ai-spector 0.3.6 → 0.3.8

package/dist/graph/InMemoryGraph.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"InMemoryGraph.d.ts","sourceRoot":"","sources":["../../src/graph/InMemoryGraph.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,SAAS,EAAE,iBAAiB,EAAE,eAAe,EAAE,MAAM,aAAa,CAAC;AAG5F,qBAAa,aAAa;IACxB,QAAQ,CAAC,SAAS,yBAAgC;IAClD,QAAQ,CAAC,QAAQ,2BAAkC;IACnD,QAAQ,CAAC,OAAO,2BAAkC;IAElD,MAAM,CAAC,IAAI,CAAC,IAAI,EAAE,iBAAiB,GAAG,aAAa;IAiBnD,MAAM,IAAI,iBAAiB;IAQ3B,uEAAuE;IACvE,mBAAmB,IAAI,iBAAiB;IAmBxC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI;IAS9B,6EAA6E;IAC7E,UAAU,CAAC,IAAI,EAAE,SAAS,GAAG,SAAS,GAAG,SAAS;IAelD,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM;IAIhC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO;IAYjC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI;IAU9B,eAAe,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO;IAczC,SAAS,CACP,EAAE,EAAE,MAAM,EACV,SAAS,EAAE,KAAK,GAAG,IAAI,GAAG,MAAM,EAChC,SAAS,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACvB,KAAK,SAAI,GACR,GAAG,CAAC,MAAM,CAAC;IAsCd,iBAAiB,IAAI,eAAe,EAAE;CA2EvC"}
+{"version":3,"file":"InMemoryGraph.d.ts","sourceRoot":"","sources":["../../src/graph/InMemoryGraph.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,SAAS,EAAE,iBAAiB,EAAE,eAAe,EAAE,MAAM,aAAa,CAAC;AAG5F,qBAAa,aAAa;IACxB,QAAQ,CAAC,SAAS,yBAAgC;IAClD,QAAQ,CAAC,QAAQ,2BAAkC;IACnD,QAAQ,CAAC,OAAO,2BAAkC;IAClD,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAqB;IAE9C,MAAM,CAAC,IAAI,CAAC,IAAI,EAAE,iBAAiB,GAAG,aAAa;IAiBnD,uEAAuE;IACvE,mBAAmB,IAAI,iBAAiB;IAmBxC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI;IAS9B,6EAA6E;IAC7E,UAAU,CAAC,IAAI,EAAE,SAAS,GAAG,SAAS,GAAG,SAAS;IAelD,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM;IAIhC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO;IAIjC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI;IAW9B,eAAe,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO;IAczC,SAAS,CACP,EAAE,EAAE,MAAM,EACV,SAAS,EAAE,KAAK,GAAG,IAAI,GAAG,MAAM,EAChC,SAAS,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACvB,KAAK,SAAI,GACR,GAAG,CAAC,MAAM,CAAC;IAsCd,iBAAiB,IAAI,eAAe,EAAE;CA4EvC"}

package/dist/graph/InMemoryGraph.js

@@ -3,6 +3,7 @@ export class InMemoryGraph {
     nodesById = new Map();
     outEdges = new Map();
     inEdges = new Map();
+    edgeKeys = new Set();
     static from(data) {
         const g = new InMemoryGraph();
         for (const node of data.nodes) {
@@ -19,13 +20,6 @@ export class InMemoryGraph {
         }
         return g;
     }
-    toJSON() {
-        return {
-            version: 1,
-            nodes: [...this.nodesById.values()],
-            edges: [...this.outEdges.values(), ...this.inEdges.values()].flat(),
-        };
-    }
     /** Dedupe edges when exporting (each edge stored once in outEdges). */
     toTraceabilityGraph() {
         const edgeSet = new Set();
@@ -70,17 +64,10 @@ export class InMemoryGraph {
         return `${edge.type}|${edge.from}|${edge.to}|${edge.role ?? ""}`;
     }
     hasEdge(edge) {
-        const key = this.edgeKey(edge);
-        for (const list of this.outEdges.values()) {
-            for (const e of list) {
-                if (this.edgeKey(e) === key) {
-                    return true;
-                }
-            }
-        }
-        return false;
+        return this.edgeKeys.has(this.edgeKey(edge));
     }
     addEdge(edge) {
+        this.edgeKeys.add(this.edgeKey(edge));
         this.outEdges.get(edge.from).push(edge);
         const inbound = this.inEdges.get(edge.to);
         if (inbound) {
@@ -147,6 +134,7 @@ export class InMemoryGraph {
             "useCase",
             "feature",
             "requirement",
+            "nfr",
             "dataEntity",
         ]);
         for (const node of this.nodesById.values()) {

package/dist/graph/InMemoryGraph.js.map

@@ -1 +1 @@
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package/dist/graph/doc-extract.d.ts.map

@@ -1 +1 @@
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package/dist/graph/doc-extract.js

@@ -2,6 +2,8 @@ import { basicDesignListChapterDocumentId, basicDesignListChapterFileToPatch, de
 import { BASIC_DESIGN_LIST_DOCUMENT_IDS, DEFAULT_BD_LIST_DOC, DEFAULT_LISTED_IN, PER_DOMAIN_TEMPLATE_DOC_BD, } from "./defaults.js";
 import { scanBasicDesignListDocuments } from "../registry/build.js";
 import { mergeStructurePatches, registryDocumentToStructurePatch, } from "../registry/structure-patch.js";
+import { extractBlockquoteAfterBoldField, extractBoldFieldDeep, extractBoldFieldInParagraph, findHeadingText, parseMarkdown, textContent, } from "../markdown/parse.js";
+import { visit } from "unist-util-visit";
 /** Registry template ids for per-domain SRS detail (see documents.json). */
 export const PER_DOMAIN_TEMPLATE_DOC = {
     useCase: "doc.srs.uc-detail",
@@ -9,16 +11,8 @@ export const PER_DOMAIN_TEMPLATE_DOC = {
 };
 const UC_ID_RE = /\b(UC-\d+)\b/gi;
 const F_ID_RE = /\b(F-\d+)\b/gi;
-const USE_CASE_ID_LINE = /\*\*Use Case ID:\*\*\s*(UC-\d+)/i;
-const USE_CASE_NAME_LINE = /\*\*Use Case Name:\*\*\s*(.+)/i;
-const FEATURE_ID_LINE = /\*\*Feature ID:\*\*\s*(F-\d+)/i;
-const FEATURE_NAME_HEADING = /^#{1,3}\s+(F-\d+)\s*[:\-–—]\s*(.+)$/im;
-const UC_HEADING = /^#{1,3}\s+(UC-\d+)\s*[:\-–—]\s*(.+)$/im;
 const TABLE_ROW_UC = /^\|\s*(UC-\d+)\s*\|/im;
 const TABLE_ROW_F = /^\|\s*(F-\d+)\s*\|/im;
-const BRIEF_DESCRIPTION_BLOCK = /\*\*Brief Description:\*\*\s*\n+>\s*([^\n]+(?:\n>[^\n]+)*)/i;
-const FEATURE_PURPOSE_BLOCK = /\*\*(?:Feature Purpose|Purpose):\*\*\s*\n+>\s*([^\n]+(?:\n>[^\n]+)*)/i;
-const PRIORITY_LINE = /\*\*Priority:\*\*\s*(High|Medium|Low)/i;
 const OVERVIEW_HEADING = /use case overview/i;
 const FEATURE_DESC_HEADING = /^1\.\s*description$/i;
 /** Normalize UC-1 → UC-01, F-2 → F-02; leaves placeholders (UC-XX) unchanged */
@@ -113,9 +107,12 @@ export function extractBasicDesignDetailMeta(content, kind, relativePath) {
             featureIds.add(id);
         }
     }
-    const idLine = content.match(FEATURE_ID_LINE);
-    if (idLine?.[1] && isRealDomainId(idLine[1])) {
-        featureIds.add(normalizeDomainId(idLine[1]));
+    const root = parseMarkdown(content);
+    const fIdVal = extractBoldFieldDeep(root, /^Feature ID$/i);
+    if (fIdVal) {
+        const m = fIdVal.match(/\b(F-\d+)\b/i);
+        if (m?.[1] && isRealDomainId(m[1]))
+            featureIds.add(normalizeDomainId(m[1]));
     }
     if (kind === "apiDetail") {
         const endpoint = content.match(ENDPOINT_SPEC_HEADING);
@@ -171,86 +168,83 @@ function buildBasicDesignDetailInstancePatch(opts) {
     return { version: 1, nodes, edges };
 }
 function primaryDomainIdFromDetailContent(content, kind) {
+    const root = parseMarkdown(content);
     if (kind === "useCaseDetail") {
-        const idLine = content.match(USE_CASE_ID_LINE);
-        if (idLine?.[1] && isRealDomainId(idLine[1])) {
-            const nameLine = content.match(USE_CASE_NAME_LINE);
-            return {
-                id: normalizeDomainId(idLine[1]),
-                title: nameLine?.[1]?.trim(),
-            };
+        const idVal = extractBoldFieldDeep(root, /^Use Case ID$/i);
+        if (idVal) {
+            const m = idVal.match(/\b(UC-\d+)\b/i);
+            if (m?.[1] && isRealDomainId(m[1])) {
+                const nameVal = extractBoldFieldDeep(root, /^Use Case Name$/i);
+                return { id: normalizeDomainId(m[1]), title: nameVal?.trim() };
+            }
         }
-        const heading = content.match(UC_HEADING);
-        if (heading?.[1] && isRealDomainId(heading[1])) {
-            return { id: normalizeDomainId(heading[1]), title: heading[2]?.trim() };
+        const hText = findHeadingText(root, /\bUC-\d+\b/);
+        if (hText) {
+            const hm = hText.match(/\b(UC-\d+)\b\s*[:\-–—]\s*(.+)$/i);
+            if (hm?.[1] && isRealDomainId(hm[1])) {
+                return { id: normalizeDomainId(hm[1]), title: hm[2]?.trim() };
+            }
         }
         return null;
     }
-    const idLine = content.match(FEATURE_ID_LINE);
-    if (idLine?.[1] && isRealDomainId(idLine[1])) {
-        const heading = content.match(FEATURE_NAME_HEADING);
-        return {
-            id: normalizeDomainId(idLine[1]),
-            title: heading?.[2]?.trim(),
-        };
+    const idVal = extractBoldFieldDeep(root, /^Feature ID$/i);
+    if (idVal) {
+        const m = idVal.match(/\b(F-\d+)\b/i);
+        if (m?.[1] && isRealDomainId(m[1])) {
+            const hText = findHeadingText(root, /\bF-\d+\b/);
+            let title;
+            if (hText) {
+                const hm = hText.match(/\b(F-\d+)\b\s*[:\-–—]\s*(.+)$/i);
+                title = hm?.[2]?.trim();
+            }
+            return { id: normalizeDomainId(m[1]), title };
+        }
     }
-    const heading = content.match(FEATURE_NAME_HEADING);
-    if (heading?.[1] && isRealDomainId(heading[1])) {
-        return { id: normalizeDomainId(heading[1]), title: heading[2]?.trim() };
+    const hText = findHeadingText(root, /\bF-\d+\b/);
+    if (hText) {
+        const hm = hText.match(/\b(F-\d+)\b\s*[:\-–—]\s*(.+)$/i);
+        if (hm?.[1] && isRealDomainId(hm[1])) {
+            return { id: normalizeDomainId(hm[1]), title: hm[2]?.trim() };
+        }
     }
     return null;
 }
-function cleanQuotedBlock(raw) {
-    return raw
-        .split(/\r?\n/)
-        .map((l) => l.replace(/^\s*>\s?/, "").trim())
-        .filter(Boolean)
-        .join(" ")
-        .replace(/\s+/g, " ")
-        .trim();
-}
 /** Rich title/description from generated detail markdown (not list-table stubs). */
 export function extractDetailDomainMeta(content, kind) {
     const primary = primaryDomainIdFromDetailContent(content, kind);
-    if (!primary) {
+    if (!primary)
         return null;
-    }
+    const root = parseMarkdown(content);
     const meta = {};
-    if (primary.title) {
+    if (primary.title)
         meta.title = primary.title;
-    }
-    const nameLine = content.match(USE_CASE_NAME_LINE);
-    if (nameLine?.[1]?.trim()) {
-        meta.title = nameLine[1].trim();
-    }
+    const nameVal = extractBoldFieldDeep(root, /^Use Case Name$/i);
+    if (nameVal?.trim())
+        meta.title = nameVal.trim();
     if (kind === "useCaseDetail") {
-        const brief = content.match(BRIEF_DESCRIPTION_BLOCK);
-        if (brief?.[1]) {
-            meta.description = cleanQuotedBlock(brief[1]);
-        }
-        const priority = content.match(PRIORITY_LINE);
-        if (priority?.[1]) {
-            meta.priority = priority[1];
+        const brief = extractBlockquoteAfterBoldField(root, /^Brief Description$/i);
+        if (brief)
+            meta.description = brief;
+        const priorityVal = extractBoldFieldDeep(root, /^Priority$/i);
+        if (priorityVal && /^(High|Medium|Low)$/i.test(priorityVal.trim())) {
+            meta.priority = priorityVal.trim();
         }
         if (!meta.description) {
             const sections = parseDetailSections(content, "doc.temp");
             const overview = sections.find((s) => OVERVIEW_HEADING.test(s.heading));
-            if (overview) {
+            if (overview)
                 meta.description = snippetAfterHeading(content, overview.heading);
-            }
         }
     }
     else {
-        const purpose = content.match(FEATURE_PURPOSE_BLOCK);
-        if (purpose?.[1]) {
-            meta.description = cleanQuotedBlock(purpose[1]);
-        }
+        const purpose = extractBlockquoteAfterBoldField(root, /^(?:Feature Purpose|Purpose)$/i);
+        if (purpose)
+            meta.description = purpose;
         if (!meta.description) {
             const sections = parseDetailSections(content, "doc.temp");
             const descSec = sections.find((s) => FEATURE_DESC_HEADING.test(s.heading));
-            if (descSec) {
+            if (descSec)
                 meta.description = snippetAfterHeading(content, descSec.heading);
-            }
         }
     }
     return meta;
@@ -333,37 +327,64 @@ function parseTableSatisfies(line, parsed) {
 }
 export function extractDomainFromMarkdown(content, relativePath) {
     const parsed = emptyParsed();
-    const lines = content.split(/\r?\n/);
+    const root = parseMarkdown(content);
+    // --- 1. Headings: ## UC-01: Title, ## F-01: Title ---
+    for (const node of root.children) {
+        if (node.type !== "heading")
+            continue;
+        const text = textContent(node);
+        const ucm = text.match(/\b(UC-\d+)\b\s*[:\-–—]\s*(.+)$/i);
+        if (ucm?.[1] && isRealDomainId(ucm[1])) {
+            addUseCase(parsed, ucm[1], { title: ucm[2]?.trim() });
+        }
+        const fm = text.match(/\b(F-\d+)\b\s*[:\-–—]\s*(.+)$/i);
+        if (fm?.[1] && isRealDomainId(fm[1])) {
+            addFeature(parsed, fm[1], { title: fm[2]?.trim() });
+        }
+    }
+    // --- 2. Bold field patterns in paragraphs (AST-based) ---
     let pendingUcId;
-    for (let i = 0; i < lines.length; i++) {
-        const line = lines[i];
-        const ucIdLine = line.match(USE_CASE_ID_LINE);
-        if (ucIdLine) {
-            pendingUcId = normalizeDomainId(ucIdLine[1]);
-            addUseCase(parsed, pendingUcId, {});
+    for (const node of root.children) {
+        if (node.type === "heading" && pendingUcId) {
+            pendingUcId = undefined;
+        }
+        if (node.type !== "paragraph")
             continue;
+        const para = node;
+        const ucIdVal = extractBoldFieldInParagraph(para, /^Use Case ID$/i);
+        if (ucIdVal) {
+            const m = ucIdVal.match(/\b(UC-\d+)\b/i);
+            if (m?.[1] && isRealDomainId(m[1])) {
+                pendingUcId = normalizeDomainId(m[1]);
+                addUseCase(parsed, pendingUcId, {});
+            }
         }
         if (pendingUcId) {
-            const nameLine = line.match(USE_CASE_NAME_LINE);
-            if (nameLine) {
-                addUseCase(parsed, pendingUcId, { title: nameLine[1] });
-                pendingUcId = undefined;
-                continue;
-            }
-            if (line.startsWith("### ") || line.startsWith("## ")) {
+            const nameVal = extractBoldFieldInParagraph(para, /^Use Case Name$/i);
+            if (nameVal) {
+                addUseCase(parsed, pendingUcId, { title: nameVal });
                 pendingUcId = undefined;
             }
         }
-        const ucHeading = line.match(UC_HEADING);
-        if (ucHeading) {
-            addUseCase(parsed, ucHeading[1], { title: ucHeading[2] });
+        const fIdVal = extractBoldFieldInParagraph(para, /^Feature ID$/i);
+        if (fIdVal) {
+            const m = fIdVal.match(/\b(F-\d+)\b/i);
+            if (m?.[1] && isRealDomainId(m[1]))
+                addFeature(parsed, m[1], {});
         }
-        const fHeading = line.match(FEATURE_NAME_HEADING);
-        if (fHeading) {
-            addFeature(parsed, fHeading[1], { title: fHeading[2] });
+    }
+    // --- 3. Actor extraction from paragraphs and list items (AST-based) ---
+    visit(root, "paragraph", (para) => {
+        const actorVal = extractBoldFieldInParagraph(para, /^Primary Actor$/i);
+        if (actorVal && !/^tbd$/i.test(actorVal) && actorVal.length > 1) {
+            const id = `actor.${slugActorId(actorVal)}`;
+            parsed.actors.set(id, { title: actorVal });
         }
+    });
+    // --- 4. Table rows (line-based: handles GFM and non-GFM pipe tables) ---
+    for (const line of content.split(/\r?\n/)) {
         const ucRow = line.match(TABLE_ROW_UC);
-        if (ucRow) {
+        if (ucRow?.[1]) {
             const cells = line.split("|").map((c) => c.trim());
             const title = cells[2] || cells[1];
             addUseCase(parsed, ucRow[1], {
@@ -371,7 +392,7 @@ export function extractDomainFromMarkdown(content, relativePath) {
             });
         }
         const fRow = line.match(TABLE_ROW_F);
-        if (fRow) {
+        if (fRow?.[1]) {
             const cells = line.split("|").map((c) => c.trim());
             const title = cells[2] || cells[1];
             addFeature(parsed, fRow[1], {
@@ -383,16 +404,16 @@ export function extractDomainFromMarkdown(content, relativePath) {
             parseTableSatisfies(line, parsed);
         }
     }
+    // --- 5. Global catch-all scan (picks up any remaining UC/F references) ---
     for (const m of content.matchAll(UC_ID_RE)) {
-        if (m[1] && isRealDomainId(m[1])) {
+        if (m[1] && isRealDomainId(m[1]))
             addUseCase(parsed, m[1], {});
-        }
     }
     for (const m of content.matchAll(F_ID_RE)) {
-        if (m[1] && isRealDomainId(m[1])) {
+        if (m[1] && isRealDomainId(m[1]))
             addFeature(parsed, m[1], {});
-        }
     }
+    // --- 6. Rich metadata from SRS detail files ---
     const srsDetailKind = classifySrsDetailFile(relativePath);
     if (srsDetailKind) {
         const rich = extractDetailDomainMeta(content, srsDetailKind);
@@ -408,6 +429,7 @@ export function extractDomainFromMarkdown(content, relativePath) {
             }
         }
     }
+    // --- 7. Basic-design detail metadata ---
     const bdKind = classifyBasicDesignDetailFile(relativePath);
     if (bdKind) {
         const meta = extractBasicDesignDetailMeta(content, bdKind, relativePath);
@@ -417,26 +439,17 @@ export function extractDomainFromMarkdown(content, relativePath) {
             });
         }
     }
-    const actorSection = /(?:\*\*Primary Actor:\*\*|Primary Actor:)\s*\*?\*?\s*([^\n*]+)/gi;
-    for (const m of content.matchAll(actorSection)) {
-        const name = m[1]?.trim();
-        if (name && !/^tbd$/i.test(name) && name.length > 1) {
-            const id = `actor.${slugActorId(name)}`;
-            parsed.actors.set(id, { title: name });
-        }
-    }
     return parsed;
 }
-const SCREEN_PURPOSE_BLOCK = /##\s*1\.\s*Screen:[\s\S]*?\*\*Purpose:\*\*\s*\n+>\s*([^\n]+(?:\n>[^\n]+)*)/i;
 function extractBasicDesignDetailDescription(content, kind) {
     if (kind === "apiDetail") {
         const meta = extractDetailDomainMeta(content, "featureDetail");
         return meta?.description;
     }
-    const purpose = content.match(SCREEN_PURPOSE_BLOCK);
-    if (purpose?.[1]) {
-        return cleanQuotedBlock(purpose[1]);
-    }
+    const root = parseMarkdown(content);
+    const purpose = extractBlockquoteAfterBoldField(root, /^Purpose$/i);
+    if (purpose)
+        return purpose;
     const sections = parseDetailSections(content, "doc.temp");
     const screenHeading = sections.find((s) => /^##\s*1\.\s*screen/i.test(s.heading));
     if (screenHeading) {
@@ -538,13 +551,13 @@ function buildDetailInstancePatch(opts) {
     const sectionPatch = detailSectionsToPatch(opts.docId, sections, opts.content);
     nodes.push(...sectionPatch.nodes);
     edges.push(...sectionPatch.edges);
-    for (const sec of sections) {
-        edges.push({ type: "definedIn", from: opts.domainId, to: sec.id });
-        edges.push({ type: "describedIn", from: opts.domainId, to: sec.id });
-    }
-    if (sections.length === 0) {
-        edges.push({ type: "definedIn", from: opts.domainId, to: opts.docId });
-    }
+    // Anchor to the primary (first) section only — one definedIn is enough for validation
+    // and avoids flooding the graph with edges to every section.
+    edges.push({
+        type: "definedIn",
+        from: opts.domainId,
+        to: sections[0]?.id ?? opts.docId,
+    });
     return { version: 1, nodes, edges };
 }
 function srsDetailFileToPatch(relativePath, content) {
@@ -708,7 +721,7 @@ export async function buildDocExtractPatch(entries, _projectRoot, options) {
         perFile.push(extractDomainFromMarkdown(e.content, e.relativePath));
     }
     const merged = mergeParsedDomains(perFile);
-    const allNodes = [];
+    const allNodesMap = new Map();
     const allEdges = [];
     const edgeKeys = new Set();
     let detailDocuments = 0;
@@ -717,8 +730,9 @@ export async function buildDocExtractPatch(entries, _projectRoot, options) {
     let bdDetailDocuments = 0;
     const mergePatchInto = (patch) => {
         for (const n of patch.nodes) {
-            if (!allNodes.some((x) => x.id === n.id && x.type === n.type)) {
-                allNodes.push(n);
+            const existing = allNodesMap.get(n.id);
+            if (!existing) {
+                allNodesMap.set(n.id, n);
                 if (n.type === "document" && n.output && !n.outputPattern) {
                     const out = String(n.output).replace(/\\/g, "/");
                     const isBdInstance = n.id.startsWith("doc.bd.api-") ||
@@ -742,8 +756,6 @@ export async function buildDocExtractPatch(entries, _projectRoot, options) {
                 }
             }
             else {
-                const idx = allNodes.findIndex((x) => x.id === n.id);
-                const existing = allNodes[idx];
                 const merged = { ...existing, ...n };
                 if (!n.title && existing.title) {
                     merged.title = existing.title;
@@ -751,10 +763,10 @@ export async function buildDocExtractPatch(entries, _projectRoot, options) {
                 if (!n.description && existing.description) {
                     merged.description = existing.description;
                 }
-                allNodes[idx] = merged;
-                if (n.type === "document" && n.output && !existing.output) {
-                    allNodes[idx] = { ...allNodes[idx], output: n.output };
+                if (n.type === "document" && !n.output && existing.output) {
+                    merged.output = existing.output;
                 }
+                allNodesMap.set(n.id, merged);
             }
         }
         for (const edge of patch.edges) {
@@ -784,7 +796,7 @@ export async function buildDocExtractPatch(entries, _projectRoot, options) {
         }));
     }
     return {
-        patch: { version: 1, nodes: allNodes, edges: allEdges },
+        patch: { version: 1, nodes: [...allNodesMap.values()], edges: allEdges },
         stats: {
             useCases: merged.useCases.size,
             features: merged.features.size,