graphifyy 0.3.17 → 0.3.28

package/dist/cli.js

@@ -15,6 +15,73 @@ var __export = (target, all) => {
     __defProp(target, name, { get: all[name], enumerable: true });
 };
 
+// src/graph.ts
+import Graph from "graphology";
+function createGraph(directed = false) {
+  return new Graph({ type: directed ? "directed" : "undirected", multi: false });
+}
+function isDirectedGraph(G) {
+  return G.type === "directed";
+}
+function loadGraphFromData(raw) {
+  const G = createGraph(raw.directed === true);
+  for (const [key, value] of Object.entries(raw.graph ?? {})) {
+    G.setAttribute(key, value);
+  }
+  for (const node of raw.nodes ?? []) {
+    const { id, ...attrs } = node;
+    G.mergeNode(id, attrs);
+  }
+  for (const link of raw.links ?? raw.edges ?? []) {
+    const { source, target, ...attrs } = link;
+    if (!G.hasNode(source) || !G.hasNode(target)) continue;
+    try {
+      G.mergeEdge(source, target, attrs);
+    } catch {
+    }
+  }
+  if (raw.hyperedges && raw.hyperedges.length > 0) {
+    G.setAttribute("hyperedges", raw.hyperedges);
+  }
+  return G;
+}
+function toUndirectedGraph(G) {
+  if (!isDirectedGraph(G)) return G.copy();
+  const copy = createGraph(false);
+  for (const [key, value] of Object.entries(G.getAttributes())) {
+    copy.setAttribute(key, value);
+  }
+  G.forEachNode((nodeId, attrs) => {
+    copy.mergeNode(nodeId, attrs);
+  });
+  G.forEachEdge((_edge, attrs, source, target) => {
+    if (!copy.hasNode(source) || !copy.hasNode(target)) return;
+    try {
+      copy.mergeEdge(source, target, attrs);
+    } catch {
+    }
+  });
+  return copy;
+}
+function forEachTraversalNeighbor(G, node, callback) {
+  if (isDirectedGraph(G)) {
+    G.forEachOutboundNeighbor(node, callback);
+    return;
+  }
+  G.forEachNeighbor(node, callback);
+}
+function traversalNeighbors(G, node) {
+  const neighbors = [];
+  forEachTraversalNeighbor(G, node, (neighbor) => {
+    neighbors.push(neighbor);
+  });
+  return neighbors;
+}
+var init_graph = __esm({
+  "src/graph.ts"() {
+  }
+});
+
 // src/hooks.ts
 var hooks_exports = {};
 __export(hooks_exports, {
@@ -43,7 +110,7 @@ function installHook(hooksDir, name, script, marker) {
     writeFileSync(hookPath, content.trimEnd() + "\n\n" + script);
     return `appended to existing ${name} hook at ${hookPath}`;
   }
-  writeFileSync(hookPath, "#!/bin/bash\n" + script);
+  writeFileSync(hookPath, "#!/bin/sh\n" + script);
   chmodSync(hookPath, 493);
   return `installed at ${hookPath}`;
 }
@@ -56,7 +123,7 @@ function uninstallHook(hooksDir, name, marker, markerEnd) {
     escapeRegExp(marker) + "[\\s\\S]*?" + escapeRegExp(markerEnd) + "\\n?"
   );
   let newContent = content.replace(regex, "").trim();
-  if (!newContent || newContent === "#!/bin/bash") {
+  if (!newContent || ["#!/bin/bash", "#!/bin/sh"].includes(newContent)) {
     unlinkSync(hookPath);
     return `removed ${name} hook at ${hookPath}`;
   }
@@ -369,7 +436,7 @@ __export(cluster_exports, {
 });
 import louvain from "graphology-communities-louvain";
 function partition(G) {
-  const result = louvain(G);
+  const result = louvain(G.type === "directed" ? toUndirectedGraph(G) : G);
   const map = /* @__PURE__ */ new Map();
   for (const [node, cid] of Object.entries(result)) {
     map.set(node, cid);
@@ -475,11 +542,72 @@ var MAX_COMMUNITY_FRACTION, MIN_SPLIT_SIZE;
 var init_cluster = __esm({
   "src/cluster.ts"() {
     init_collections();
+    init_graph();
     MAX_COMMUNITY_FRACTION = 0.25;
     MIN_SPLIT_SIZE = 10;
   }
 });
 
+// src/types.ts
+var init_types = __esm({
+  "src/types.ts"() {
+  }
+});
+
+// src/detect.ts
+import {
+  readdirSync,
+  readFileSync as readFileSync2,
+  writeFileSync as writeFileSync2,
+  statSync,
+  existsSync as existsSync3,
+  mkdirSync as mkdirSync2,
+  lstatSync
+} from "fs";
+import { join as join2, resolve as resolve2, extname, basename, relative, sep, dirname } from "path";
+import { createHash } from "crypto";
+var CODE_EXTENSIONS, DOC_EXTENSIONS, PAPER_EXTENSIONS, IMAGE_EXTENSIONS;
+var init_detect = __esm({
+  "src/detect.ts"() {
+    init_types();
+    CODE_EXTENSIONS = /* @__PURE__ */ new Set([
+      ".py",
+      ".ts",
+      ".js",
+      ".jsx",
+      ".tsx",
+      ".go",
+      ".rs",
+      ".java",
+      ".cpp",
+      ".cc",
+      ".cxx",
+      ".c",
+      ".h",
+      ".hpp",
+      ".rb",
+      ".swift",
+      ".kt",
+      ".kts",
+      ".cs",
+      ".scala",
+      ".php",
+      ".lua",
+      ".toc",
+      ".zig",
+      ".ps1",
+      ".ex",
+      ".exs",
+      ".m",
+      ".mm",
+      ".jl"
+    ]);
+    DOC_EXTENSIONS = /* @__PURE__ */ new Set([".md", ".txt", ".rst"]);
+    PAPER_EXTENSIONS = /* @__PURE__ */ new Set([".pdf"]);
+    IMAGE_EXTENSIONS = /* @__PURE__ */ new Set([".png", ".jpg", ".jpeg", ".gif", ".webp", ".svg"]);
+  }
+});
+
 // src/analyze.ts
 var analyze_exports = {};
 __export(analyze_exports, {
@@ -521,10 +649,11 @@ function isConceptNode(G, nodeId) {
   return false;
 }
 function fileCategory(path) {
-  const ext = path.includes(".") ? path.split(".").pop()?.toLowerCase() ?? "" : "";
+  const ext = path.includes(".") ? `.${path.split(".").pop()?.toLowerCase() ?? ""}` : "";
   if (CODE_EXTENSIONS.has(ext)) return "code";
   if (PAPER_EXTENSIONS.has(ext)) return "paper";
   if (IMAGE_EXTENSIONS.has(ext)) return "image";
+  if (DOC_EXTENSIONS.has(ext)) return "doc";
   return "doc";
 }
 function topLevelDir(path) {
@@ -718,10 +847,10 @@ function suggestQuestions(G, communities, communityLabels, topN = 7) {
       const cid = nodeCommunity.get(nodeId);
       const commLabel = cid !== void 0 ? labelMap.get(cid) ?? `Community ${cid}` : "unknown";
       const neighborComms = /* @__PURE__ */ new Set();
-      G.forEachNeighbor(nodeId, (n) => {
+      for (const n of traversalNeighbors(G, nodeId)) {
         const nc = nodeCommunity.get(n);
         if (nc !== void 0 && nc !== cid) neighborComms.add(nc);
-      });
+      }
       if (neighborComms.size > 0) {
         const otherLabels = [...neighborComms].map((c) => labelMap.get(c) ?? `Community ${c}`);
         questions.push({
@@ -850,30 +979,12 @@ function graphDiff(GOld, GNew) {
     summary: parts.length > 0 ? parts.join(", ") : "no changes"
   };
 }
-var CODE_EXTENSIONS, PAPER_EXTENSIONS, IMAGE_EXTENSIONS;
 var init_analyze = __esm({
   "src/analyze.ts"() {
     init_collections();
     init_cluster();
-    CODE_EXTENSIONS = /* @__PURE__ */ new Set([
-      "py",
-      "ts",
-      "tsx",
-      "js",
-      "go",
-      "rs",
-      "java",
-      "rb",
-      "cpp",
-      "c",
-      "h",
-      "cs",
-      "kt",
-      "scala",
-      "php"
-    ]);
-    PAPER_EXTENSIONS = /* @__PURE__ */ new Set(["pdf"]);
-    IMAGE_EXTENSIONS = /* @__PURE__ */ new Set(["png", "jpg", "jpeg", "webp", "gif", "svg"]);
+    init_graph();
+    init_detect();
   }
 });
 
@@ -882,42 +993,27 @@ var serve_exports = {};
 __export(serve_exports, {
   serve: () => serve
 });
-import { readFileSync as readFileSync2 } from "fs";
-import Graph from "graphology";
+import { readFileSync as readFileSync3 } from "fs";
 import { bidirectional } from "graphology-shortest-path/unweighted.js";
-import { basename } from "path";
+import { basename as basename2, dirname as dirname2, resolve as resolve3 } from "path";
 function loadGraph(graphPath) {
   let safePath;
   try {
-    safePath = validateGraphPath(graphPath);
+    safePath = validateGraphPath(graphPath, dirname2(resolve3(graphPath)));
   } catch (err) {
     console.error(`error: ${err instanceof Error ? err.message : err}`);
     process.exit(1);
   }
   let data;
   try {
-    data = JSON.parse(readFileSync2(safePath, "utf-8"));
+    data = JSON.parse(readFileSync3(safePath, "utf-8"));
   } catch (err) {
     console.error(
       `error: graph.json is corrupted (${err instanceof Error ? err.message : err}). Re-run the graphify skill to rebuild it (for Codex: $graphify .).`
     );
     process.exit(1);
   }
-  const G = new Graph({ type: "undirected", multi: false });
-  const nodes = data.nodes ?? [];
-  for (const node of nodes) {
-    const { id, ...attrs } = node;
-    G.mergeNode(id, attrs);
-  }
-  const links = data.links ?? data.edges ?? [];
-  for (const link of links) {
-    const { source, target, ...attrs } = link;
-    try {
-      G.mergeEdge(source, target, attrs);
-    } catch {
-    }
-  }
-  return G;
+  return loadGraphFromData(data);
 }
 function communitiesFromGraph(G) {
   const communities = /* @__PURE__ */ new Map();
@@ -930,6 +1026,15 @@ function communitiesFromGraph(G) {
   });
   return communities;
 }
+function communityName(G, cid) {
+  if (cid === void 0 || cid === null) return null;
+  const labels = G.getAttribute("community_labels");
+  const fromGraph = labels?.[String(cid)];
+  if (typeof fromGraph === "string" && fromGraph.length > 0) {
+    return sanitizeLabel(fromGraph);
+  }
+  return null;
+}
 function scoreNodes(G, terms) {
   const scored = [];
   G.forEachNode((nid, data) => {
@@ -948,7 +1053,7 @@ function bfs(G, startNodes, depth) {
   for (let i = 0; i < depth; i++) {
     const nextFrontier = /* @__PURE__ */ new Set();
     for (const n of frontier) {
-      G.forEachNeighbor(n, (neighbor) => {
+      forEachTraversalNeighbor(G, n, (neighbor) => {
         if (!visited.has(neighbor)) {
           nextFrontier.add(neighbor);
           edges.push([n, neighbor]);
@@ -968,7 +1073,7 @@ function dfs(G, startNodes, depth) {
     const [node, d] = stack.pop();
     if (visited.has(node) || d > depth) continue;
     visited.add(node);
-    G.forEachNeighbor(node, (neighbor) => {
+    forEachTraversalNeighbor(G, node, (neighbor) => {
       if (!visited.has(neighbor)) {
         stack.push([neighbor, d + 1]);
         edges.push([node, neighbor]);
@@ -1047,7 +1152,7 @@ function toolGetNode(G, args) {
     `  ID: ${nid}`,
     `  Source: ${d.source_file ?? ""} ${d.source_location ?? ""}`,
     `  Type: ${d.file_type ?? ""}`,
-    `  Community: ${d.community ?? ""}`,
+    `  Community: ${d.community_name ? `${d.community ?? ""} (${d.community_name})` : communityName(G, d.community) ?? String(d.community ?? "")}`,
     `  Degree: ${G.degree(nid)}`
   ].join("\n");
 }
@@ -1058,7 +1163,7 @@ function toolGetNeighbors(G, args) {
   if (matches.length === 0) return `No node matching '${label}' found.`;
   const nid = matches[0];
   const lines = [`Neighbors of ${G.getNodeAttribute(nid, "label") ?? nid}:`];
-  G.forEachNeighbor(nid, (neighbor) => {
+  forEachTraversalNeighbor(G, nid, (neighbor) => {
     const edgeKey = G.edge(nid, neighbor);
     if (!edgeKey) return;
     const d = G.getEdgeAttributes(edgeKey);
@@ -1074,7 +1179,8 @@ function toolGetCommunity(communities, G, args) {
   const cid = Number(args.community_id);
   const nodes = communities.get(cid);
   if (!nodes || nodes.length === 0) return `Community ${cid} not found.`;
-  const lines = [`Community ${cid} (${nodes.length} nodes):`];
+  const label = communityName(G, cid);
+  const lines = [label ? `Community ${cid} - ${label} (${nodes.length} nodes):` : `Community ${cid} (${nodes.length} nodes):`];
   for (const n of nodes) {
     const d = G.getNodeAttributes(n);
     lines.push(`  ${d.label ?? n} [${d.source_file ?? ""}]`);
@@ -1296,8 +1402,13 @@ async function serve(graphPath = "graphify-out/graph.json", transport) {
     if (!handler) {
       return { content: [{ type: "text", text: `Unknown tool: ${name}` }] };
     }
-    const text = handler(args ?? {});
-    return { content: [{ type: "text", text }] };
+    try {
+      const text = handler(args ?? {});
+      return { content: [{ type: "text", text }] };
+    } catch (err) {
+      const message = err instanceof Error ? err.message : String(err);
+      return { content: [{ type: "text", text: `Error executing ${name}: ${message}` }] };
+    }
   });
   const serverTransport = transport ?? new StdioServerTransport();
   let keepAlive;
@@ -1305,14 +1416,14 @@ async function serve(graphPath = "graphify-out/graph.json", transport) {
     keepAlive = setInterval(() => void 0, 6e4);
     process.stdin?.resume();
   }
-  const closed = new Promise((resolve7) => {
+  const closed = new Promise((resolve9) => {
     const previousOnClose = server.onclose;
     server.onclose = () => {
       if (keepAlive) {
         clearInterval(keepAlive);
       }
       previousOnClose?.();
-      resolve7();
+      resolve9();
     };
   });
   await server.connect(serverTransport);
@@ -1323,9 +1434,10 @@ async function serve(graphPath = "graphify-out/graph.json", transport) {
 var isDirectExecution;
 var init_serve = __esm({
   "src/serve.ts"() {
+    init_graph();
     init_security();
     init_analyze();
-    isDirectExecution = typeof process !== "undefined" && typeof process.argv[1] === "string" && /^serve\.(?:js|mjs|cjs|ts)$/.test(basename(process.argv[1]));
+    isDirectExecution = typeof process !== "undefined" && typeof process.argv[1] === "string" && /^serve\.(?:js|mjs|cjs|ts)$/.test(basename2(process.argv[1]));
     if (isDirectExecution) {
       const graphPath = process.argv[2] ?? "graphify-out/graph.json";
       serve(graphPath).catch((err) => {
@@ -1337,21 +1449,33 @@ var init_serve = __esm({
 });
 
 // src/cache.ts
-import { createHash } from "crypto";
-import { readFileSync as readFileSync3, writeFileSync as writeFileSync2, mkdirSync as mkdirSync2, readdirSync, unlinkSync as unlinkSync2, renameSync, existsSync as existsSync3 } from "fs";
-import { join as join2, resolve as resolve2 } from "path";
+import { createHash as createHash2 } from "crypto";
+import { readFileSync as readFileSync4, writeFileSync as writeFileSync3, mkdirSync as mkdirSync3, readdirSync as readdirSync2, unlinkSync as unlinkSync2, renameSync, existsSync as existsSync4 } from "fs";
+import { extname as extname2, join as join3, resolve as resolve5 } from "path";
+function bodyContent(content) {
+  const text = content.toString("utf-8");
+  if (!text.startsWith("---")) {
+    return content;
+  }
+  const end = text.indexOf("\n---", 3);
+  if (end === -1) {
+    return content;
+  }
+  return Buffer.from(text.slice(end + 4), "utf-8");
+}
 function fileHash(filePath) {
-  const content = readFileSync3(filePath);
-  const resolved = resolve2(filePath);
-  const h = createHash("sha256");
+  const raw = readFileSync4(filePath);
+  const content = extname2(filePath).toLowerCase() === ".md" ? bodyContent(raw) : raw;
+  const resolved = resolve5(filePath);
+  const h = createHash2("sha256");
   h.update(content);
   h.update("\0");
   h.update(resolved);
   return h.digest("hex");
 }
 function cacheDir(root = ".") {
-  const d = join2(root, "graphify-out", "cache");
-  mkdirSync2(d, { recursive: true });
+  const d = join3(root, "graphify-out", "cache");
+  mkdirSync3(d, { recursive: true });
   return d;
 }
 function loadCached(filePath, root = ".") {
@@ -1361,20 +1485,20 @@ function loadCached(filePath, root = ".") {
   } catch {
     return null;
   }
-  const entry = join2(cacheDir(root), `${h}.json`);
-  if (!existsSync3(entry)) return null;
+  const entry = join3(cacheDir(root), `${h}.json`);
+  if (!existsSync4(entry)) return null;
   try {
-    return JSON.parse(readFileSync3(entry, "utf-8"));
+    return JSON.parse(readFileSync4(entry, "utf-8"));
   } catch {
     return null;
   }
 }
 function saveCached(filePath, result, root = ".") {
   const h = fileHash(filePath);
-  const entry = join2(cacheDir(root), `${h}.json`);
+  const entry = join3(cacheDir(root), `${h}.json`);
   const tmp = entry + ".tmp";
   try {
-    writeFileSync2(tmp, JSON.stringify(result));
+    writeFileSync3(tmp, JSON.stringify(result));
     renameSync(tmp, entry);
   } catch {
     try {
@@ -1415,8 +1539,8 @@ __export(extract_exports, {
   extractWithDiagnostics: () => extractWithDiagnostics,
   extractZig: () => extractZig
 });
-import { readFileSync as readFileSync4, readdirSync as readdirSync2, lstatSync, realpathSync, existsSync as existsSync4 } from "fs";
-import { resolve as resolve3, basename as basename2, extname, dirname, join as join3, sep } from "path";
+import { readFileSync as readFileSync5, readdirSync as readdirSync3, lstatSync as lstatSync2, realpathSync, existsSync as existsSync5 } from "fs";
+import { resolve as resolve7, basename as basename3, extname as extname3, dirname as dirname3, join as join4, sep as sep2 } from "path";
 import { createRequire } from "module";
 import * as TreeSitter from "web-tree-sitter";
 function getModuleRequire() {
@@ -1454,14 +1578,14 @@ function resolveGrammarWasm(langName) {
   for (const candidate of candidates) {
     try {
       const resolved = moduleRequire.resolve(candidate);
-      if (existsSync4(resolved)) return resolved;
+      if (existsSync5(resolved)) return resolved;
     } catch {
     }
   }
-  const nmDir = join3(process.cwd(), "node_modules");
+  const nmDir = join4(process.cwd(), "node_modules");
   for (const candidate of candidates) {
-    const p = join3(nmDir, candidate);
-    if (existsSync4(p)) return p;
+    const p = join4(nmDir, candidate);
+    if (existsSync5(p)) return p;
   }
   return null;
 }
@@ -1866,13 +1990,13 @@ async function _extractGeneric(filePath, config) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     tree = parseText(parser, source);
   } catch (e) {
     return { nodes: [], edges: [], error: String(e) };
   }
   const root = tree.rootNode;
-  const stem = basename2(filePath, extname(filePath));
+  const stem = basename3(filePath, extname3(filePath));
   const strPath = filePath;
   const nodes = [];
   const edges = [];
@@ -1902,7 +2026,7 @@ async function _extractGeneric(filePath, config) {
     });
   }
   const fileNid = _makeId(stem);
-  addNode(fileNid, basename2(filePath), 1);
+  addNode(fileNid, basename3(filePath), 1);
   function walk(node, parentClassNid = null) {
     const t = node.type;
     if (config.importTypes.has(t)) {
@@ -2241,10 +2365,10 @@ async function _extractGeneric(filePath, config) {
               source: callerNid,
               target: tgtNid,
               relation: "calls",
-              confidence: "INFERRED",
+              confidence: "EXTRACTED",
               source_file: strPath,
               source_location: `L${line}`,
-              weight: 0.8
+              weight: 1
             });
           }
         }
@@ -2274,13 +2398,13 @@ async function _extractPythonRationale(filePath, result) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     const tree = parseText(parser, source);
     root = tree.rootNode;
   } catch {
     return;
   }
-  const stem = basename2(filePath, extname(filePath));
+  const stem = basename3(filePath, extname3(filePath));
   const strPath = filePath;
   const { nodes, edges } = result;
   const seenIds = new Set(nodes.map((n) => n.id));
@@ -2376,7 +2500,7 @@ async function extractPython(filePath) {
   return result;
 }
 async function extractJs(filePath) {
-  const ext = extname(filePath);
+  const ext = extname3(filePath);
   const config = ext === ".ts" || ext === ".tsx" ? _TS_CONFIG : _JS_CONFIG;
   return _extractGeneric(filePath, config);
 }
@@ -2421,13 +2545,13 @@ async function extractJulia(filePath) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     tree = parseText(parser, source);
   } catch (e) {
     return { nodes: [], edges: [], error: String(e) };
   }
   const root = tree.rootNode;
-  const stem = basename2(filePath, extname(filePath));
+  const stem = basename3(filePath, extname3(filePath));
   const strPath = filePath;
   const nodes = [];
   const edges = [];
@@ -2443,7 +2567,7 @@ async function extractJulia(filePath) {
     edges.push({ source: src, target: tgt, relation, confidence, source_file: strPath, source_location: `L${line}`, weight });
   }
   const fileNid = _makeId(stem);
-  addNode(fileNid, basename2(filePath), 1);
+  addNode(fileNid, basename3(filePath), 1);
   function funcNameFromSignature(sigNode) {
     for (const child of sigNode.children) {
       if (child.type === "call_expression") {
@@ -2617,14 +2741,14 @@ async function extractGo(filePath) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     tree = parseText(parser, source);
   } catch (e) {
     return { nodes: [], edges: [], error: String(e) };
   }
   const root = tree.rootNode;
-  const stem = basename2(filePath, extname(filePath));
-  const pkgScope = dirname(filePath).split(sep).pop() || stem;
+  const stem = basename3(filePath, extname3(filePath));
+  const pkgScope = dirname3(filePath).split(sep2).pop() || stem;
   const strPath = filePath;
   const nodes = [];
   const edges = [];
@@ -2640,7 +2764,7 @@ async function extractGo(filePath) {
     edges.push({ source: src, target: tgt, relation, confidence, source_file: strPath, source_location: `L${line}`, weight });
   }
   const fileNid = _makeId(stem);
-  addNode(fileNid, basename2(filePath), 1);
+  addNode(fileNid, basename3(filePath), 1);
   function walk(node) {
     const t = node.type;
     if (t === "function_declaration") {
@@ -2767,10 +2891,10 @@ async function extractGo(filePath) {
               source: callerNid,
               target: tgtNid,
               relation: "calls",
-              confidence: "INFERRED",
+              confidence: "EXTRACTED",
               source_file: strPath,
               source_location: `L${line}`,
-              weight: 0.8
+              weight: 1
             });
           }
         }
@@ -2799,13 +2923,13 @@ async function extractRust(filePath) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     tree = parseText(parser, source);
   } catch (e) {
     return { nodes: [], edges: [], error: String(e) };
   }
   const root = tree.rootNode;
-  const stem = basename2(filePath, extname(filePath));
+  const stem = basename3(filePath, extname3(filePath));
   const strPath = filePath;
   const nodes = [];
   const edges = [];
@@ -2821,7 +2945,7 @@ async function extractRust(filePath) {
     edges.push({ source: src, target: tgt, relation, confidence, source_file: strPath, source_location: `L${line}`, weight });
   }
   const fileNid = _makeId(stem);
-  addNode(fileNid, basename2(filePath), 1);
+  addNode(fileNid, basename3(filePath), 1);
   function walk(node, parentImplNid = null) {
     const t = node.type;
     if (t === "function_item") {
@@ -2922,10 +3046,10 @@ async function extractRust(filePath) {
               source: callerNid,
               target: tgtNid,
               relation: "calls",
-              confidence: "INFERRED",
+              confidence: "EXTRACTED",
               source_file: strPath,
               source_location: `L${line}`,
-              weight: 0.8
+              weight: 1
             });
           }
         }
@@ -2954,13 +3078,13 @@ async function extractZig(filePath) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     tree = parseText(parser, source);
   } catch (e) {
     return { nodes: [], edges: [], error: String(e) };
   }
   const root = tree.rootNode;
-  const stem = basename2(filePath, extname(filePath));
+  const stem = basename3(filePath, extname3(filePath));
   const strPath = filePath;
   const nodes = [];
   const edges = [];
@@ -2976,7 +3100,7 @@ async function extractZig(filePath) {
     edges.push({ source: src, target: tgt, relation, confidence, source_file: strPath, source_location: `L${line}`, weight });
   }
   const fileNid = _makeId(stem);
-  addNode(fileNid, basename2(filePath), 1);
+  addNode(fileNid, basename3(filePath), 1);
   function extractImport(node) {
     for (const child of node.children) {
       if (child.type === "builtin_function") {
@@ -3084,7 +3208,7 @@ async function extractZig(filePath) {
           const pair = `${callerNid}|${tgtNid}`;
           if (!seenCallPairs.has(pair)) {
             seenCallPairs.add(pair);
-            addEdge(callerNid, tgtNid, "calls", node.startPosition.row + 1, "INFERRED", 0.8);
+            addEdge(callerNid, tgtNid, "calls", node.startPosition.row + 1, "EXTRACTED", 1);
           }
         }
       }
@@ -3112,13 +3236,13 @@ async function extractPowershell(filePath) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     tree = parseText(parser, source);
   } catch (e) {
     return { nodes: [], edges: [], error: String(e) };
   }
   const root = tree.rootNode;
-  const stem = basename2(filePath, extname(filePath));
+  const stem = basename3(filePath, extname3(filePath));
   const strPath = filePath;
   const nodes = [];
   const edges = [];
@@ -3134,7 +3258,7 @@ async function extractPowershell(filePath) {
     edges.push({ source: src, target: tgt, relation, confidence, source_file: strPath, source_location: `L${line}`, weight });
   }
   const fileNid = _makeId(stem);
-  addNode(fileNid, basename2(filePath), 1);
+  addNode(fileNid, basename3(filePath), 1);
   const _PS_SKIP = /* @__PURE__ */ new Set([
     "using",
     "return",
@@ -3267,7 +3391,7 @@ async function extractPowershell(filePath) {
             const pair = `${callerNid}|${tgtNid}`;
             if (!seenCallPairs.has(pair)) {
               seenCallPairs.add(pair);
-              addEdge(callerNid, tgtNid, "calls", node.startPosition.row + 1, "INFERRED", 0.8);
+              addEdge(callerNid, tgtNid, "calls", node.startPosition.row + 1, "EXTRACTED", 1);
             }
           }
         }
@@ -3296,13 +3420,13 @@ async function extractObjc(filePath) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     tree = parseText(parser, source);
   } catch (e) {
     return { nodes: [], edges: [], error: String(e) };
   }
   const root = tree.rootNode;
-  const stem = basename2(filePath, extname(filePath));
+  const stem = basename3(filePath, extname3(filePath));
   const strPath = filePath;
   const nodes = [];
   const edges = [];
@@ -3318,7 +3442,7 @@ async function extractObjc(filePath) {
     edges.push({ source: src, target: tgt, relation, confidence, source_file: strPath, source_location: `L${line}`, weight });
   }
   const fileNid = _makeId(stem);
-  addNode(fileNid, basename2(filePath), 1);
+  addNode(fileNid, basename3(filePath), 1);
   function _read(node) {
     return source.slice(node.startIndex, node.endIndex);
   }
@@ -3473,7 +3597,7 @@ async function extractObjc(filePath) {
                 const pair = `${callerNid}|${candidate}`;
                 if (!seenCalls.has(pair) && callerNid !== candidate) {
                   seenCalls.add(pair);
-                  addEdge(callerNid, candidate, "calls", bodyNode.startPosition.row + 1, "INFERRED", 0.8);
+                  addEdge(callerNid, candidate, "calls", bodyNode.startPosition.row + 1, "EXTRACTED", 1);
                 }
               }
             }
@@ -3499,13 +3623,13 @@ async function extractElixir(filePath) {
   try {
     const parser = new Parser2();
     parser.setLanguage(lang);
-    source = readFileSync4(filePath, "utf-8");
+    source = readFileSync5(filePath, "utf-8");
     tree = parseText(parser, source);
   } catch (e) {
     return { nodes: [], edges: [], error: String(e) };
   }
   const root = tree.rootNode;
-  const stem = basename2(filePath, extname(filePath));
+  const stem = basename3(filePath, extname3(filePath));
   const strPath = filePath;
   const nodes = [];
   const edges = [];
@@ -3521,7 +3645,7 @@ async function extractElixir(filePath) {
     edges.push({ source: src, target: tgt, relation, confidence, source_file: strPath, source_location: `L${line}`, weight });
   }
   const fileNid = _makeId(stem);
-  addNode(fileNid, basename2(filePath), 1);
+  addNode(fileNid, basename3(filePath), 1);
   const _IMPORT_KEYWORDS = /* @__PURE__ */ new Set(["alias", "import", "require", "use"]);
   function getAliasText(node) {
     for (const child of node.children) {
@@ -3664,7 +3788,7 @@ async function extractElixir(filePath) {
         const pair = `${callerNid}|${tgtNid}`;
         if (!seenCallPairs.has(pair)) {
           seenCallPairs.add(pair);
-          addEdge(callerNid, tgtNid, "calls", node.startPosition.row + 1, "INFERRED", 0.8);
+          addEdge(callerNid, tgtNid, "calls", node.startPosition.row + 1, "EXTRACTED", 1);
         }
       }
     }
@@ -3691,7 +3815,7 @@ async function _resolveCrossFileImports(perFile, paths) {
     for (const node of fileResult.nodes ?? []) {
       const src = node.source_file ?? "";
       if (!src) continue;
-      const fileStem = basename2(src, extname(src));
+      const fileStem = basename3(src, extname3(src));
       const label = node.label ?? "";
       const nid = node.id ?? "";
       if (label && !label.endsWith(")") && !label.endsWith(".py") && !label.startsWith("_")) {
@@ -3703,7 +3827,7 @@ async function _resolveCrossFileImports(perFile, paths) {
   const newEdges = [];
   const stemToPath = /* @__PURE__ */ new Map();
   for (const p of paths) {
-    stemToPath.set(basename2(p, extname(p)), p);
+    stemToPath.set(basename3(p, extname3(p)), p);
   }
   for (let idx = 0; idx < perFile.length; idx++) {
     let walkImports = function(node) {
@@ -3767,7 +3891,7 @@ async function _resolveCrossFileImports(perFile, paths) {
     };
     const fileResult = perFile[idx];
     const filePath = paths[idx];
-    const fileStem = basename2(filePath, extname(filePath));
+    const fileStem = basename3(filePath, extname3(filePath));
     const strPath = filePath;
     const localClasses = fileResult.nodes.filter(
       (n) => n.source_file === strPath && !n.label.endsWith(")") && !n.label.endsWith(".py") && n.id !== _makeId(fileStem)
@@ -3776,7 +3900,7 @@ async function _resolveCrossFileImports(perFile, paths) {
     let source;
     let tree;
     try {
-      source = readFileSync4(filePath, "utf-8");
+      source = readFileSync5(filePath, "utf-8");
       tree = parseText(parser, source);
     } catch {
       continue;
@@ -3793,9 +3917,9 @@ async function extractWithDiagnostics(paths) {
     if (paths.length === 0) {
       root = ".";
     } else if (paths.length === 1) {
-      root = dirname(paths[0]);
+      root = dirname3(paths[0]);
     } else {
-      const parts = paths.map((p) => p.split(sep));
+      const parts = paths.map((p) => p.split(sep2));
       const minLen = Math.min(...parts.map((p) => p.length));
       let commonLen = 0;
       for (let i = 0; i < minLen; i++) {
@@ -3803,7 +3927,7 @@ async function extractWithDiagnostics(paths) {
         if (uniqueAtLevel.size === 1) commonLen++;
         else break;
       }
-      root = commonLen > 0 ? parts[0].slice(0, commonLen).join(sep) : ".";
+      root = commonLen > 0 ? parts[0].slice(0, commonLen).join(sep2) : ".";
     }
   } catch {
     root = ".";
@@ -3816,7 +3940,7 @@ async function extractWithDiagnostics(paths) {
 `);
     }
     const filePath = paths[i];
-    const ext = extname(filePath);
+    const ext = extname3(filePath);
     const extractor = _DISPATCH[ext];
     if (!extractor) continue;
     const cached = loadCached(filePath, root);
@@ -3842,9 +3966,9 @@ async function extractWithDiagnostics(paths) {
     allNodes.push(...result.nodes ?? []);
     allEdges.push(...result.edges ?? []);
   }
-  const pyPaths = paths.filter((p) => extname(p) === ".py");
+  const pyPaths = paths.filter((p) => extname3(p) === ".py");
   if (pyPaths.length > 0) {
-    const pyResults = perFile.filter((_r, i) => extname(paths[i]) === ".py");
+    const pyResults = perFile.filter((_r, i) => extname3(paths[i]) === ".py");
     try {
       const crossFileEdges = await _resolveCrossFileImports(pyResults, pyPaths);
       allEdges.push(...crossFileEdges);
@@ -3867,9 +3991,9 @@ async function extract(paths) {
 }
 function collectFiles(target, options) {
   const followSymlinks = options?.followSymlinks ?? false;
-  const resolved = resolve3(target);
+  const resolved = resolve7(target);
   try {
-    const stat = lstatSync(resolved);
+    const stat = lstatSync2(resolved);
     if (stat.isFile()) return [resolved];
   } catch {
     return [];
@@ -3878,16 +4002,16 @@ function collectFiles(target, options) {
   function walkDir(dir, visited) {
     let entries;
     try {
-      entries = readdirSync2(dir);
+      entries = readdirSync3(dir);
     } catch {
       return;
     }
     for (const entry of entries) {
       if (entry.startsWith(".")) continue;
-      const fullPath = join3(dir, entry);
+      const fullPath = join4(dir, entry);
       let stat;
       try {
-        stat = lstatSync(fullPath);
+        stat = lstatSync2(fullPath);
       } catch {
         continue;
       }
@@ -3898,17 +4022,17 @@ function collectFiles(target, options) {
             const real = realpathSync(fullPath);
             if (visited.has(real)) continue;
             visited.add(real);
-            const parentReal = realpathSync(dirname(fullPath));
-            if (parentReal === real || parentReal.startsWith(real + sep)) continue;
+            const parentReal = realpathSync(dirname3(fullPath));
+            if (parentReal === real || parentReal.startsWith(real + sep2)) continue;
           } catch {
             continue;
           }
         }
-        const pathParts = fullPath.split(sep);
+        const pathParts = fullPath.split(sep2);
         if (pathParts.some((part) => part.startsWith("."))) continue;
         walkDir(fullPath, visited);
       } else if (stat.isFile()) {
-        const ext = extname(entry);
+        const ext = extname3(entry);
         if (_EXTENSIONS.has(ext)) {
           results.push(fullPath);
         }
@@ -4270,8 +4394,7 @@ __export(build_exports, {
   build: () => build,
   buildFromJson: () => buildFromJson
 });
-import Graph2 from "graphology";
-function buildFromJson(extraction) {
+function buildFromJson(extraction, options) {
   const errors = validateExtraction(extraction);
   const realErrors = errors.filter((e) => !e.includes("does not match any node id"));
   if (realErrors.length > 0) {
@@ -4279,7 +4402,7 @@ function buildFromJson(extraction) {
       `[graphify] Extraction warning (${realErrors.length} issues): ${realErrors[0]}`
     );
   }
-  const G = new Graph2({ type: "undirected", multi: false });
+  const G = createGraph(options?.directed === true);
   for (const node of extraction.nodes ?? []) {
     const { id, ...attrs } = node;
     G.mergeNode(id, attrs);
@@ -4301,7 +4424,7 @@ function buildFromJson(extraction) {
   }
   return G;
 }
-function build(extractions) {
+function build(extractions, options) {
   const combined = {
     nodes: [],
     edges: [],
@@ -4316,10 +4439,11 @@ function build(extractions) {
     combined.input_tokens += ext.input_tokens ?? 0;
     combined.output_tokens += ext.output_tokens ?? 0;
   }
-  return buildFromJson(combined);
+  return buildFromJson(combined, options);
 }
 var init_build = __esm({
   "src/build.ts"() {
+    init_graph();
     init_validate();
   }
 });
@@ -4499,7 +4623,7 @@ __export(export_exports, {
   toJson: () => toJson,
   toSvg: () => toSvg
 });
-import { writeFileSync as writeFileSync3 } from "fs";
+import { writeFileSync as writeFileSync4 } from "fs";
 function nodeCommunityMap2(communities) {
   const communityMap = toNumericMap(communities);
   const result = /* @__PURE__ */ new Map();
@@ -4527,14 +4651,17 @@ function normalizeCommunityLabels(labelsOrOptions) {
   }
   return toNumericMap(labelsOrOptions.communityLabels);
 }
-function toJson(G, communities, outputPath) {
+function toJson(G, communities, outputPath, communityLabelsOrOptions) {
   const nodeComm = nodeCommunityMap2(communities);
+  const communityLabels = normalizeCommunityLabels(communityLabelsOrOptions);
   const nodes = [];
   G.forEachNode((nodeId, attrs) => {
+    const communityId = nodeComm.get(nodeId) ?? null;
     nodes.push({
       id: nodeId,
       ...attrs,
-      community: nodeComm.get(nodeId) ?? null
+      community: communityId,
+      community_name: communityId !== null ? sanitizeLabel(communityLabels?.get(communityId) ?? `Community ${communityId}`) : null
     });
   });
   const links = [];
@@ -4551,15 +4678,20 @@ function toJson(G, communities, outputPath) {
     links.push(link);
   });
   const hyperedges = G.getAttribute("hyperedges") ?? [];
+  const communityLabelsObject = communityLabels ? Object.fromEntries(
+    [...communityLabels.entries()].sort((a, b) => a[0] - b[0]).map(([cid, label]) => [String(cid), sanitizeLabel(label)])
+  ) : {};
   const output = {
-    directed: false,
+    directed: isDirectedGraph(G),
     multigraph: false,
-    graph: {},
+    graph: {
+      community_labels: communityLabelsObject
+    },
     nodes,
     links,
     hyperedges
   };
-  writeFileSync3(outputPath, JSON.stringify(output, null, 2), "utf-8");
+  writeFileSync4(outputPath, JSON.stringify(output, null, 2), "utf-8");
 }
 function toCypher(G, outputPath) {
   const lines = ["// Neo4j Cypher import - generated by the graphify skill", ""];
@@ -4581,7 +4713,7 @@ function toCypher(G, outputPath) {
       `MATCH (a {id: '${uEsc}'}), (b {id: '${vEsc}'}) MERGE (a)-[:${rel} {confidence: '${conf}'}]->(b);`
     );
   });
-  writeFileSync3(outputPath, lines.join("\n"), "utf-8");
+  writeFileSync4(outputPath, lines.join("\n"), "utf-8");
 }
 function neo4jLabel(label) {
   const sanitized = label.replace(/[^A-Za-z0-9_]/g, "");
@@ -4820,9 +4952,24 @@ function focusNode(nodeId) {
   showInfo(nodeId);
 }
 
+let hoveredNodeId = null;
+network.on('hoverNode', params => {
+  hoveredNodeId = params.node;
+  container.style.cursor = 'pointer';
+});
+network.on('blurNode', () => {
+  hoveredNodeId = null;
+  container.style.cursor = 'default';
+});
+container.addEventListener('click', () => {
+  if (hoveredNodeId !== null) {
+    showInfo(hoveredNodeId);
+    network.selectNodes([hoveredNodeId]);
+  }
+});
 network.on('click', params => {
   if (params.nodes.length > 0) showInfo(params.nodes[0]);
-  else document.getElementById('info-content').innerHTML = '<span class="empty">Click a node to inspect it</span>';
+  else if (hoveredNodeId === null) document.getElementById('info-content').innerHTML = '<span class="empty">Click a node to inspect it</span>';
 });
 
 const searchInput = document.getElementById('search');
@@ -4977,7 +5124,7 @@ ${htmlScript(nodesJson, edgesJson, legendJson)}
 ${hyperedgeScript(hyperedgesJson)}
 </body>
 </html>`;
-  writeFileSync3(outputPath, html, "utf-8");
+  writeFileSync4(outputPath, html, "utf-8");
 }
 function toGraphml(G, communities, outputPath) {
   const nodeComm = nodeCommunityMap2(communities);
@@ -4993,7 +5140,7 @@ function toGraphml(G, communities, outputPath) {
   lines.push('  <key id="community" for="node" attr.name="community" attr.type="int"/>');
   lines.push('  <key id="relation" for="edge" attr.name="relation" attr.type="string"/>');
   lines.push('  <key id="confidence" for="edge" attr.name="confidence" attr.type="string"/>');
-  lines.push('  <graph id="G" edgedefault="undirected">');
+  lines.push(`  <graph id="G" edgedefault="${isDirectedGraph(G) ? "directed" : "undirected"}">`);
   G.forEachNode((nodeId, data) => {
     lines.push(`    <node id="${xmlEsc(nodeId)}">`);
     lines.push(`      <data key="label">${xmlEsc(data.label ?? nodeId)}</data>`);
@@ -5010,7 +5157,7 @@ function toGraphml(G, communities, outputPath) {
   });
   lines.push("  </graph>");
   lines.push("</graphml>");
-  writeFileSync3(outputPath, lines.join("\n"), "utf-8");
+  writeFileSync4(outputPath, lines.join("\n"), "utf-8");
 }
 function toSvg(G, communities, outputPath, communityLabelsOrOptions, figsize = [20, 14]) {
   const communityMap = toNumericMap(communities);
@@ -5083,7 +5230,7 @@ function toSvg(G, communities, outputPath, communityLabelsOrOptions, figsize = [
     }
   }
   svgParts.push("</svg>");
-  writeFileSync3(outputPath, svgParts.join("\n"), "utf-8");
+  writeFileSync4(outputPath, svgParts.join("\n"), "utf-8");
 }
 function toCanvas(G, communities, outputPath, communityLabelsOrOptions, nodeFilenames) {
   const communityMap = toNumericMap(communities);
@@ -5092,7 +5239,7 @@ function toCanvas(G, communities, outputPath, communityLabelsOrOptions, nodeFile
   const providedNodeFilenames = options?.nodeFilenames ?? nodeFilenames;
   const CANVAS_COLORS = ["1", "2", "3", "4", "5", "6"];
   function safeName(label) {
-    return label.replace(/[\\/*?:"<>|#^[\]]/g, "").trim() || "unnamed";
+    return label.replace(/\r\n/g, " ").replace(/\r/g, " ").replace(/\n/g, " ").replace(/[\\/*?:"<>|#^[\]]/g, "").trim() || "unnamed";
   }
   let filenameMap;
   if (!providedNodeFilenames) {
@@ -5171,13 +5318,13 @@ function toCanvas(G, communities, outputPath, communityLabelsOrOptions, nodeFile
   for (let idx = 0; idx < sortedCids.length; idx++) {
     const cid = sortedCids[idx];
     const members = communityMap.get(cid) ?? [];
-    const communityName = communityLabels?.get(cid) ?? `Community ${cid}`;
+    const communityName2 = communityLabels?.get(cid) ?? `Community ${cid}`;
     const [gx, gy, gw, gh] = groupLayout.get(cid) ?? [0, 0, 600, 400];
     const canvasColor = CANVAS_COLORS[idx % CANVAS_COLORS.length];
     canvasNodes.push({
       id: `g${cid}`,
       type: "group",
-      label: communityName,
+      label: communityName2,
       x: gx,
       y: gy,
       width: gw,
@@ -5227,12 +5374,13 @@ function toCanvas(G, communities, outputPath, communityLabelsOrOptions, nodeFile
     });
   }
   const canvasData = { nodes: canvasNodes, edges: canvasEdges };
-  writeFileSync3(outputPath, JSON.stringify(canvasData, null, 2), "utf-8");
+  writeFileSync4(outputPath, JSON.stringify(canvasData, null, 2), "utf-8");
 }
 var COMMUNITY_COLORS, MAX_NODES_FOR_VIZ, CONFIDENCE_SCORE_DEFAULTS;
 var init_export = __esm({
   "src/export.ts"() {
     init_security();
+    init_graph();
     init_collections();
     COMMUNITY_COLORS = [
       "#4E79A7",
@@ -5261,8 +5409,8 @@ __export(watch_exports, {
   rebuildCode: () => rebuildCode,
   watch: () => watch
 });
-import { existsSync as existsSync5, mkdirSync as mkdirSync3, writeFileSync as writeFileSync4, unlinkSync as unlinkSync3 } from "fs";
-import { resolve as pathResolve2, extname as extname2, basename as basename3 } from "path";
+import { existsSync as existsSync6, mkdirSync as mkdirSync4, writeFileSync as writeFileSync5, unlinkSync as unlinkSync3 } from "fs";
+import { resolve as pathResolve2, extname as extname4, basename as basename4 } from "path";
 async function rebuildCode(watchPath, followSymlinks = false) {
   try {
     const { collectFiles: collectFiles2, extractWithDiagnostics: extractWithDiagnostics2 } = await Promise.resolve().then(() => (init_extract(), extract_exports));
@@ -5314,7 +5462,7 @@ async function rebuildCode(watchPath, followSymlinks = false) {
     }
     const questions = suggestQuestions2(G, communities, labels);
     const outDir = pathResolve2(watchPath, "graphify-out");
-    mkdirSync3(outDir, { recursive: true });
+    mkdirSync4(outDir, { recursive: true });
     const report = generate2(
       G,
       communities,
@@ -5327,10 +5475,10 @@ async function rebuildCode(watchPath, followSymlinks = false) {
       watchPath,
       questions
     );
-    writeFileSync4(pathResolve2(outDir, "GRAPH_REPORT.md"), report, "utf-8");
-    toJson2(G, communities, pathResolve2(outDir, "graph.json"));
+    writeFileSync5(pathResolve2(outDir, "GRAPH_REPORT.md"), report, "utf-8");
+    toJson2(G, communities, pathResolve2(outDir, "graph.json"), { communityLabels: labels });
     const flagPath = pathResolve2(outDir, "needs_update");
-    if (existsSync5(flagPath)) {
+    if (existsSync6(flagPath)) {
       unlinkSync3(flagPath);
     }
     console.log(
@@ -5349,9 +5497,9 @@ async function rebuildCode(watchPath, followSymlinks = false) {
 }
 function notifyOnly(watchPath) {
   const outDir = pathResolve2(watchPath, "graphify-out");
-  mkdirSync3(outDir, { recursive: true });
+  mkdirSync4(outDir, { recursive: true });
   const flagPath = pathResolve2(outDir, "needs_update");
-  writeFileSync4(flagPath, "1", "utf-8");
+  writeFileSync5(flagPath, "1", "utf-8");
   console.log(`
 [graphify watch] New or changed files detected in ${watchPath}`);
   console.log(
@@ -5363,7 +5511,7 @@ function notifyOnly(watchPath) {
   console.log(`[graphify watch] Flag written to ${flagPath}`);
 }
 function hasNonCode(changedPaths) {
-  return changedPaths.some((p) => !CODE_EXTENSIONS2.has(extname2(p).toLowerCase()));
+  return changedPaths.some((p) => !CODE_EXTENSIONS.has(extname4(p).toLowerCase()));
 }
 async function watch(watchPath, debounce = 3) {
   let chokidar;
@@ -5387,7 +5535,7 @@ async function watch(watchPath, debounce = 3) {
     ]
   });
   watcher.on("all", (_event, filePath) => {
-    const ext = extname2(filePath).toLowerCase();
+    const ext = extname4(filePath).toLowerCase();
     if (!WATCHED_EXTENSIONS.has(ext)) return;
     const parts = filePath.split("/");
     if (parts.some((part) => part.startsWith(".") && part !== ".")) return;
@@ -5426,62 +5574,17 @@ async function watch(watchPath, debounce = 3) {
   process.on("SIGINT", cleanup);
   process.on("SIGTERM", cleanup);
 }
-var WATCHED_EXTENSIONS, CODE_EXTENSIONS2, isDirectExecution2;
+var WATCHED_EXTENSIONS, isDirectExecution2;
 var init_watch = __esm({
   "src/watch.ts"() {
+    init_detect();
     WATCHED_EXTENSIONS = /* @__PURE__ */ new Set([
-      ".py",
-      ".ts",
-      ".js",
-      ".go",
-      ".rs",
-      ".java",
-      ".cpp",
-      ".c",
-      ".rb",
-      ".swift",
-      ".kt",
-      ".cs",
-      ".scala",
-      ".php",
-      ".cc",
-      ".cxx",
-      ".hpp",
-      ".h",
-      ".kts",
-      ".md",
-      ".txt",
-      ".rst",
-      ".pdf",
-      ".png",
-      ".jpg",
-      ".jpeg",
-      ".webp",
-      ".gif",
-      ".svg"
-    ]);
-    CODE_EXTENSIONS2 = /* @__PURE__ */ new Set([
-      ".py",
-      ".ts",
-      ".js",
-      ".go",
-      ".rs",
-      ".java",
-      ".cpp",
-      ".c",
-      ".rb",
-      ".swift",
-      ".kt",
-      ".cs",
-      ".scala",
-      ".php",
-      ".cc",
-      ".cxx",
-      ".hpp",
-      ".h",
-      ".kts"
+      ...CODE_EXTENSIONS,
+      ...DOC_EXTENSIONS,
+      ...PAPER_EXTENSIONS,
+      ...IMAGE_EXTENSIONS
     ]);
-    isDirectExecution2 = typeof process !== "undefined" && typeof process.argv[1] === "string" && /^watch\.(?:js|mjs|cjs|ts)$/.test(basename3(process.argv[1]));
+    isDirectExecution2 = typeof process !== "undefined" && typeof process.argv[1] === "string" && /^watch\.(?:js|mjs|cjs|ts)$/.test(basename4(process.argv[1]));
     if (isDirectExecution2) {
       const watchPath = process.argv[2] ?? ".";
       const debounce = process.argv[3] ? parseFloat(process.argv[3]) : 3;
@@ -5499,8 +5602,7 @@ __export(benchmark_exports, {
   printBenchmark: () => printBenchmark,
   runBenchmark: () => runBenchmark
 });
-import { readFileSync as readFileSync5, existsSync as existsSync6 } from "fs";
-import Graph3 from "graphology";
+import { readFileSync as readFileSync6, existsSync as existsSync7 } from "fs";
 function estimateTokens(text) {
   return Math.max(1, Math.floor(text.length / CHARS_PER_TOKEN));
 }
@@ -5521,7 +5623,7 @@ function querySubgraphTokens(G, question, depth = 3) {
   for (let d = 0; d < depth; d++) {
     const nextFrontier = /* @__PURE__ */ new Set();
     for (const n of frontier) {
-      G.forEachNeighbor(n, (neighbor) => {
+      forEachTraversalNeighbor(G, n, (neighbor) => {
         if (!visited.has(neighbor)) {
           nextFrontier.add(neighbor);
           edgesSeen.push([n, neighbor]);
@@ -5548,26 +5650,12 @@ function querySubgraphTokens(G, question, depth = 3) {
   return estimateTokens(lines.join("\n"));
 }
 function loadGraph2(graphPath) {
-  const raw = JSON.parse(readFileSync5(graphPath, "utf-8"));
-  const G = new Graph3({ type: "undirected" });
-  for (const node of raw.nodes ?? []) {
-    const { id, ...attrs } = node;
-    G.mergeNode(id, attrs);
-  }
-  for (const link of raw.links ?? []) {
-    const { source, target, ...attrs } = link;
-    if (G.hasNode(source) && G.hasNode(target)) {
-      try {
-        G.mergeEdge(source, target, attrs);
-      } catch {
-      }
-    }
-  }
-  return G;
+  const raw = JSON.parse(readFileSync6(graphPath, "utf-8"));
+  return loadGraphFromData(raw);
 }
 function runBenchmark(graphPath = "graphify-out/graph.json", corpusWordsOrOptions, questions) {
   const options = typeof corpusWordsOrOptions === "number" ? { corpusWords: corpusWordsOrOptions, questions } : corpusWordsOrOptions ?? {};
-  if (!existsSync6(graphPath)) {
+  if (!existsSync7(graphPath)) {
     return { error: `Graph file not found: ${graphPath}. Build the graph first.` };
   }
   const G = loadGraph2(graphPath);
@@ -5627,6 +5715,7 @@ graphify token reduction benchmark`);
 var CHARS_PER_TOKEN, SAMPLE_QUESTIONS;
 var init_benchmark = __esm({
   "src/benchmark.ts"() {
+    init_graph();
     CHARS_PER_TOKEN = 4;
     SAMPLE_QUESTIONS = [
       "how does authentication work",
@@ -5639,24 +5728,26 @@ var init_benchmark = __esm({
 });
 
 // src/cli.ts
+init_graph();
 import {
-  readFileSync as readFileSync6,
-  writeFileSync as writeFileSync5,
-  existsSync as existsSync7,
-  mkdirSync as mkdirSync4,
-  copyFileSync,
+  readFileSync as readFileSync7,
+  writeFileSync as writeFileSync6,
+  existsSync as existsSync8,
+  mkdirSync as mkdirSync5,
   realpathSync as realpathSync2,
-  statSync
+  statSync as statSync2,
+  unlinkSync as unlinkSync4,
+  rmdirSync
 } from "fs";
-import { join as join4, resolve as resolve5, dirname as dirname2 } from "path";
+import { join as join5, resolve as resolve8, dirname as dirname4 } from "path";
 import { homedir, platform } from "os";
 import { fileURLToPath } from "url";
 import { Command } from "commander";
 var __filename = fileURLToPath(import.meta.url);
-var __dirname = dirname2(__filename);
+var __dirname = dirname4(__filename);
 function getVersion() {
   try {
-    const pkg = JSON.parse(readFileSync6(join4(__dirname, "..", "package.json"), "utf-8"));
+    const pkg = JSON.parse(readFileSync7(join5(__dirname, "..", "package.json"), "utf-8"));
     return pkg.version ?? "unknown";
   } catch {
     return "unknown";
@@ -5666,42 +5757,57 @@ var VERSION = getVersion();
 var PLATFORM_CONFIG = {
   claude: {
     skill_file: "skill.md",
-    skill_dst: join4(".claude", "skills", "graphify", "SKILL.md"),
+    skill_dst: join5(".claude", "skills", "graphify", "SKILL.md"),
     claude_md: true
   },
   codex: {
     skill_file: "skill-codex.md",
-    skill_dst: join4(".agents", "skills", "graphify", "SKILL.md"),
+    skill_dst: join5(".agents", "skills", "graphify", "SKILL.md"),
+    claude_md: false
+  },
+  gemini: {
+    skill_file: "skill-gemini.toml",
+    skill_dst: join5(".gemini", "commands", "graphify.toml"),
     claude_md: false
   },
   opencode: {
     skill_file: "skill-opencode.md",
-    skill_dst: join4(".config", "opencode", "skills", "graphify", "SKILL.md"),
+    skill_dst: join5(".config", "opencode", "skills", "graphify", "SKILL.md"),
+    claude_md: false
+  },
+  aider: {
+    skill_file: "skill.md",
+    skill_dst: join5(".aider", "graphify", "SKILL.md"),
+    claude_md: false
+  },
+  copilot: {
+    skill_file: "skill.md",
+    skill_dst: join5(".copilot", "skills", "graphify", "SKILL.md"),
     claude_md: false
   },
   claw: {
     skill_file: "skill-claw.md",
-    skill_dst: join4(".claw", "skills", "graphify", "SKILL.md"),
+    skill_dst: join5(".claw", "skills", "graphify", "SKILL.md"),
     claude_md: false
   },
   droid: {
     skill_file: "skill-droid.md",
-    skill_dst: join4(".factory", "skills", "graphify", "SKILL.md"),
+    skill_dst: join5(".factory", "skills", "graphify", "SKILL.md"),
     claude_md: false
   },
   trae: {
     skill_file: "skill-trae.md",
-    skill_dst: join4(".trae", "skills", "graphify", "SKILL.md"),
+    skill_dst: join5(".trae", "skills", "graphify", "SKILL.md"),
     claude_md: false
   },
   "trae-cn": {
     skill_file: "skill-trae.md",
-    skill_dst: join4(".trae-cn", "skills", "graphify", "SKILL.md"),
+    skill_dst: join5(".trae-cn", "skills", "graphify", "SKILL.md"),
     claude_md: false
   },
   windows: {
     skill_file: "skill-windows.md",
-    skill_dst: join4(".claude", "skills", "graphify", "SKILL.md"),
+    skill_dst: join5(".claude", "skills", "graphify", "SKILL.md"),
     claude_md: true
   }
 };
@@ -5724,18 +5830,233 @@ Rules:
 - If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
 - After modifying code files in this session, run \`npx graphify hook-rebuild\` to keep the graph current
 `;
+var GEMINI_MD_SECTION = `## graphify
+
+This project has a graphify knowledge graph at graphify-out/.
+
+Rules:
+- Before answering architecture or codebase questions, read graphify-out/GRAPH_REPORT.md for god nodes and community structure
+- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
+- In Gemini CLI, the reliable explicit custom command is \`/graphify ...\`
+- If the user asks to build, update, query, path, or explain the graph, use the installed \`/graphify\` custom command or the configured \`graphify\` MCP server instead of ad-hoc file traversal
+- After modifying code files in this session, run \`npx graphify hook-rebuild\` to keep the graph current
+`;
+var GEMINI_MCP_SERVER = {
+  command: "graphify",
+  args: ["serve", "graphify-out/graph.json"],
+  trust: false,
+  description: "graphify knowledge graph MCP server"
+};
+var OPENCODE_PLUGIN_ENTRY = ".opencode/plugins/graphify.js";
+var OPENCODE_PLUGIN_JS = `// graphify OpenCode plugin
+// Injects a knowledge graph reminder before bash tool calls when the graph exists.
+import { existsSync } from "fs";
+import { join } from "path";
+
+export const GraphifyPlugin = async ({ directory }) => {
+  let reminded = false;
+
+  return {
+    "tool.execute.before": async (input, output) => {
+      if (reminded) return;
+      if (!existsSync(join(directory, "graphify-out", "graph.json"))) return;
+
+      if (input.tool === "bash") {
+        output.args.command =
+          'echo "[graphify] Knowledge graph available. Read graphify-out/GRAPH_REPORT.md for god nodes and architecture context before searching files." && ' +
+          output.args.command;
+        reminded = true;
+      }
+    },
+  };
+};
+`;
 var MD_MARKER = "## graphify";
+var CURSOR_RULE = `---
+description: graphify knowledge graph context
+alwaysApply: true
+---
+
+This project has a graphify knowledge graph at graphify-out/.
+
+- Before answering architecture or codebase questions, read graphify-out/GRAPH_REPORT.md for god nodes and community structure
+- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
+- After modifying code files in this session, run \`npx graphify hook-rebuild\` to keep the graph current
+`;
+var AIDER_SEMANTIC_SECTION = `#### Part B - Semantic extraction (sequential extraction on Aider)
+
+**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic extraction to do.
+
+> **Aider platform:** Multi-agent support is still early on Aider. Extraction runs sequentially - read and extract each uncached file yourself instead of dispatching parallel Agent calls.
+
+Print: \`Semantic extraction: N files (sequential - Aider)\`
+
+**Step B0 - Check extraction cache first**
+
+Before reading any docs, papers, or images, check which files already have cached semantic extraction results:
+
+\`\`\`bash
+node -e "
+const fs = require('fs');
+const { checkSemanticCache } = require('graphifyy');
+
+const detect = JSON.parse(fs.readFileSync('graphify-out/.graphify_detect.json', 'utf-8'));
+const allFiles = Object.values(detect.files).flat();
+
+const [cachedNodes, cachedEdges, cachedHyperedges, uncached] = checkSemanticCache(allFiles);
+
+if (cachedNodes.length || cachedEdges.length || cachedHyperedges.length) {
+    fs.writeFileSync('graphify-out/.graphify_cached.json', JSON.stringify({nodes: cachedNodes, edges: cachedEdges, hyperedges: cachedHyperedges}));
+}
+fs.writeFileSync('graphify-out/.graphify_uncached.txt', uncached.join('\\n'));
+console.log(\`Cache: \${allFiles.length - uncached.length} files hit, \${uncached.length} files need extraction\`);
+"
+\`\`\`
+
+Only extract files listed in \`graphify-out/.graphify_uncached.txt\`. If all files are cached, skip to Part C directly.
+
+**Step B1 - Split into chunks**
+
+Load files from \`graphify-out/.graphify_uncached.txt\`. Split them into logical batches of 20-25 files, but process them sequentially on Aider. Keep files from the same directory together. Each image still deserves focused attention because vision context is expensive.
+
+**Step B2 - Sequential extraction (Aider)**
+
+Process each uncached file one at a time. For each file:
+
+1. Read the file contents.
+2. Extract nodes, edges, and hyperedges using the same graphify rules:
+   - EXTRACTED: relationship explicit in source (import, call, citation, "see section 3.2")
+   - INFERRED: reasonable inference (shared structure, implied dependency)
+   - AMBIGUOUS: uncertain - flag it instead of omitting it
+   - Code files: only add semantic edges AST cannot find. Do not re-extract imports.
+   - Doc/paper files: extract named concepts, entities, citations, and rationale nodes (WHY decisions were made -> \`rationale_for\` edges)
+   - Image files: use vision to understand what the image is, not just OCR
+   - If \`--mode deep\` was given, be more aggressive with INFERRED edges
+   - Add \`semantically_similar_to\` only for genuinely non-obvious cross-cutting similarities
+   - Add hyperedges only when 3+ nodes clearly participate in one shared concept or flow
+   - \`confidence_score\` is REQUIRED on every edge: EXTRACTED=1.0, INFERRED=0.6-0.9, AMBIGUOUS=0.1-0.3
+3. Accumulate the results across all files.
+
+Write the accumulated result to \`graphify-out/.graphify_semantic_new.json\` using this exact schema:
+
+\`\`\`json
+{"nodes":[{"id":"filestem_entityname","label":"Human Readable Name","file_type":"code|document|paper|image","source_file":"relative/path","source_location":null,"source_url":null,"captured_at":null,"author":null,"contributor":null}],"edges":[{"source":"node_id","target":"node_id","relation":"calls|implements|references|cites|conceptually_related_to|shares_data_with|semantically_similar_to|rationale_for","confidence":"EXTRACTED|INFERRED|AMBIGUOUS","confidence_score":1.0,"source_file":"relative/path","source_location":null,"weight":1.0}],"hyperedges":[{"id":"snake_case_id","label":"Human Readable Label","nodes":["node_id1","node_id2","node_id3"],"relation":"participate_in|implement|form","confidence":"EXTRACTED|INFERRED","confidence_score":0.75,"source_file":"relative/path"}],"input_tokens":0,"output_tokens":0}
+\`\`\`
+
+**Step B3 - Cache and merge**
+
+If more than half the sequential batches failed, stop and tell the user.
+
+Save new results to cache:
+
+\`\`\`bash
+node -e "
+const fs = require('fs');
+const { saveSemanticCache } = require('graphifyy');
+
+const raw = fs.existsSync('graphify-out/.graphify_semantic_new.json') ? JSON.parse(fs.readFileSync('graphify-out/.graphify_semantic_new.json', 'utf-8')) : {nodes:[],edges:[],hyperedges:[]};
+const saved = saveSemanticCache(raw.nodes || [], raw.edges || [], raw.hyperedges || []);
+console.log(\`Cached \${saved} files\`);
+"
+\`\`\`
+
+Merge cached + new results into \`graphify-out/.graphify_semantic.json\`:
+
+\`\`\`bash
+node -e "
+const fs = require('fs');
+
+const cached = fs.existsSync('graphify-out/.graphify_cached.json') ? JSON.parse(fs.readFileSync('graphify-out/.graphify_cached.json', 'utf-8')) : {nodes:[],edges:[],hyperedges:[]};
+const fresh = fs.existsSync('graphify-out/.graphify_semantic_new.json') ? JSON.parse(fs.readFileSync('graphify-out/.graphify_semantic_new.json', 'utf-8')) : {nodes:[],edges:[],hyperedges:[]};
+
+const allNodes = [...cached.nodes, ...(fresh.nodes || [])];
+const allEdges = [...cached.edges, ...(fresh.edges || [])];
+const allHyperedges = [...(cached.hyperedges || []), ...(fresh.hyperedges || [])];
+
+const seen = new Set();
+const dedupedNodes = [];
+for (const node of allNodes) {
+  if (seen.has(node.id)) continue;
+  seen.add(node.id);
+  dedupedNodes.push(node);
+}
+
+fs.writeFileSync('graphify-out/.graphify_semantic.json', JSON.stringify({
+  nodes: dedupedNodes,
+  edges: allEdges,
+  hyperedges: allHyperedges,
+  input_tokens: fresh.input_tokens || 0,
+  output_tokens: fresh.output_tokens || 0
+}, null, 2));
+
+console.log(\`Extraction complete - \${dedupedNodes.length} nodes, \${allEdges.length} edges (\${cached.nodes.length} from cache, \${(fresh.nodes || []).length} new)\`);
+"
+\`\`\`
+
+Clean up temp files: \`rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json\``;
 function findSkillFile(filename) {
   const paths = [
-    join4(__dirname, "..", "src", "skills", filename),
-    join4(__dirname, "skills", filename),
-    join4(__dirname, "..", "skills", filename)
+    join5(__dirname, "..", "src", "skills", filename),
+    join5(__dirname, "skills", filename),
+    join5(__dirname, "..", "skills", filename)
   ];
   for (const p of paths) {
-    if (existsSync7(p)) return p;
+    if (existsSync8(p)) return p;
   }
   return null;
 }
+function renderAiderSkill(baseSkill) {
+  return baseSkill.replace(
+    /#### Part B - Semantic extraction \(parallel subagents\)[\s\S]*?(?=\n#### Part C - Merge AST \+ semantic into final extraction)/,
+    AIDER_SEMANTIC_SECTION
+  );
+}
+function loadSkillContent(platformName) {
+  const cfg = PLATFORM_CONFIG[platformName];
+  if (!cfg) {
+    console.error(`error: unknown platform '${platformName}'. Choose from: ${Object.keys(PLATFORM_CONFIG).join(", ")}`);
+    process.exit(1);
+  }
+  const skillSrc = findSkillFile(cfg.skill_file);
+  if (!skillSrc) {
+    console.error(`error: ${cfg.skill_file} not found in package - reinstall graphify`);
+    process.exit(1);
+  }
+  const baseSkill = readFileSync7(skillSrc, "utf-8");
+  if (platformName === "aider") {
+    const rendered = renderAiderSkill(baseSkill);
+    if (rendered === baseSkill) {
+      throw new Error("failed to render Aider skill overrides");
+    }
+    return rendered;
+  }
+  return baseSkill;
+}
+function uninstallSkill(platformName) {
+  const cfg = PLATFORM_CONFIG[platformName];
+  if (!cfg) {
+    console.error(`error: unknown platform '${platformName}'. Choose from: ${Object.keys(PLATFORM_CONFIG).join(", ")}`);
+    process.exit(1);
+  }
+  const skillDst = join5(homedir(), cfg.skill_dst);
+  const removed = [];
+  if (existsSync8(skillDst)) {
+    unlinkSync4(skillDst);
+    removed.push(`skill removed: ${skillDst}`);
+  }
+  const versionFile = join5(dirname4(skillDst), ".graphify_version");
+  if (existsSync8(versionFile)) {
+    unlinkSync4(versionFile);
+  }
+  for (let dir = dirname4(skillDst); dir !== dirname4(dir); dir = dirname4(dir)) {
+    try {
+      rmdirSync(dir);
+    } catch {
+      break;
+    }
+  }
+  console.log(removed.length > 0 ? removed.join("; ") : "nothing to remove");
+}
 function getInvocationExample(platformName) {
   return platformName === "codex" ? "$graphify ." : "/graphify .";
 }
@@ -5762,35 +6083,154 @@ function getAgentsMdSection(platformName) {
   }
   return lines.join("\n") + "\n";
 }
+function installGeminiMcp(projectDir) {
+  const geminiDir = join5(projectDir, ".gemini");
+  if (existsSync8(geminiDir) && !statSync2(geminiDir).isDirectory()) {
+    console.log("  .gemini/settings.json  ->  skipped (cannot create config dir because .gemini is a file)");
+    return;
+  }
+  const settingsPath = join5(geminiDir, "settings.json");
+  mkdirSync5(dirname4(settingsPath), { recursive: true });
+  let settings = {};
+  if (existsSync8(settingsPath)) {
+    try {
+      settings = JSON.parse(readFileSync7(settingsPath, "utf-8"));
+    } catch {
+    }
+  }
+  const mcpServers = settings.mcpServers ?? {};
+  const existing = mcpServers.graphify;
+  if (JSON.stringify(existing) === JSON.stringify(GEMINI_MCP_SERVER)) {
+    console.log("  .gemini/settings.json  ->  graphify MCP already registered (no change)");
+    return;
+  }
+  mcpServers.graphify = GEMINI_MCP_SERVER;
+  settings.mcpServers = mcpServers;
+  writeFileSync6(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
+  console.log("  .gemini/settings.json  ->  graphify MCP server registered");
+}
+function uninstallGeminiMcp(projectDir) {
+  const settingsPath = join5(projectDir, ".gemini", "settings.json");
+  if (!existsSync8(settingsPath)) return;
+  let settings;
+  try {
+    settings = JSON.parse(readFileSync7(settingsPath, "utf-8"));
+  } catch {
+    return;
+  }
+  const mcpServers = { ...settings.mcpServers ?? {} };
+  if (!("graphify" in mcpServers)) return;
+  delete mcpServers.graphify;
+  if (Object.keys(mcpServers).length === 0) {
+    delete settings.mcpServers;
+  } else {
+    settings.mcpServers = mcpServers;
+  }
+  writeFileSync6(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
+  console.log("  .gemini/settings.json  ->  graphify MCP server removed");
+}
+function cursorInstall(projectDir = ".") {
+  const rulePath = join5(projectDir, ".cursor", "rules", "graphify.mdc");
+  mkdirSync5(dirname4(rulePath), { recursive: true });
+  if (existsSync8(rulePath)) {
+    console.log(`graphify rule already exists at ${resolve8(rulePath)} (no change)`);
+  } else {
+    writeFileSync6(rulePath, CURSOR_RULE, "utf-8");
+    console.log(`graphify rule written to ${resolve8(rulePath)}`);
+  }
+  console.log();
+  console.log("Cursor will now always include the knowledge graph context.");
+  console.log("Run `$graphify .` or `/graphify .` in your assistant first if you have not built the graph yet.");
+}
+function cursorUninstall(projectDir = ".") {
+  const rulePath = join5(projectDir, ".cursor", "rules", "graphify.mdc");
+  if (!existsSync8(rulePath)) {
+    console.log("No graphify Cursor rule found - nothing to do");
+    return;
+  }
+  const { unlinkSync: unlinkSync5 } = __require("fs");
+  unlinkSync5(rulePath);
+  console.log(`graphify Cursor rule removed from ${resolve8(rulePath)}`);
+}
+function installOpenCodePlugin(projectDir) {
+  const opencodeDir = join5(projectDir, ".opencode");
+  if (existsSync8(opencodeDir) && !statSync2(opencodeDir).isDirectory()) {
+    console.log(`  ${OPENCODE_PLUGIN_ENTRY}  ->  skipped (cannot create plugin dir because .opencode is a file)`);
+    return;
+  }
+  const pluginPath = join5(projectDir, ".opencode", "plugins", "graphify.js");
+  mkdirSync5(dirname4(pluginPath), { recursive: true });
+  writeFileSync6(pluginPath, OPENCODE_PLUGIN_JS, "utf-8");
+  console.log(`  ${OPENCODE_PLUGIN_ENTRY}  ->  tool.execute.before hook written`);
+  const configPath = join5(projectDir, "opencode.json");
+  let config = {};
+  if (existsSync8(configPath)) {
+    try {
+      config = JSON.parse(readFileSync7(configPath, "utf-8"));
+    } catch {
+      config = {};
+    }
+  }
+  const plugins = Array.isArray(config.plugin) ? [...config.plugin] : [];
+  if (plugins.includes(OPENCODE_PLUGIN_ENTRY)) {
+    console.log("  opencode.json  ->  plugin already registered (no change)");
+    return;
+  }
+  plugins.push(OPENCODE_PLUGIN_ENTRY);
+  config.plugin = plugins;
+  writeFileSync6(configPath, JSON.stringify(config, null, 2), "utf-8");
+  console.log("  opencode.json  ->  plugin registered");
+}
+function uninstallOpenCodePlugin(projectDir) {
+  const pluginPath = join5(projectDir, ".opencode", "plugins", "graphify.js");
+  if (existsSync8(pluginPath)) {
+    const { unlinkSync: unlinkSync5 } = __require("fs");
+    unlinkSync5(pluginPath);
+    console.log(`  ${OPENCODE_PLUGIN_ENTRY}  ->  removed`);
+  }
+  const configPath = join5(projectDir, "opencode.json");
+  if (!existsSync8(configPath)) return;
+  let config;
+  try {
+    config = JSON.parse(readFileSync7(configPath, "utf-8"));
+  } catch {
+    return;
+  }
+  const plugins = Array.isArray(config.plugin) ? [...config.plugin] : [];
+  if (!plugins.includes(OPENCODE_PLUGIN_ENTRY)) return;
+  const filtered = plugins.filter((entry) => entry !== OPENCODE_PLUGIN_ENTRY);
+  if (filtered.length === 0) {
+    delete config.plugin;
+  } else {
+    config.plugin = filtered;
+  }
+  writeFileSync6(configPath, JSON.stringify(config, null, 2), "utf-8");
+  console.log("  opencode.json  ->  plugin deregistered");
+}
 function installSkill(platformName) {
   const cfg = PLATFORM_CONFIG[platformName];
   if (!cfg) {
     console.error(`error: unknown platform '${platformName}'. Choose from: ${Object.keys(PLATFORM_CONFIG).join(", ")}`);
     process.exit(1);
   }
-  const skillSrc = findSkillFile(cfg.skill_file);
-  if (!skillSrc) {
-    console.error(`error: ${cfg.skill_file} not found in package - reinstall graphify`);
-    process.exit(1);
-  }
-  const skillDst = join4(homedir(), cfg.skill_dst);
-  mkdirSync4(dirname2(skillDst), { recursive: true });
-  copyFileSync(skillSrc, skillDst);
-  writeFileSync5(join4(dirname2(skillDst), ".graphify_version"), VERSION, "utf-8");
+  const skillDst = join5(homedir(), cfg.skill_dst);
+  mkdirSync5(dirname4(skillDst), { recursive: true });
+  writeFileSync6(skillDst, loadSkillContent(platformName), "utf-8");
+  writeFileSync6(join5(dirname4(skillDst), ".graphify_version"), VERSION, "utf-8");
   console.log(`  skill installed  ->  ${skillDst}`);
   if (cfg.claude_md) {
-    const claudeMd = join4(homedir(), ".claude", "CLAUDE.md");
-    if (existsSync7(claudeMd)) {
-      const content = readFileSync6(claudeMd, "utf-8");
+    const claudeMd = join5(homedir(), ".claude", "CLAUDE.md");
+    if (existsSync8(claudeMd)) {
+      const content = readFileSync7(claudeMd, "utf-8");
       if (content.includes("graphify")) {
         console.log(`  CLAUDE.md        ->  already registered (no change)`);
       } else {
-        writeFileSync5(claudeMd, content.trimEnd() + SKILL_REGISTRATION, "utf-8");
+        writeFileSync6(claudeMd, content.trimEnd() + SKILL_REGISTRATION, "utf-8");
         console.log(`  CLAUDE.md        ->  skill registered in ${claudeMd}`);
       }
     } else {
-      mkdirSync4(dirname2(claudeMd), { recursive: true });
-      writeFileSync5(claudeMd, SKILL_REGISTRATION.trimStart(), "utf-8");
+      mkdirSync5(dirname4(claudeMd), { recursive: true });
+      writeFileSync6(claudeMd, SKILL_REGISTRATION.trimStart(), "utf-8");
       console.log(`  CLAUDE.md        ->  created at ${claudeMd}`);
     }
   }
@@ -5808,33 +6248,32 @@ function installSkill(platformName) {
   console.log();
 }
 function installClaudeHook(projectDir) {
-  const settingsPath = join4(projectDir, ".claude", "settings.json");
-  mkdirSync4(dirname2(settingsPath), { recursive: true });
+  const settingsPath = join5(projectDir, ".claude", "settings.json");
+  mkdirSync5(dirname4(settingsPath), { recursive: true });
   let settings = {};
-  if (existsSync7(settingsPath)) {
+  if (existsSync8(settingsPath)) {
     try {
-      settings = JSON.parse(readFileSync6(settingsPath, "utf-8"));
+      settings = JSON.parse(readFileSync7(settingsPath, "utf-8"));
     } catch {
     }
   }
   const hooks = settings.hooks ?? {};
   const preTool = hooks.PreToolUse ?? [];
-  if (preTool.some((h) => h.matcher === "Glob|Grep" && JSON.stringify(h).includes("graphify"))) {
-    console.log(`  .claude/settings.json  ->  hook already registered (no change)`);
-    return;
-  }
-  preTool.push(SETTINGS_HOOK);
-  hooks.PreToolUse = preTool;
+  const filtered = preTool.filter(
+    (h) => !(h.matcher === "Glob|Grep" && JSON.stringify(h).includes("graphify"))
+  );
+  filtered.push(SETTINGS_HOOK);
+  hooks.PreToolUse = filtered;
   settings.hooks = hooks;
-  writeFileSync5(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
+  writeFileSync6(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
   console.log(`  .claude/settings.json  ->  PreToolUse hook registered`);
 }
 function uninstallClaudeHook(projectDir) {
-  const settingsPath = join4(projectDir, ".claude", "settings.json");
-  if (!existsSync7(settingsPath)) return;
+  const settingsPath = join5(projectDir, ".claude", "settings.json");
+  if (!existsSync8(settingsPath)) return;
   let settings;
   try {
-    settings = JSON.parse(readFileSync6(settingsPath, "utf-8"));
+    settings = JSON.parse(readFileSync7(settingsPath, "utf-8"));
   } catch {
     return;
   }
@@ -5846,25 +6285,25 @@ function uninstallClaudeHook(projectDir) {
   if (filtered.length === preTool.length) return;
   hooks.PreToolUse = filtered;
   settings.hooks = hooks;
-  writeFileSync5(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
+  writeFileSync6(settingsPath, JSON.stringify(settings, null, 2), "utf-8");
   console.log(`  .claude/settings.json  ->  PreToolUse hook removed`);
 }
 function claudeInstall(projectDir = ".") {
   let alreadyConfigured = false;
-  const target = join4(projectDir, "CLAUDE.md");
-  if (existsSync7(target)) {
-    const content = readFileSync6(target, "utf-8");
+  const target = join5(projectDir, "CLAUDE.md");
+  if (existsSync8(target)) {
+    const content = readFileSync7(target, "utf-8");
     if (content.includes(MD_MARKER)) {
       alreadyConfigured = true;
       console.log("graphify already configured in CLAUDE.md");
     } else {
-      writeFileSync5(target, content.trimEnd() + "\n\n" + CLAUDE_MD_SECTION, "utf-8");
+      writeFileSync6(target, content.trimEnd() + "\n\n" + CLAUDE_MD_SECTION, "utf-8");
     }
   } else {
-    writeFileSync5(target, CLAUDE_MD_SECTION, "utf-8");
+    writeFileSync6(target, CLAUDE_MD_SECTION, "utf-8");
   }
   if (!alreadyConfigured) {
-    console.log(`graphify section written to ${resolve5(target)}`);
+    console.log(`graphify section written to ${resolve8(target)}`);
   }
   installClaudeHook(projectDir);
   console.log();
@@ -5872,68 +6311,112 @@ function claudeInstall(projectDir = ".") {
   console.log("codebase questions and rebuild it after code changes.");
 }
 function claudeUninstall(projectDir = ".") {
-  const target = join4(projectDir, "CLAUDE.md");
-  if (!existsSync7(target)) {
+  const target = join5(projectDir, "CLAUDE.md");
+  if (!existsSync8(target)) {
     console.log("No CLAUDE.md found in current directory - nothing to do");
     return;
   }
-  const content = readFileSync6(target, "utf-8");
+  const content = readFileSync7(target, "utf-8");
   if (!content.includes(MD_MARKER)) {
     console.log("graphify section not found in CLAUDE.md - nothing to do");
     return;
   }
   const cleaned = content.replace(/\n*## graphify\n[\s\S]*?(?=\n## |\s*$)/, "").trim();
   if (cleaned) {
-    writeFileSync5(target, cleaned + "\n", "utf-8");
-    console.log(`graphify section removed from ${resolve5(target)}`);
+    writeFileSync6(target, cleaned + "\n", "utf-8");
+    console.log(`graphify section removed from ${resolve8(target)}`);
   } else {
-    const { unlinkSync: unlinkSync4 } = __require("fs");
-    unlinkSync4(target);
-    console.log(`CLAUDE.md was empty after removal - deleted ${resolve5(target)}`);
+    const { unlinkSync: unlinkSync5 } = __require("fs");
+    unlinkSync5(target);
+    console.log(`CLAUDE.md was empty after removal - deleted ${resolve8(target)}`);
   }
   uninstallClaudeHook(projectDir);
 }
+function geminiInstall(projectDir = ".") {
+  let alreadyConfigured = false;
+  const target = join5(projectDir, "GEMINI.md");
+  if (existsSync8(target)) {
+    const content = readFileSync7(target, "utf-8");
+    if (content.includes(MD_MARKER)) {
+      alreadyConfigured = true;
+      console.log("graphify already configured in GEMINI.md");
+    } else {
+      writeFileSync6(target, content.trimEnd() + "\n\n" + GEMINI_MD_SECTION, "utf-8");
+    }
+  } else {
+    writeFileSync6(target, GEMINI_MD_SECTION, "utf-8");
+  }
+  if (!alreadyConfigured) {
+    console.log(`graphify section written to ${resolve8(target)}`);
+  }
+  installGeminiMcp(projectDir);
+  console.log();
+  console.log("Gemini CLI will now check the knowledge graph before answering");
+  console.log("codebase questions and can access graphify via the configured MCP server.");
+  console.log();
+  console.log("Note: install the `/graphify` custom command globally with");
+  console.log("`graphify install --platform gemini` if you have not done that yet.");
+}
+function geminiUninstall(projectDir = ".") {
+  const target = join5(projectDir, "GEMINI.md");
+  if (!existsSync8(target)) {
+    console.log("No GEMINI.md found in current directory - nothing to do");
+  } else {
+    const content = readFileSync7(target, "utf-8");
+    if (!content.includes(MD_MARKER)) {
+      console.log("graphify section not found in GEMINI.md - nothing to do");
+    } else {
+      const cleaned = content.replace(/\n*## graphify\n[\s\S]*?(?=\n## |\s*$)/, "").trim();
+      if (cleaned) {
+        writeFileSync6(target, cleaned + "\n", "utf-8");
+        console.log(`graphify section removed from ${resolve8(target)}`);
+      } else {
+        const { unlinkSync: unlinkSync5 } = __require("fs");
+        unlinkSync5(target);
+        console.log(`GEMINI.md was empty after removal - deleted ${resolve8(target)}`);
+      }
+    }
+  }
+  uninstallGeminiMcp(projectDir);
+}
 function installCodexHook(projectDir) {
-  const hooksDir = join4(projectDir, ".codex");
-  if (existsSync7(hooksDir) && !statSync(hooksDir).isDirectory()) {
+  const hooksDir = join5(projectDir, ".codex");
+  if (existsSync8(hooksDir) && !statSync2(hooksDir).isDirectory()) {
     console.log("  .codex/hooks.json  ->  skipped (cannot create hook dir because .codex is a file)");
     return;
   }
-  const hooksPath = join4(hooksDir, "hooks.json");
-  mkdirSync4(hooksDir, { recursive: true });
+  const hooksPath = join5(hooksDir, "hooks.json");
+  mkdirSync5(hooksDir, { recursive: true });
   let existing = {};
-  if (existsSync7(hooksPath)) {
+  if (existsSync8(hooksPath)) {
     try {
-      existing = JSON.parse(readFileSync6(hooksPath, "utf-8"));
+      existing = JSON.parse(readFileSync7(hooksPath, "utf-8"));
     } catch {
     }
   }
   const hooks = existing.hooks ?? {};
   const preTool = hooks.PreToolUse ?? [];
-  if (preTool.some((h) => JSON.stringify(h).includes("graphify"))) {
-    console.log(`  .codex/hooks.json  ->  hook already registered (no change)`);
-    return;
-  }
-  preTool.push({
+  const filtered = preTool.filter((h) => !JSON.stringify(h).includes("graphify"));
+  filtered.push({
     matcher: "Bash",
     hooks: [
       {
         type: "command",
-        command: `[ -f graphify-out/graph.json ] && echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","additionalContext":"graphify: Knowledge graph exists. Read graphify-out/GRAPH_REPORT.md for god nodes and community structure before searching raw files."}}' || true`
+        command: `[ -f graphify-out/graph.json ] && echo '{"hookSpecificOutput":{"hookEventName":"PreToolUse","permissionDecision":"allow"},"systemMessage":"graphify: Knowledge graph exists. Read graphify-out/GRAPH_REPORT.md for god nodes and community structure before searching raw files."}' || true`
       }
     ]
   });
-  hooks.PreToolUse = preTool;
+  hooks.PreToolUse = filtered;
   existing.hooks = hooks;
-  writeFileSync5(hooksPath, JSON.stringify(existing, null, 2), "utf-8");
+  writeFileSync6(hooksPath, JSON.stringify(existing, null, 2), "utf-8");
   console.log(`  .codex/hooks.json  ->  PreToolUse hook registered`);
 }
 function uninstallCodexHook(projectDir) {
-  const hooksPath = join4(projectDir, ".codex", "hooks.json");
-  if (!existsSync7(hooksPath)) return;
+  const hooksPath = join5(projectDir, ".codex", "hooks.json");
+  if (!existsSync8(hooksPath)) return;
   let existing;
   try {
-    existing = JSON.parse(readFileSync6(hooksPath, "utf-8"));
+    existing = JSON.parse(readFileSync7(hooksPath, "utf-8"));
   } catch {
     return;
   }
@@ -5942,67 +6425,71 @@ function uninstallCodexHook(projectDir) {
   const filtered = preTool.filter((h) => !JSON.stringify(h).includes("graphify"));
   hooks.PreToolUse = filtered;
   existing.hooks = hooks;
-  writeFileSync5(hooksPath, JSON.stringify(existing, null, 2), "utf-8");
+  writeFileSync6(hooksPath, JSON.stringify(existing, null, 2), "utf-8");
   console.log(`  .codex/hooks.json  ->  PreToolUse hook removed`);
 }
 function agentsInstall(projectDir, platformName) {
   let alreadyConfigured = false;
-  const target = join4(projectDir, "AGENTS.md");
+  const target = join5(projectDir, "AGENTS.md");
   const section = getAgentsMdSection(platformName);
-  if (existsSync7(target)) {
-    const content = readFileSync6(target, "utf-8");
+  if (existsSync8(target)) {
+    const content = readFileSync7(target, "utf-8");
     if (content.includes(MD_MARKER)) {
       alreadyConfigured = true;
       console.log(`graphify already configured in AGENTS.md`);
     } else {
-      writeFileSync5(target, content.trimEnd() + "\n\n" + section, "utf-8");
+      writeFileSync6(target, content.trimEnd() + "\n\n" + section, "utf-8");
     }
   } else {
-    writeFileSync5(target, section, "utf-8");
+    writeFileSync6(target, section, "utf-8");
   }
   if (!alreadyConfigured) {
-    console.log(`graphify section written to ${resolve5(target)}`);
+    console.log(`graphify section written to ${resolve8(target)}`);
   }
   if (platformName === "codex") {
     installCodexHook(projectDir);
+  } else if (platformName === "opencode") {
+    installOpenCodePlugin(projectDir);
   }
   console.log();
   console.log(`${platformName.charAt(0).toUpperCase() + platformName.slice(1)} will now check the knowledge graph before answering`);
   console.log("codebase questions and rebuild it after code changes.");
-  if (platformName !== "codex") {
+  if (!["codex", "opencode"].includes(platformName)) {
     console.log();
     console.log("Note: unlike Claude Code, there is no PreToolUse hook equivalent for");
     console.log(`${platformName.charAt(0).toUpperCase() + platformName.slice(1)} \u2014 the AGENTS.md rules are the always-on mechanism.`);
   }
 }
 function agentsUninstall(projectDir, platformName) {
-  const target = join4(projectDir, "AGENTS.md");
-  if (!existsSync7(target)) {
+  const target = join5(projectDir, "AGENTS.md");
+  if (!existsSync8(target)) {
     console.log("No AGENTS.md found in current directory - nothing to do");
-    return;
-  }
-  const content = readFileSync6(target, "utf-8");
-  if (!content.includes(MD_MARKER)) {
-    console.log("graphify section not found in AGENTS.md - nothing to do");
-    return;
-  }
-  const cleaned = content.replace(/\n*## graphify\n[\s\S]*?(?=\n## |\s*$)/, "").trim();
-  if (cleaned) {
-    writeFileSync5(target, cleaned + "\n", "utf-8");
-    console.log(`graphify section removed from ${resolve5(target)}`);
   } else {
-    const { unlinkSync: unlinkSync4 } = __require("fs");
-    unlinkSync4(target);
-    console.log(`AGENTS.md was empty after removal - deleted ${resolve5(target)}`);
+    const content = readFileSync7(target, "utf-8");
+    if (!content.includes(MD_MARKER)) {
+      console.log("graphify section not found in AGENTS.md - nothing to do");
+    } else {
+      const cleaned = content.replace(/\n*## graphify\n[\s\S]*?(?=\n## |\s*$)/, "").trim();
+      if (cleaned) {
+        writeFileSync6(target, cleaned + "\n", "utf-8");
+        console.log(`graphify section removed from ${resolve8(target)}`);
+      } else {
+        const { unlinkSync: unlinkSync5 } = __require("fs");
+        unlinkSync5(target);
+        console.log(`AGENTS.md was empty after removal - deleted ${resolve8(target)}`);
+      }
+    }
   }
   if (platformName === "codex") {
     uninstallCodexHook(projectDir);
+  } else if (platformName === "opencode") {
+    uninstallOpenCodePlugin(projectDir);
   }
 }
 function checkSkillVersion(skillDst) {
-  const versionFile = join4(dirname2(skillDst), ".graphify_version");
-  if (!existsSync7(versionFile)) return;
-  const installed = readFileSync6(versionFile, "utf-8").trim();
+  const versionFile = join5(dirname4(skillDst), ".graphify_version");
+  if (!existsSync8(versionFile)) return;
+  const installed = readFileSync7(versionFile, "utf-8").trim();
   if (installed !== VERSION) {
     console.log(
       `  warning: skill is from graphify ${installed}, package is ${VERSION}. Run 'graphify install' to update.`
@@ -6041,7 +6528,7 @@ function getPlatformsToCheck(argv) {
 async function main() {
   for (const platformName of getPlatformsToCheck(process.argv.slice(2))) {
     const cfg = PLATFORM_CONFIG[platformName];
-    checkSkillVersion(join4(homedir(), cfg.skill_dst));
+    checkSkillVersion(join5(homedir(), cfg.skill_dst));
   }
   const program = new Command();
   program.name("graphify").description("AI coding assistant skill - turn any folder into a queryable knowledge graph").version(VERSION);
@@ -6053,13 +6540,28 @@ async function main() {
     sub.command("install").description(`Write graphify section to CLAUDE.md + PreToolUse hook`).action(() => claudeInstall());
     sub.command("uninstall").description(`Remove graphify section from CLAUDE.md + PreToolUse hook`).action(() => claudeUninstall());
   }
-  for (const cmd of ["codex", "opencode", "claw", "droid", "trae", "trae-cn"]) {
+  for (const cmd of ["gemini"]) {
+    const sub = program.command(cmd).description(`${cmd} skill management`);
+    sub.command("install").description("Write graphify section to GEMINI.md + project MCP config").action(() => geminiInstall());
+    sub.command("uninstall").description("Remove graphify section from GEMINI.md + project MCP config").action(() => geminiUninstall());
+  }
+  {
+    const sub = program.command("cursor").description("cursor skill management");
+    sub.command("install").description("Write .cursor/rules/graphify.mdc").action(() => cursorInstall());
+    sub.command("uninstall").description("Remove .cursor/rules/graphify.mdc").action(() => cursorUninstall());
+  }
+  {
+    const sub = program.command("copilot").description("copilot skill management");
+    sub.command("install").description("Copy graphify skill to ~/.copilot/skills").action(() => installSkill("copilot"));
+    sub.command("uninstall").description("Remove graphify skill from ~/.copilot/skills").action(() => uninstallSkill("copilot"));
+  }
+  for (const cmd of ["aider", "codex", "opencode", "claw", "droid", "trae", "trae-cn"]) {
     const sub = program.command(cmd).description(`${cmd} skill management`);
     sub.command("install").description(
-      cmd === "codex" ? "Write graphify section to AGENTS.md + PreToolUse hook" : "Write graphify section to AGENTS.md"
+      cmd === "codex" ? "Write graphify section to AGENTS.md + PreToolUse hook" : cmd === "opencode" ? "Write graphify section to AGENTS.md + tool.execute.before plugin" : "Write graphify section to AGENTS.md"
     ).action(() => agentsInstall(".", cmd));
     sub.command("uninstall").description(
-      cmd === "codex" ? "Remove graphify section from AGENTS.md + PreToolUse hook" : "Remove graphify section from AGENTS.md"
+      cmd === "codex" ? "Remove graphify section from AGENTS.md + PreToolUse hook" : cmd === "opencode" ? "Remove graphify section from AGENTS.md + plugin" : "Remove graphify section from AGENTS.md"
     ).action(() => {
       agentsUninstall(".", cmd);
     });
@@ -6090,7 +6592,7 @@ async function main() {
     const { readFileSync: rf } = await import("fs");
     const { resolve: res } = await import("path");
     const gp = res(opts.graph);
-    if (!existsSync7(gp)) {
+    if (!existsSync8(gp)) {
       console.error(`error: graph file not found: ${gp}`);
       process.exit(1);
     }
@@ -6099,22 +6601,8 @@ async function main() {
       process.exit(1);
     }
     try {
-      const Graph4 = (await import("graphology")).default;
       const raw = JSON.parse(rf(gp, "utf-8"));
-      const G = new Graph4({ type: "undirected" });
-      for (const node of raw.nodes ?? []) {
-        const { id, ...attrs } = node;
-        G.mergeNode(id, attrs);
-      }
-      for (const link of raw.links ?? []) {
-        const { source, target, ...attrs } = link;
-        if (G.hasNode(source) && G.hasNode(target)) {
-          try {
-            G.mergeEdge(source, target, attrs);
-          } catch {
-          }
-        }
-      }
+      const G = loadGraphFromData(raw);
       const terms = question.toLowerCase().split(/\s+/).filter((t) => t.length > 2);
       const scored = [];
       G.forEachNode((nid, data) => {
@@ -6139,7 +6627,7 @@ async function main() {
           if (d > 2) continue;
           if (d > 0 && visited.has(node)) continue;
           visited.add(node);
-          G.forEachNeighbor(node, (neighbor) => {
+          forEachTraversalNeighbor(G, node, (neighbor) => {
             if (!visited.has(neighbor)) {
               stack.push([neighbor, d + 1]);
               edgesSeen.push([node, neighbor]);
@@ -6151,7 +6639,7 @@ async function main() {
         for (let depth = 0; depth < 2; depth++) {
           const nextFrontier = /* @__PURE__ */ new Set();
           for (const n of frontier) {
-            G.forEachNeighbor(n, (neighbor) => {
+            forEachTraversalNeighbor(G, n, (neighbor) => {
               if (!visited.has(neighbor)) {
                 nextFrontier.add(neighbor);
                 edgesSeen.push([n, neighbor]);
@@ -6198,9 +6686,9 @@ async function main() {
     const { runBenchmark: runBenchmark2, printBenchmark: printBenchmark2 } = await Promise.resolve().then(() => (init_benchmark(), benchmark_exports));
     const gp = graphPath ?? "graphify-out/graph.json";
     let corpusWords;
-    if (existsSync7(".graphify_detect.json")) {
+    if (existsSync8(".graphify_detect.json")) {
       try {
-        const data = JSON.parse(readFileSync6(".graphify_detect.json", "utf-8"));
+        const data = JSON.parse(readFileSync7(".graphify_detect.json", "utf-8"));
         corpusWords = data.total_words;
       } catch {
       }
@@ -6219,7 +6707,7 @@ function isDirectCliExecution() {
   try {
     return realpathSync2(process.argv[1]) === __filename;
   } catch {
-    return resolve5(process.argv[1]) === __filename;
+    return resolve8(process.argv[1]) === __filename;
   }
 }
 if (isDirectCliExecution()) {
@@ -6230,9 +6718,14 @@ if (isDirectCliExecution()) {
 }
 export {
   agentsInstall,
+  cursorInstall,
+  cursorUninstall,
+  geminiInstall,
+  geminiUninstall,
   getAgentsMdSection,
   getInvocationExample,
   getPlatformsToCheck,
+  installClaudeHook,
   installCodexHook,
   main
 };