s as styles, d as db, p as parser$1 } from "./styles-ca3715f6-CKhYSe7r.js";
-import { r as getConfig, u as select, v as log$1, w as configureSvgSize, C as common$1, R as curveBasis, O as utils } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { G as Graph } from "./graph-jZhookGR.js";
-import { l as layout } from "./layout-BsbNXXgR.js";
-import { l as line } from "./line-OzQTpJsh.js";
-import "./index-B2UUF9y9.js";
+import { s as styles, d as db, p as parser$1 } from "./styles-ca3715f6-B0PvBknL.js";
+import { r as getConfig, u as select, v as log$1, w as configureSvgSize, C as common$1, R as curveBasis, O as utils } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { G as Graph } from "./graph-CZfltE7S.js";
+import { l as layout } from "./layout-5MwFTPs7.js";
+import { l as line } from "./line-D0U74KO0.js";
+import "./index-CUsEKU8Q.js";
 import "./array-DgktLKBx.js";
 import "./path-Cp2qmpkd.js";
 const drawStartState = (g) => g.append("circle").attr("class", "start-state").attr("r", getConfig().state.sizeUnit).attr("cx", getConfig().state.padding + getConfig().state.sizeUnit).attr("cy", getConfig().state.padding + getConfig().state.sizeUnit);

package/app/out/renderer/assets/{stateDiagram-v2-c2b004d7-Dm203Z8l.js → stateDiagram-v2-c2b004d7-B3sEkrB8.js}

@@ -1,13 +1,13 @@
-import { s as styles, d as db, p as parser$1, D as DEFAULT_NESTED_DOC_DIR, a as DEFAULT_STATE_TYPE, b as DIVIDER_TYPE, S as STMT_RELATION, c as STMT_STATE } from "./styles-ca3715f6-CKhYSe7r.js";
-import { G as Graph } from "./graph-jZhookGR.js";
-import { v as log$1, r as getConfig, u as select, O as utils, w as configureSvgSize, C as common$1 } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { r as render } from "./index-5325376f-CbxmatXv.js";
-import "./layout-BsbNXXgR.js";
-import "./index-B2UUF9y9.js";
-import "./clone-D-DQ4nnY.js";
-import "./edges-96097737-DycnAYk_.js";
-import "./createText-1719965b-ciE8YuqI.js";
-import "./line-OzQTpJsh.js";
+import { s as styles, d as db, p as parser$1, D as DEFAULT_NESTED_DOC_DIR, a as DEFAULT_STATE_TYPE, b as DIVIDER_TYPE, S as STMT_RELATION, c as STMT_STATE } from "./styles-ca3715f6-B0PvBknL.js";
+import { G as Graph } from "./graph-CZfltE7S.js";
+import { v as log$1, r as getConfig, u as select, O as utils, w as configureSvgSize, C as common$1 } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { r as render } from "./index-5325376f-DWTrHDEo.js";
+import "./layout-5MwFTPs7.js";
+import "./index-CUsEKU8Q.js";
+import "./clone-PHFwh58n.js";
+import "./edges-96097737-DBk1JhZS.js";
+import "./createText-1719965b-CE_0jsfj.js";
+import "./line-D0U74KO0.js";
 import "./array-DgktLKBx.js";
 import "./path-Cp2qmpkd.js";
 const SHAPE_STATE = "rect";

package/app/out/renderer/assets/{styles-b4e223ce-BV4b1eAh.js → styles-b4e223ce-BGytHk8n.js}

@@ -1,4 +1,4 @@
-import { H as getDiagramTitle, J as setDiagramTitle, m as setAccDescription, n as getAccDescription, o as getAccTitle, q as setAccTitle, r as getConfig, C as common$1, O as utils, v as log$1, M as clear$1, z as sanitizeText$2, aj as parseGenericTypes, u as select } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
+import { H as getDiagramTitle, J as setDiagramTitle, m as setAccDescription, n as getAccDescription, o as getAccTitle, q as setAccTitle, r as getConfig, C as common$1, O as utils, v as log$1, M as clear$1, z as sanitizeText$2, aj as parseGenericTypes, u as select } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
 var parser = function() {
   var o = function(k, v, o2, l) {
     for (o2 = o2 || {}, l = k.length; l--; o2[k[l]] = v)

package/app/out/renderer/assets/{styles-ca3715f6-CKhYSe7r.js → styles-ca3715f6-B0PvBknL.js}

@@ -1,4 +1,4 @@
-import { H as getDiagramTitle, J as setDiagramTitle, m as setAccDescription, n as getAccDescription, q as setAccTitle, o as getAccTitle, r as getConfig, C as common$1, v as log$1, M as clear$1, ao as generateId } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
+import { H as getDiagramTitle, J as setDiagramTitle, m as setAccDescription, n as getAccDescription, q as setAccTitle, o as getAccTitle, r as getConfig, C as common$1, v as log$1, M as clear$1, ao as generateId } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
 var parser = function() {
   var o = function(k, v, o2, l) {
     for (o2 = o2 || {}, l = k.length; l--; o2[k[l]] = v)

package/app/out/renderer/assets/{styles-d45a18b0-DTCMfE-4.js → styles-d45a18b0-C6F384ai.js}

@@ -1,7 +1,7 @@
-import { aN as Selection, aO as root, aP as array, aQ as isPlainObject, aR as isFunction, v as log$1, r as getConfig, u as select, O as utils, ak as setupGraphViewbox$1, al as getStylesFromArray, am as interpolateToCurve, an as curveLinear, ah as renderKatexSanitized, C as common$1, S as evaluate, at as rgba } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { G as Graph } from "./graph-jZhookGR.js";
-import { r as render } from "./index-5325376f-CbxmatXv.js";
-import { c as channel } from "./channel-Bll9CBqI.js";
+import { aN as Selection, aO as root, aP as array, aQ as isPlainObject, aR as isFunction, v as log$1, r as getConfig, u as select, O as utils, ak as setupGraphViewbox$1, al as getStylesFromArray, am as interpolateToCurve, an as curveLinear, ah as renderKatexSanitized, C as common$1, S as evaluate, at as rgba } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { G as Graph } from "./graph-CZfltE7S.js";
+import { r as render } from "./index-5325376f-DWTrHDEo.js";
+import { c as channel } from "./channel-jk5Np8ud.js";
 function selectAll(selector) {
   return typeof selector === "string" ? new Selection([document.querySelectorAll(selector)], [document.documentElement]) : new Selection([array(selector)], root);
 }

package/app/out/renderer/assets/{svgDrawCommon-b86b1483-DK4i-dfJ.js → svgDrawCommon-b86b1483-BXgThwM_.js}

@@ -1,4 +1,4 @@
-import { G as lineBreakRegex, A as dist } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
+import { G as lineBreakRegex, A as dist } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
 const drawRect = (element, rectData) => {
   const rectElement = element.append("rect");
   rectElement.attr("x", rectData.x);

package/app/out/renderer/assets/{timeline-definition-faaaa080-CE2LmuDH.js → timeline-definition-faaaa080-iNn5igPR.js}

@@ -1,6 +1,6 @@
-import { r as getConfig, v as log$1, u as select, ak as setupGraphViewbox$1, ap as commonDb, aq as isDark, ar as lighten, as as darken, M as clear$1 } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { a as arc } from "./arc-BAWS3N-F.js";
-import "./index-B2UUF9y9.js";
+import { r as getConfig, v as log$1, u as select, ak as setupGraphViewbox$1, ap as commonDb, aq as isDark, ar as lighten, as as darken, M as clear$1 } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { a as arc } from "./arc-CPL9nDFE.js";
+import "./index-CUsEKU8Q.js";
 import "./path-Cp2qmpkd.js";
 var parser = function() {
   var o = function(k, v, o2, l) {

package/app/out/renderer/assets/{xychartDiagram-f5964ef8-Bd8KT9X9.js → xychartDiagram-f5964ef8-oF_gxlk1.js}

@@ -1,10 +1,10 @@
-import { m as setAccDescription, n as getAccDescription, H as getDiagramTitle, J as setDiagramTitle, o as getAccTitle, q as setAccTitle, v as log$1, Z as selectSvgElement, w as configureSvgSize, M as clear$1, ai as getConfig$1, z as sanitizeText$2, aM as cleanAndMerge, ab as defaultConfig$2, ac as getThemeVariables$2 } from "./MilkdownMarkdownEditor-CuTa5j4S.js";
-import { a as computeDimensionOfText } from "./createText-1719965b-ciE8YuqI.js";
+import { m as setAccDescription, n as getAccDescription, H as getDiagramTitle, J as setDiagramTitle, o as getAccTitle, q as setAccTitle, v as log$1, Z as selectSvgElement, w as configureSvgSize, M as clear$1, ai as getConfig$1, z as sanitizeText$2, aM as cleanAndMerge, ab as defaultConfig$2, ac as getThemeVariables$2 } from "./MilkdownMarkdownEditor-Bj7JSjF5.js";
+import { a as computeDimensionOfText } from "./createText-1719965b-CE_0jsfj.js";
 import { i as initRange } from "./init-ZxktEp_H.js";
 import { o as ordinal } from "./ordinal-DSZU4PqD.js";
-import { l as linear } from "./linear-DO5pdnqi.js";
-import { l as line } from "./line-OzQTpJsh.js";
-import "./index-B2UUF9y9.js";
+import { l as linear } from "./linear-BclyBoiT.js";
+import { l as line } from "./line-D0U74KO0.js";
+import "./index-CUsEKU8Q.js";
 import "./array-DgktLKBx.js";
 import "./path-Cp2qmpkd.js";
 function range(start, stop, step) {

package/app/out/renderer/index.html

@@ -4,8 +4,8 @@
     <meta charset="UTF-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Research Pilot</title>
-    <script type="module" crossorigin src="./assets/index-B2UUF9y9.js"></script>
-    <link rel="stylesheet" crossorigin href="./assets/index-lAZsmnj1.css">
+    <script type="module" crossorigin src="./assets/index-CUsEKU8Q.js"></script>
+    <link rel="stylesheet" crossorigin href="./assets/index-CogwQwDN.css">
   </head>
   <body class="overflow-hidden">
     <div id="root"></div>

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "research-copilot",
-  "version": "0.2.16",
+  "version": "0.2.20",
   "description": "AI-powered research assistant for scientists — literature search, data analysis, academic writing, and project management",
   "type": "module",
   "bin": {
@@ -12,6 +12,7 @@
     "app/build/",
     "app/package.json",
     "lib/skills/",
+    "scripts/",
     "README.md",
     "LICENSE"
   ],

package/scripts/backfill-papers.mjs

@@ -0,0 +1,142 @@
+#!/usr/bin/env node
+// Backfill paper artifacts from existing literature-run review.json files.
+// Usage: node scripts/backfill-papers.mjs <projectPath>
+import { readFileSync, writeFileSync, mkdirSync, readdirSync, existsSync } from 'fs'
+import { join } from 'path'
+import { randomUUID } from 'crypto'
+
+const projectPath = process.argv[2]
+if (!projectPath) {
+  console.error('Usage: node scripts/backfill-papers.mjs <projectPath>')
+  process.exit(1)
+}
+
+const litRunsDir = join(projectPath, '.research-pilot/literature-runs')
+const papersDir = join(projectPath, '.research-pilot/artifacts/papers')
+mkdirSync(papersDir, { recursive: true })
+
+// Load existing papers for dedup
+const existingPapers = []
+if (existsSync(papersDir)) {
+  for (const f of readdirSync(papersDir)) {
+    if (!f.endsWith('.json')) continue
+    try {
+      const p = JSON.parse(readFileSync(join(papersDir, f), 'utf-8'))
+      existingPapers.push(p)
+    } catch {}
+  }
+}
+
+function normalizeTitle(t) {
+  return t.toLowerCase().replace(/[^\w\s]/g, ' ').replace(/\s+/g, ' ').trim()
+}
+
+function isDuplicate(title, year) {
+  const nt = normalizeTitle(title)
+  return existingPapers.some(p => {
+    const pt = normalizeTitle(p.title)
+    if (pt !== nt) return false
+    if (!year || !p.year) return true
+    return p.year === year
+  })
+}
+
+function generateCiteKey(authors, year) {
+  const firstAuthor = (authors?.[0] ?? 'unknown').split(/\s+/).pop()?.toLowerCase() ?? 'unknown'
+  return `${firstAuthor}${year ?? 'nd'}`
+}
+
+const AUTO_SAVE_THRESHOLD = 7
+let saved = 0
+let skippedDup = 0
+let skippedScore = 0
+
+if (!existsSync(litRunsDir)) {
+  console.error(`No literature-runs dir at ${litRunsDir}`)
+  process.exit(1)
+}
+
+const runs = readdirSync(litRunsDir)
+for (const runId of runs) {
+  const reviewPath = join(litRunsDir, runId, 'review.json')
+  if (!existsSync(reviewPath)) continue
+
+  let data
+  try {
+    data = JSON.parse(readFileSync(reviewPath, 'utf-8'))
+  } catch { continue }
+
+  const papers = data.review?.relevantPapers ?? []
+  const subTopics = data.plan?.subTopics ?? []
+  const roundLabel = `R-${runId}`
+
+  for (const paper of papers) {
+    if ((paper.relevanceScore ?? 0) < AUTO_SAVE_THRESHOLD) {
+      skippedScore++
+      continue
+    }
+    if (isDuplicate(paper.title, paper.year)) {
+      skippedDup++
+      continue
+    }
+
+    const authors = paper.authors?.length > 0 ? paper.authors : ['Unknown']
+    const citeKey = generateCiteKey(authors, paper.year)
+    const doi = (paper.doi ?? '').trim() || `unknown:${citeKey}`
+    const now = new Date().toISOString()
+    const id = randomUUID()
+
+    // Match subtopic
+    const matchedSubTopic = subTopics.find(st =>
+      paper.relevanceJustification?.toLowerCase().includes(st.name.toLowerCase())
+    )?.name
+
+    const artifact = {
+      id,
+      type: 'paper',
+      title: paper.title,
+      authors,
+      abstract: paper.abstract ?? '',
+      citeKey,
+      doi,
+      bibtex: `@article{${citeKey},\n  title = {${paper.title}},\n  author = {${authors.join(' and ')}},${paper.year ? `\n  year = {${paper.year}},` : ''}${paper.venue ? `\n  journal = {${paper.venue}},` : ''}${doi ? `\n  doi = {${doi}},` : ''}${paper.url ? `\n  url = {${paper.url}},` : ''}\n}`,
+      year: paper.year ?? undefined,
+      venue: paper.venue ?? undefined,
+      url: paper.url ?? undefined,
+      tags: [],
+      provenance: {
+        source: 'agent',
+        sessionId: 'backfill',
+        agentId: 'literature-team',
+        extractedFrom: 'agent-response'
+      },
+      createdAt: now,
+      updatedAt: now,
+      externalSource: paper.source,
+      relevanceScore: paper.relevanceScore,
+      citationCount: paper.citationCount ?? undefined,
+      relevanceJustification: paper.relevanceJustification,
+      subTopic: matchedSubTopic,
+      addedInRound: roundLabel,
+      addedByTask: 'deep_literature_study',
+      identityConfidence: paper.doi ? 'high' : 'medium',
+      semanticScholarId: paper.source === 'semantic_scholar' ? paper.id : undefined,
+      arxivId: paper.source === 'arxiv' ? paper.id : undefined,
+    }
+
+    // Remove undefined keys for clean JSON
+    for (const [k, v] of Object.entries(artifact)) {
+      if (v === undefined) delete artifact[k]
+    }
+
+    const filePath = join(papersDir, `${id}.json`)
+    writeFileSync(filePath, JSON.stringify(artifact, null, 2), 'utf-8')
+
+    // Track for dedup within this run
+    existingPapers.push(artifact)
+    saved++
+    console.log(`  + ${paper.title.slice(0, 80)}  (score: ${paper.relevanceScore})`)
+  }
+}
+
+console.log(`\nDone: ${saved} papers saved, ${skippedDup} duplicates skipped, ${skippedScore} below threshold (< ${AUTO_SAVE_THRESHOLD})`)

package/scripts/fix-node-pty-perms.mjs

@@ -0,0 +1,32 @@
+import { chmodSync, readdirSync, statSync } from 'node:fs'
+import { createRequire } from 'node:module'
+import path from 'node:path'
+
+// spawn-helper is only used on Unix platforms; Windows uses conpty.
+if (process.platform === 'win32') process.exit(0)
+
+const require = createRequire(import.meta.url)
+
+try {
+  // Resolve from package.json so we rely only on node-pty's public layout,
+  // not internal modules or runtime-loaded native bindings.
+  const ptyDir = path.dirname(require.resolve('node-pty/package.json'))
+  const prebuildsDir = path.join(ptyDir, 'prebuilds')
+
+  for (const entry of readdirSync(prebuildsDir, { withFileTypes: true })) {
+    if (!entry.isDirectory()) continue
+    const helper = path.join(prebuildsDir, entry.name, 'spawn-helper')
+    try {
+      const stat = statSync(helper)
+      if ((stat.mode & 0o111) !== 0o111) {
+        chmodSync(helper, stat.mode | 0o755)
+        console.log(`[postinstall] fixed node-pty helper permissions: ${helper}`)
+      }
+    } catch {
+      // Arch dirs without spawn-helper (e.g., win32-*) — skip silently.
+    }
+  }
+} catch (error) {
+  const message = error instanceof Error ? error.message : String(error)
+  console.warn(`[postinstall] skipped node-pty helper permission fix: ${message}`)
+}