@dreamtree-org/graphify 1.1.3 → 1.2.0

package/dist/cli/index.js

@@ -503,6 +503,29 @@ function packageRoot() {
   const packageJsonPath = require2.resolve("@dreamtree-org/graphify/package.json");
   return path4.dirname(packageJsonPath);
 }
+var MCP_SERVER_ENTRY = {
+  command: "npx",
+  args: ["-y", "@dreamtree-org/graphify", "--mcp"]
+};
+async function upsertMcpServer(filePath, serversKey = "mcpServers") {
+  let config = {};
+  try {
+    config = JSON.parse(await fs6.readFile(filePath, "utf-8"));
+  } catch (error) {
+    if (error.code !== "ENOENT") {
+      throw new Error(`cannot update ${filePath} \u2014 it exists but is not valid JSON; fix or remove it and re-run.`, {
+        cause: error
+      });
+    }
+  }
+  const servers = config[serversKey] ?? {};
+  servers["graphify"] = MCP_SERVER_ENTRY;
+  config[serversKey] = servers;
+  await fs6.mkdir(path4.dirname(filePath), { recursive: true });
+  await fs6.writeFile(filePath, `${JSON.stringify(config, null, 2)}
+`, "utf-8");
+  return filePath;
+}
 var MD_MARKER_BEGIN = "<!-- >>> graphify >>> -->";
 var MD_MARKER_END = "<!-- <<< graphify <<< -->";
 async function writeOwnedFile(filePath, content) {
@@ -537,7 +560,8 @@ var PLATFORMS = {
   claude: async (cwd, content) => {
     const target = path4.join(cwd, ".claude", "skills", "graphify", "SKILL.md");
     await writeOwnedFile(target, content);
-    return { host: "Claude Code", path: target };
+    const mcpPath = await upsertMcpServer(path4.join(cwd, ".mcp.json"));
+    return { host: "Claude Code", path: target, mcpPath };
   },
   cursor: async (cwd, content) => {
     const target = path4.join(cwd, ".cursor", "rules", "graphify.mdc");
@@ -550,7 +574,8 @@ alwaysApply: false
 ---
 ${body}`
     );
-    return { host: "Cursor", path: target };
+    const mcpPath = await upsertMcpServer(path4.join(cwd, ".cursor", "mcp.json"));
+    return { host: "Cursor", path: target, mcpPath };
   },
   windsurf: async (cwd, content) => {
     const target = path4.join(cwd, ".windsurf", "rules", "graphify.md");
@@ -570,10 +595,32 @@ ${body}`
   gemini: async (cwd, content) => {
     const target = path4.join(cwd, "GEMINI.md");
     await upsertMarkedBlock(target, content.replace(/^---[\s\S]*?---\n/, ""));
-    return { host: "Gemini CLI", path: target };
+    const mcpPath = await upsertMcpServer(path4.join(cwd, ".gemini", "settings.json"));
+    return { host: "Gemini CLI", path: target, mcpPath };
   }
 };
 var SUPPORTED_PLATFORMS = Object.keys(PLATFORMS).sort((a, b) => a.localeCompare(b));
+var PLATFORM_MARKERS = {
+  cursor: [".cursor"],
+  windsurf: [".windsurf"],
+  cline: [".clinerules"],
+  agents: ["AGENTS.md"],
+  gemini: ["GEMINI.md", ".gemini"]
+};
+async function detectPlatforms(cwd = process.cwd()) {
+  const platforms = ["claude"];
+  for (const [platform, markers] of Object.entries(PLATFORM_MARKERS)) {
+    for (const marker of markers) {
+      try {
+        await fs6.access(path4.join(cwd, marker));
+        platforms.push(platform);
+        break;
+      } catch {
+      }
+    }
+  }
+  return platforms;
+}
 async function runInstall(platforms = ["claude"], cwd = process.cwd()) {
   const sourcePath = path4.join(packageRoot(), "src", "skill", "SKILL.md");
   const content = await fs6.readFile(sourcePath, "utf-8");
@@ -589,7 +636,8 @@ async function runInstall(platforms = ["claude"], cwd = process.cwd()) {
     results.push(await installer(cwd, content));
   }
   for (const result of results) {
-    console.log(`Installed graphify for ${result.host} -> ${result.path}`);
+    const mcpNote = result.mcpPath ? ` (MCP server registered in ${result.mcpPath})` : "";
+    console.log(`Installed graphify for ${result.host} -> ${result.path}${mcpNote}`);
   }
   return results;
 }
@@ -699,7 +747,7 @@ async function watchAndRebuild(root, runOnce) {
   });
 }
 var program = new Command();
-program.name("graphify").description("Turn a folder of code/docs/papers into a queryable knowledge graph.").argument("[path]", "path to scan, or a GitHub URL", ".").option("--mode <mode>", "extraction mode (deep for richer INFERRED edges \u2014 reserved, no-op in v1)").option("--update", "incremental rebuild \u2014 reuse cached extractions for unchanged files").option("--watch", "rebuild on file change").option("--cluster-only", "rerun clustering on an existing graph").option("--leiden", "use Leiden instead of Louvain for community detection (v2 \u2014 better community quality)").option("--max-iterations <n>", "Leiden only: cap on outer iterations for very large graphs", Number).option("--no-viz", "skip graph.html").option("--svg", "also export graph.svg (not implemented in v1)").option("--graphml", "also export graph.graphml (not implemented in v1)").option("--neo4j", "generate graphify-out/cypher.txt for Neo4j (not implemented in v1)").option("--mcp", "start MCP stdio server instead of running the pipeline").option("--mysql <dsn>", "also extract a MySQL schema (mysql://user:pass@host:port/db) into the graph").action(async (targetArg, options) => {
+program.name("graphify").description("Turn a folder of code/docs/papers into a queryable knowledge graph.").argument("[path]", "path to scan, or a GitHub URL", ".").option("--mode <mode>", "extraction mode (deep for richer INFERRED edges \u2014 reserved, no-op in v1)").option("--update", "incremental rebuild \u2014 reuse cached extractions for unchanged files").option("--watch", "rebuild on file change").option("--cluster-only", "rerun clustering on an existing graph").option("--leiden", "use Leiden instead of Louvain for community detection (v2 \u2014 better community quality)").option("--max-iterations <n>", "Leiden only: cap on outer iterations for very large graphs", Number).option("--no-viz", "skip graph.html").option("--svg", "also export graph.svg (not implemented in v1)").option("--graphml", "also export graph.graphml (not implemented in v1)").option("--neo4j", "generate graphify-out/cypher.txt for Neo4j (not implemented in v1)").option("--mcp", "start MCP stdio server instead of running the pipeline").option("--no-install", "skip auto-installing the agent skill + MCP config after the build").option("--mysql <dsn>", "also extract a MySQL schema (mysql://user:pass@host:port/db) into the graph").action(async (targetArg, options) => {
   try {
     if (options.mcp) {
       const outDir = path5.resolve(targetArg === "." ? process.cwd() : targetArg, "graphify-out");
@@ -708,7 +756,8 @@ program.name("graphify").description("Turn a folder of code/docs/papers into a q
       return;
     }
     let root = targetArg;
-    if (looksLikeGitUrl(targetArg)) {
+    const cloned = looksLikeGitUrl(targetArg);
+    if (cloned) {
       console.error(`Cloning ${targetArg} ...`);
       root = await cloneRepo(targetArg);
     }
@@ -734,6 +783,13 @@ program.name("graphify").description("Turn a folder of code/docs/papers into a q
       onProgress: (m) => console.error(m)
     });
     await runOnce();
+    if (options.install && !cloned) {
+      try {
+        await runInstall(await detectPlatforms(root), root);
+      } catch (error) {
+        console.error(`graphify: agent skill/MCP install skipped: ${error.message}`);
+      }
+    }
     if (options.watch) {
       console.error(`Watching ${root} for changes (Ctrl+C to stop) ...`);
       await watchAndRebuild(root, runOnce);
@@ -815,7 +871,7 @@ program.command("benchmark [questions...]").description("measure token savings o
     process.exitCode = 1;
   }
 });
-program.command("install").description("install the skill/rules files into local agents (claude, cursor, windsurf, cline, agents, gemini, all)").option("--platform <names...>", "platform(s) to install for", ["claude"]).action(async (options) => {
+program.command("install").description("install the skill/rules files + project MCP config into local agents (claude, cursor, windsurf, cline, agents, gemini, all)").option("--platform <names...>", "platform(s) to install for", ["claude"]).action(async (options) => {
   try {
     await runInstall(options.platform);
   } catch (error) {

package/dist/cli/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/cli/index.ts","../../src/cli/commands/affected.ts","../../src/cli/commands/benchmark.ts","../../src/cli/commands/check.ts","../../src/cli/commands/context.ts","../../src/cli/commands/explain.ts","../../src/cli/commands/review.ts","../../src/cli/commands/tests.ts","../../src/cli/commands/global.ts","../../src/cli/commands/hook.ts","../../src/cli/commands/install.ts","../../src/cli/commands/path.ts","../../src/cli/commands/query.ts"],"sourcesContent":["#!/usr/bin/env node\nimport { execFile } from 'node:child_process';\nimport * as fs from 'node:fs/promises';\nimport * as os from 'node:os';\nimport * as path from 'node:path';\nimport { promisify } from 'node:util';\nimport { watch as watchFiles } from 'chokidar';\nimport { Command } from 'commander';\nimport { analyze } from '../analyze.js';\nimport { cluster } from '../cluster.js';\nimport { exportGraph } from '../export.js';\nimport { loadGraph } from '../graphStore.js';\nimport { runPipeline } from '../pipeline.js';\nimport { renderReport } from '../report.js';\nimport { validateDsn, validateUrl } from '../security.js';\nimport type { ExtractionResult } from '../types.js';\nimport { runAffected } from './commands/affected.js';\nimport { runBenchmark } from './commands/benchmark.js';\nimport { runCheck } from './commands/check.js';\nimport { runContext } from './commands/context.js';\nimport { runExplain } from './commands/explain.js';\nimport { runReview } from './commands/review.js';\nimport { runTests } from './commands/tests.js';\nimport { runGlobalAdd, runGlobalBuild, runGlobalList, runGlobalRemove, runMerge } from './commands/global.js';\nimport { runHookInstall, runHookUninstall } from './commands/hook.js';\nimport { loadResults, renderLessons, saveResult, type ResultOutcome, type ResultType } from '../memory.js';\nimport { runInstall } from './commands/install.js';\nimport { runPath } from './commands/path.js';\nimport { runQuery } from './commands/query.js';\n\nconst execFileAsync = promisify(execFile);\n\ninterface DefaultCommandOptions {\n  mode?: string;\n  update?: boolean;\n  watch?: boolean;\n  clusterOnly?: boolean;\n  viz: boolean; // commander negatable --no-viz -> options.viz\n  svg?: boolean;\n  graphml?: boolean;\n  neo4j?: boolean;\n  mcp?: boolean;\n  leiden?: boolean;\n  maxIterations?: number;\n  mysql?: string;\n}\n\nfunction looksLikeGitUrl(value: string): boolean {\n  if (!/^https?:\\/\\//i.test(value)) return false;\n  return /github\\.com|gitlab\\.com|bitbucket\\.org/i.test(value) || value.endsWith('.git');\n}\n\n/** Clone `url` into a fresh temp directory using an argv-array child_process call (never shell: true, never a shell string built from input). */\nasync function cloneRepo(url: string): Promise<string> {\n  const validated = validateUrl(url);\n  const dest = await fs.mkdtemp(path.join(os.tmpdir(), 'graphify-clone-'));\n  await execFileAsync('git', ['clone', '--depth', '1', validated, dest]);\n  return dest;\n}\n\nfunction exportOptionsFrom(options: DefaultCommandOptions) {\n  return { html: options.viz, svg: options.svg, graphml: options.graphml, neo4j: options.neo4j };\n}\n\nfunction clusterOptionsFrom(options: DefaultCommandOptions) {\n  return {\n    algorithm: options.leiden ? ('leiden' as const) : ('louvain' as const),\n    maxIterations: options.maxIterations,\n  };\n}\n\nasync function runClusterOnly(root: string, options: DefaultCommandOptions): Promise<void> {\n  const outDir = path.join(root, 'graphify-out');\n  const graph = await loadGraph(outDir);\n  cluster(graph, clusterOptionsFrom(options));\n  const analysis = analyze(graph);\n  const report = renderReport(graph, analysis);\n  await exportGraph(graph, { outDir, ...exportOptionsFrom(options) }, report);\n  console.error(`Re-clustered the existing graph (${clusterOptionsFrom(options).algorithm}).`);\n}\n\n/** Watch `root` (ignoring graphify-out/, node_modules/, .git/) and re-run `runOnce` on any change, debounced. Never resolves — the process stays alive until interrupted, matching normal watch-mode CLI behavior. */\nasync function watchAndRebuild(root: string, runOnce: () => Promise<unknown>): Promise<void> {\n  const watcher = watchFiles(root, {\n    ignored: (filePath: string) => /(^|[/\\\\])(node_modules|\\.git|graphify-out)([/\\\\]|$)/.test(filePath),\n    ignoreInitial: true,\n  });\n\n  let timer: ReturnType<typeof setTimeout> | null = null;\n  let running = false;\n  const schedule = (): void => {\n    if (timer) clearTimeout(timer);\n    timer = setTimeout(() => {\n      if (running) return;\n      running = true;\n      console.error('Change detected, rebuilding...');\n      runOnce()\n        .catch((error: unknown) => console.error(`graphify --watch: rebuild failed: ${(error as Error).message}`))\n        .finally(() => {\n          running = false;\n        });\n    }, 300);\n  };\n\n  watcher.on('add', schedule).on('change', schedule).on('unlink', schedule);\n\n  await new Promise<never>(() => {\n    /* keep the process alive until the user interrupts it (Ctrl+C) */\n  });\n}\n\nconst program = new Command();\n\nprogram\n  .name('graphify')\n  .description('Turn a folder of code/docs/papers into a queryable knowledge graph.')\n  .argument('[path]', 'path to scan, or a GitHub URL', '.')\n  .option('--mode <mode>', 'extraction mode (deep for richer INFERRED edges — reserved, no-op in v1)')\n  .option('--update', 'incremental rebuild — reuse cached extractions for unchanged files')\n  .option('--watch', 'rebuild on file change')\n  .option('--cluster-only', 'rerun clustering on an existing graph')\n  .option('--leiden', 'use Leiden instead of Louvain for community detection (v2 — better community quality)')\n  .option('--max-iterations <n>', 'Leiden only: cap on outer iterations for very large graphs', Number)\n  .option('--no-viz', 'skip graph.html')\n  .option('--svg', 'also export graph.svg (not implemented in v1)')\n  .option('--graphml', 'also export graph.graphml (not implemented in v1)')\n  .option('--neo4j', 'generate graphify-out/cypher.txt for Neo4j (not implemented in v1)')\n  .option('--mcp', 'start MCP stdio server instead of running the pipeline')\n  .option('--mysql <dsn>', 'also extract a MySQL schema (mysql://user:pass@host:port/db) into the graph')\n  .action(async (targetArg: string, options: DefaultCommandOptions) => {\n    try {\n      if (options.mcp) {\n        const outDir = path.resolve(targetArg === '.' ? process.cwd() : targetArg, 'graphify-out');\n        const { startServer } = await import('../mcp/server.js');\n        await startServer(path.join(outDir, 'graph.json'));\n        return;\n      }\n\n      let root = targetArg;\n      if (looksLikeGitUrl(targetArg)) {\n        console.error(`Cloning ${targetArg} ...`);\n        root = await cloneRepo(targetArg);\n      }\n      root = path.resolve(root);\n\n      if (options.mode) {\n        console.error(`--mode ${options.mode} is reserved for a future richer-INFERRED-edges pass — currently a no-op.`);\n      }\n\n      if (options.clusterOnly) {\n        await runClusterOnly(root, options);\n        return;\n      }\n\n      let extraExtractions: ExtractionResult[] | undefined;\n      if (options.mysql) {\n        const { extractMysql } = await import('../extractors/mysql.js');\n        console.error(`Extracting MySQL schema from ${validateDsn(options.mysql).safeDisplay} ...`);\n        extraExtractions = [await extractMysql(options.mysql)];\n      }\n\n      const runOnce = () =>\n        runPipeline(root, {\n          ...exportOptionsFrom(options),\n          ...clusterOptionsFrom(options),\n          extraExtractions,\n          update: options.update,\n          onProgress: (m) => console.error(m),\n        });\n      await runOnce();\n\n      if (options.watch) {\n        console.error(`Watching ${root} for changes (Ctrl+C to stop) ...`);\n        await watchAndRebuild(root, runOnce);\n      }\n    } catch (error) {\n      console.error(`graphify: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('query <question>')\n  .description('BFS (default) or DFS traversal answering a question against the existing graph')\n  .option('--dfs', 'depth-first traversal (trace a specific path)')\n  .option('--budget <tokens>', 'cap answer at N tokens', Number)\n  .action(async (question: string, options: { dfs?: boolean; budget?: number }) => {\n    try {\n      await runQuery(question, options);\n    } catch (error) {\n      console.error(`graphify query: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('path <from> <to>')\n  .description('shortest path between two named nodes')\n  .action(async (from: string, to: string) => {\n    try {\n      await runPath(from, to);\n    } catch (error) {\n      console.error(`graphify path: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('explain <node>')\n  .description('plain-language explanation of a node')\n  .action(async (node: string) => {\n    try {\n      await runExplain(node);\n    } catch (error) {\n      console.error(`graphify explain: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('affected <node>')\n  .description('reverse impact analysis — everything that (transitively) depends on a node')\n  .option('--depth <n>', 'how many reverse hops to follow (default 3)', Number)\n  .option('--limit <n>', 'cap on affected nodes reported (default 200)', Number)\n  .action(async (node: string, options: { depth?: number; limit?: number }) => {\n    try {\n      await runAffected(node, options);\n    } catch (error) {\n      console.error(`graphify affected: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('context <task>')\n  .description('token-budgeted working-set pack — the actual code for a task, in one call')\n  .option('--budget <tokens>', 'approximate token cap for the pack (default 4000)', Number)\n  .action(async (task: string, options: { budget?: number }) => {\n    try {\n      await runContext(task, options);\n    } catch (error) {\n      console.error(`graphify context: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('tests [node]')\n  .description('structural test selection — the minimal test files worth running for a change')\n  .option('--changed [rev]', 'select for the working-tree diff (optionally vs a revision) instead of a node')\n  .action(async (node: string | undefined, options: { changed?: string | boolean }) => {\n    try {\n      await runTests(node, options);\n    } catch (error) {\n      console.error(`graphify tests: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('review <base> [head]')\n  .description('structural review between two git revisions: added/removed/rewired symbols with blast radius + tests')\n  .action(async (base: string, head?: string) => {\n    try {\n      await runReview(base, head);\n    } catch (error) {\n      console.error(`graphify review: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('check')\n  .description('check the graph against dependency rules (graphify.rules.json) — exits 1 on violations')\n  .option('--rules <file>', 'rules file (default ./graphify.rules.json)')\n  .action(async (options: { rules?: string }) => {\n    try {\n      await runCheck(options);\n    } catch (error) {\n      console.error(`graphify check: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('benchmark [questions...]')\n  .description('measure token savings of graph answers vs reading the files they touch')\n  .action(async (questions: string[]) => {\n    try {\n      await runBenchmark(questions);\n    } catch (error) {\n      console.error(`graphify benchmark: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('install')\n  .description('install the skill/rules files into local agents (claude, cursor, windsurf, cline, agents, gemini, all)')\n  .option('--platform <names...>', 'platform(s) to install for', ['claude'])\n  .action(async (options: { platform: string[] }) => {\n    try {\n      await runInstall(options.platform);\n    } catch (error) {\n      console.error(`graphify install: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nconst globalCommand = program\n  .command('global')\n  .description('manage the cross-project global graph (registry at ~/.graphify/global.json)');\n\nglobalCommand\n  .command('add [path]')\n  .description('register a project (must already have graphify-out/graph.json)')\n  .action(async (target?: string) => {\n    try {\n      await runGlobalAdd(target);\n    } catch (error) {\n      console.error(`graphify global add: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nglobalCommand\n  .command('remove <name>')\n  .description('unregister a project by name')\n  .action(async (name: string) => {\n    try {\n      await runGlobalRemove(name);\n    } catch (error) {\n      console.error(`graphify global remove: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nglobalCommand\n  .command('list')\n  .description('list registered projects')\n  .action(async () => {\n    try {\n      await runGlobalList();\n    } catch (error) {\n      console.error(`graphify global list: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nglobalCommand\n  .command('build')\n  .description('merge every registered project into one global graph')\n  .option('--out <dir>', 'output directory (default ~/.graphify/global-out)')\n  .action(async (options: { out?: string }) => {\n    try {\n      await runGlobalBuild(options);\n    } catch (error) {\n      console.error(`graphify global build: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('merge <dirs...>')\n  .description('one-shot merge of two or more built project graphs into one')\n  .option('--out <dir>', 'output directory (default ./graphify-merged)')\n  .action(async (dirs: string[], options: { out?: string }) => {\n    try {\n      await runMerge(dirs, options);\n    } catch (error) {\n      console.error(`graphify merge: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('save-result')\n  .description('save a Q&A result to graphify-out/memory/ for the graph feedback loop')\n  .requiredOption('--question <q>', 'the question that was asked')\n  .requiredOption('--answer <a>', 'the answer that was given')\n  .option('--nodes <ids...>', 'node ids/labels cited in the answer', [])\n  .option('--type <t>', 'query|path|explain|affected', 'query')\n  .option('--outcome <o>', 'useful|dead_end|corrected', 'useful')\n  .option('--correction <text>', 'what the right answer was (pairs with --outcome corrected)')\n  .action(async (options: {\n    question: string;\n    answer: string;\n    nodes: string[];\n    type: string;\n    outcome: string;\n    correction?: string;\n  }) => {\n    try {\n      const memoryDir = path.join(process.cwd(), 'graphify-out', 'memory');\n      const file = await saveResult(\n        {\n          question: options.question,\n          answer: options.answer,\n          nodes: options.nodes,\n          type: options.type as ResultType,\n          outcome: options.outcome as ResultOutcome,\n          correction: options.correction,\n        },\n        memoryDir,\n      );\n      console.log(`Saved -> ${file}`);\n    } catch (error) {\n      console.error(`graphify save-result: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('reflect')\n  .description('aggregate graphify-out/memory/ into a recency-weighted lessons doc')\n  .option('--half-life-days <n>', 'a result loses half its weight every N days (default 30)', Number)\n  .option('--out <file>', 'output path (default graphify-out/reflections/LESSONS.md)')\n  .action(async (options: { halfLifeDays?: number; out?: string }) => {\n    try {\n      const memoryDir = path.join(process.cwd(), 'graphify-out', 'memory');\n      const results = await loadResults(memoryDir);\n      const lessons = renderLessons(results, { halfLifeDays: options.halfLifeDays });\n      const outPath = path.resolve(options.out ?? path.join(process.cwd(), 'graphify-out', 'reflections', 'LESSONS.md'));\n      await fs.mkdir(path.dirname(outPath), { recursive: true });\n      await fs.writeFile(outPath, lessons, 'utf-8');\n      console.log(`Reflected ${results.length} result(s) -> ${outPath}`);\n    } catch (error) {\n      console.error(`graphify reflect: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nconst hookCommand = program\n  .command('hook')\n  .description('manage the git hooks that auto-rebuild the graph on commit/pull');\n\nhookCommand\n  .command('install')\n  .description('install post-commit and post-merge hooks (preserves existing hook content)')\n  .action(async () => {\n    try {\n      await runHookInstall();\n    } catch (error) {\n      console.error(`graphify hook install: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nhookCommand\n  .command('uninstall')\n  .description('remove the graphify block from the git hooks')\n  .action(async () => {\n    try {\n      await runHookUninstall();\n    } catch (error) {\n      console.error(`graphify hook uninstall: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram.parseAsync(process.argv);\n","import { loadGraph } from '../../graphStore.js';\nimport { affectedBy } from '../../impact.js';\n\nexport interface AffectedOptions {\n  depth?: number;\n  limit?: number;\n}\n\n/** Reverse impact analysis: everything that (transitively) depends on the named node. */\nexport async function runAffected(nodeName: string, options: AffectedOptions = {}): Promise<void> {\n  const graph = await loadGraph();\n  const result = affectedBy(graph, nodeName, { maxDepth: options.depth, limit: options.limit });\n\n  if (!result) {\n    console.log(`No node matched \"${nodeName}\".`);\n    return;\n  }\n\n  console.log(`Impact of changing ${result.target.label} (${result.target.id}):`);\n\n  if (result.affected.length === 0) {\n    console.log('  Nothing in the graph depends on it — no incoming dependency edges.');\n    return;\n  }\n\n  let currentDepth = 0;\n  for (const node of result.affected) {\n    if (node.depth !== currentDepth) {\n      currentDepth = node.depth;\n      console.log('');\n      console.log(currentDepth === 1 ? 'Directly affected:' : `Affected at depth ${currentDepth}:`);\n    }\n    const isPlaceholder =\n      node.sourceFile === '<unknown>' || node.sourceFile === '<external>' || node.sourceFile === '';\n    const where = isPlaceholder\n      ? '(reference only)'\n      : `${node.sourceFile}${node.sourceLocation ? `:${node.sourceLocation}` : ''}`;\n    console.log(\n      `  ${node.label} — ${where} ` +\n        `(--${node.via.relation}--> ${node.via.dependsOn}, ${node.via.confidence})`,\n    );\n  }\n\n  console.log('');\n  const { EXTRACTED, INFERRED, AMBIGUOUS } = result.byConfidence;\n  console.log(\n    `Blast radius: ${result.affected.length} node(s) within ${result.maxDepth} hop(s) — ` +\n      `${EXTRACTED} certain (EXTRACTED), ${INFERRED} likely (INFERRED), ${AMBIGUOUS} uncertain (AMBIGUOUS).`,\n  );\n  if (result.truncated) {\n    console.log('(List truncated — raise --limit to see more.)');\n  }\n}\n","import * as fs from 'node:fs/promises';\nimport type Graph from 'graphology';\nimport { loadGraph } from '../../graphStore.js';\nimport { queryGraph } from '../../query.js';\nimport { isTestFile } from '../../testmap.js';\n\n/**\n * `graphify benchmark` — measure the token savings of answering through the\n * graph instead of reading source files. For each question it compares the\n * serialized size of the graph answer against the size of every source file\n * that answer's nodes live in (the \"just read the relevant files\" baseline\n * an agent without the graph would pay). Chars/4 is the usual token\n * approximation, applied to both sides so the ratio is fair.\n */\n\nexport interface BenchmarkRow {\n  question: string;\n  graphTokens: number;\n  naiveTokens: number;\n  /** naive / graph — how many times cheaper the graph answer is. */\n  reduction: number;\n  filesRead: number;\n  filesMissing: number;\n}\n\nexport type FileReader = (path: string) => Promise<string>;\n\nconst tokensOf = (text: string): number => Math.ceil(text.length / 4);\n\nexport async function benchmarkQuestion(\n  graph: Graph,\n  question: string,\n  readFile: FileReader,\n): Promise<BenchmarkRow> {\n  const result = queryGraph(graph, question);\n  // Compact JSON, matching how queryGraph's own token budget measures itself.\n  const graphTokens = tokensOf(JSON.stringify(result));\n\n  const sourceFiles = new Set<string>();\n  for (const node of result.visited) {\n    if (node.sourceFile && !node.sourceFile.startsWith('<') && !node.sourceFile.includes('://')) {\n      sourceFiles.add(node.sourceFile);\n    }\n  }\n\n  let naiveTokens = 0;\n  let filesRead = 0;\n  let filesMissing = 0;\n  for (const file of [...sourceFiles].sort((a, b) => a.localeCompare(b))) {\n    try {\n      naiveTokens += tokensOf(await readFile(file));\n      filesRead++;\n    } catch {\n      filesMissing++;\n    }\n  }\n\n  return {\n    question,\n    graphTokens,\n    naiveTokens,\n    reduction: graphTokens > 0 && naiveTokens > 0 ? naiveTokens / graphTokens : 0,\n    filesRead,\n    filesMissing,\n  };\n}\n\n/** Files no agent would ask a \"how does X work\" question about — build config, examples, scripts, docs. */\nconst NON_QUESTION_FILE =\n  /(^|\\/)(examples?|scripts?|bench(?:mark)?s?|fixtures?|docs?|\\.github)\\/|\\.(config|conf)\\.[^/]+$|(^|\\/)(rollup|webpack|vite|vitest|jest|babel|tsup|eslint|prettier)\\.[^/]*$/i;\n\n/**\n * Default questions when none are given: the labels of the highest-degree\n * (most load-bearing) SOURCE entities. Tests, build config, and examples\n * are excluded — they score high on degree but are questions no agent\n * would ask, and they drag the measured reduction down unfairly.\n */\nexport function defaultQuestions(graph: Graph, count = 5): string[] {\n  const entries = [...graph.nodes()]\n    .map((id) => ({\n      id,\n      degree: graph.degree(id),\n      label: (graph.getNodeAttribute(id, 'label') as string | undefined) ?? id,\n      file: (graph.getNodeAttribute(id, 'sourceFile') as string | undefined) ?? '',\n    }))\n    // File nodes score high on degree but make poor questions — prefer entities.\n    .filter((e) => e.id.includes('::'))\n    .filter((e) => !isTestFile(e.file) && !NON_QUESTION_FILE.test(e.file))\n    .sort((a, b) => b.degree - a.degree || a.id.localeCompare(b.id));\n  return entries.slice(0, count).map((e) => `how does ${e.label} work`);\n}\n\nexport async function runBenchmark(questions: string[]): Promise<BenchmarkRow[]> {\n  const graph = await loadGraph();\n  const effective = questions.length > 0 ? questions : defaultQuestions(graph);\n  if (effective.length === 0) {\n    console.log('The graph has no entity nodes to benchmark against — build it first.');\n    return [];\n  }\n\n  const rows: BenchmarkRow[] = [];\n  for (const question of effective) {\n    rows.push(await benchmarkQuestion(graph, question, (p) => fs.readFile(p, 'utf-8')));\n  }\n\n  console.log('Token cost per question — graph answer vs reading the files it touches:\\n');\n  for (const row of rows) {\n    const reduction = row.reduction > 0 ? `${row.reduction.toFixed(1)}x` : 'n/a';\n    console.log(`  \"${row.question}\"`);\n    console.log(\n      `    graph: ~${row.graphTokens} tokens | files: ~${row.naiveTokens} tokens ` +\n        `(${row.filesRead} file(s)${row.filesMissing ? `, ${row.filesMissing} unreadable` : ''}) | reduction: ${reduction}`,\n    );\n  }\n\n  const scored = rows.filter((r) => r.reduction > 0);\n  if (scored.length > 0) {\n    const avg = scored.reduce((s, r) => s + r.reduction, 0) / scored.length;\n    console.log(`\\nAverage reduction: ${avg.toFixed(1)}x across ${scored.length} question(s).`);\n  } else {\n    console.log('\\nNo reduction could be measured — run from the project root so source files are readable.');\n  }\n  return rows;\n}\n","import * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport { checkRules, validateRules } from '../../check.js';\nimport { loadGraph } from '../../graphStore.js';\n\nexport interface CheckCommandOptions {\n  rules?: string;\n}\n\n/**\n * Check the graph against declared dependency rules. Exits non-zero on\n * violations so CI (and agents verifying their own edits) can gate on it.\n */\nexport async function runCheck(options: CheckCommandOptions = {}): Promise<void> {\n  const rulesPath = path.resolve(options.rules ?? 'graphify.rules.json');\n  let raw: string;\n  try {\n    raw = await fs.readFile(rulesPath, 'utf-8');\n  } catch {\n    throw new Error(\n      `No rules file at ${rulesPath} — create graphify.rules.json with ` +\n        '{ \"rules\": [{ \"name\": \"...\", \"from\": \"src/a/**\", \"disallow\": [\"src/b/**\"] }] }.',\n    );\n  }\n  const config = validateRules(JSON.parse(raw));\n\n  const graph = await loadGraph();\n  const violations = checkRules(graph, config);\n\n  if (violations.length === 0) {\n    console.log(`OK — ${config.rules.length} rule(s), no violations.`);\n    return;\n  }\n\n  console.log(`${violations.length} violation(s):`);\n  for (const v of violations) {\n    console.log(`  [${v.rule}] ${v.fromNode} --${v.relation}--> ${v.toNode}`);\n    console.log(`    ${v.fromFile} must not depend on ${v.toFile}${v.reason ? ` — ${v.reason}` : ''}`);\n  }\n  process.exitCode = 1;\n}\n","import * as fs from 'node:fs/promises';\nimport { buildContextPack, renderContextPack } from '../../context.js';\nimport { loadGraph } from '../../graphStore.js';\n\nexport interface ContextCommandOptions {\n  budget?: number;\n}\n\n/** Token-budgeted working-set pack: the actual code an agent needs for a task, in one call. */\nexport async function runContext(task: string, options: ContextCommandOptions = {}): Promise<void> {\n  const graph = await loadGraph();\n  const pack = await buildContextPack(graph, task, (p) => fs.readFile(p, 'utf-8'), {\n    tokenBudget: options.budget,\n  });\n  console.log(renderContextPack(pack));\n}\n","import { loadGraph } from '../../graphStore.js';\nimport { explainNode } from '../../query.js';\n\n/** Plain-language explanation of a single node. */\nexport async function runExplain(nodeName: string): Promise<void> {\n  const graph = await loadGraph();\n  const result = explainNode(graph, nodeName);\n\n  if (!result) {\n    console.log(`No node matched \"${nodeName}\".`);\n    return;\n  }\n\n  console.log(result.label);\n  if (result.sourceFile === '<unknown>' || result.sourceFile === '<external>' || result.sourceFile === '') {\n    // Auto-vivified endpoint (re-export alias / unresolved reference) — it\n    // has no source of its own, so \"<unknown>:L0\" would read like a bug.\n    console.log('  location: (reference only — no declaration seen; check its outgoing edges for the real definition)');\n  } else {\n    const location = result.sourceLocation ? `:${result.sourceLocation}` : '';\n    console.log(`  location: ${result.sourceFile}${location}`);\n  }\n  if (result.communityLabel) {\n    console.log(`  community: ${result.communityLabel}`);\n  }\n\n  console.log('');\n  console.log(`Calls / references out (${result.outgoing.length}):`);\n  if (result.outgoing.length === 0) {\n    console.log('  (none)');\n  } else {\n    for (const edge of result.outgoing) {\n      console.log(`  --${edge.relation}--> ${edge.target} (${edge.confidence})`);\n    }\n  }\n\n  console.log('');\n  console.log(`Referenced by (${result.incoming.length}):`);\n  if (result.incoming.length === 0) {\n    console.log('  (none)');\n  } else {\n    for (const edge of result.incoming) {\n      console.log(`  ${edge.source} --${edge.relation}--> (${edge.confidence})`);\n    }\n  }\n}\n","import { renderReview, reviewRevisions } from '../../diff.js';\n\n/** Structural review between two git revisions (head defaults to HEAD). */\nexport async function runReview(base: string, head?: string): Promise<void> {\n  const diff = await reviewRevisions(process.cwd(), base, head ?? 'HEAD');\n  console.log(renderReview(diff));\n}\n","import { execFile } from 'node:child_process';\nimport { promisify } from 'node:util';\nimport { loadGraph } from '../../graphStore.js';\nimport { testsForChangedFiles, testsForNode } from '../../testmap.js';\n\nconst execFileAsync = promisify(execFile);\n\nexport interface TestsCommandOptions {\n  /** Select tests for the working-tree diff (optionally against a rev) instead of a named node. */\n  changed?: string | boolean;\n}\n\n/** Structural test selection: the minimal test files worth running for a change. */\nexport async function runTests(nodeQuery: string | undefined, options: TestsCommandOptions = {}): Promise<void> {\n  const graph = await loadGraph();\n\n  let selection;\n  if (options.changed !== undefined && options.changed !== false) {\n    const args = ['diff', '--name-only'];\n    if (typeof options.changed === 'string') args.push(options.changed);\n    const { stdout } = await execFileAsync('git', args);\n    const changedFiles = stdout.split('\\n').map((l) => l.trim()).filter(Boolean);\n    if (changedFiles.length === 0) {\n      console.log('No changed files in the diff.');\n      return;\n    }\n    selection = testsForChangedFiles(graph, changedFiles);\n  } else if (nodeQuery) {\n    selection = testsForNode(graph, nodeQuery);\n    if (!selection) {\n      console.log(`No node matched \"${nodeQuery}\".`);\n      return;\n    }\n  } else {\n    console.log('Provide a node to select tests for, or --changed for the working-tree diff.');\n    return;\n  }\n\n  if (selection.testFiles.length === 0) {\n    console.log(\n      `No test files found in the blast radius of ${selection.target} ` +\n        `(${selection.affectedNodeCount} affected node(s) checked) — either it's untested or the tests ` +\n        'reach it through a path the graph does not capture.',\n    );\n    return;\n  }\n\n  const how =\n    selection.precision === 'usage'\n      ? 'selected by actual usage (calls/inheritance)'\n      : 'selected by import reachability — may over-include files sharing an entry point';\n  console.log(`Test files for ${selection.target} (${how}; most direct first):`);\n  for (const test of selection.testFiles) {\n    const via = test.depth === 0 ? test.via : `depth ${test.depth}, via ${test.via}`;\n    console.log(`  ${test.file}  (${via})`);\n  }\n}\n","import * as fs from 'node:fs/promises';\nimport * as os from 'node:os';\nimport * as path from 'node:path';\nimport { analyze } from '../../analyze.js';\nimport { cluster } from '../../cluster.js';\nimport { exportGraph } from '../../export.js';\nimport { loadGraph } from '../../graphStore.js';\nimport { mergeGraphs, type MergeEntry } from '../../merge.js';\nimport { renderReport } from '../../report.js';\n\n/**\n * `graphify global add|remove|list|build` — a registry of projects whose\n * built graphs get merged into one global cross-project graph, plus the\n * one-shot `graphify merge <dir...>` for merging without a registry.\n * The registry lives at ~/.graphify/global.json; the merged output defaults\n * to ~/.graphify/global-out/.\n */\n\nexport interface GlobalRegistry {\n  projects: Array<{ name: string; root: string }>;\n}\n\nfunction registryDir(): string {\n  return path.join(os.homedir(), '.graphify');\n}\n\nfunction registryPath(): string {\n  return path.join(registryDir(), 'global.json');\n}\n\nasync function readRegistry(): Promise<GlobalRegistry> {\n  try {\n    const raw = await fs.readFile(registryPath(), 'utf-8');\n    const parsed: unknown = JSON.parse(raw);\n    const projects = (parsed as GlobalRegistry).projects;\n    if (!Array.isArray(projects)) return { projects: [] };\n    return { projects: projects.filter((p) => typeof p?.name === 'string' && typeof p?.root === 'string') };\n  } catch {\n    return { projects: [] };\n  }\n}\n\nasync function writeRegistry(registry: GlobalRegistry): Promise<void> {\n  await fs.mkdir(registryDir(), { recursive: true });\n  await fs.writeFile(registryPath(), JSON.stringify(registry, null, 2), 'utf-8');\n}\n\n/** Project name for a root: its package.json \"name\" if present, else the directory basename. */\nasync function projectNameFor(root: string): Promise<string> {\n  try {\n    const raw = await fs.readFile(path.join(root, 'package.json'), 'utf-8');\n    const name = (JSON.parse(raw) as { name?: unknown }).name;\n    if (typeof name === 'string' && name.length > 0) return name;\n  } catch {\n    // no package.json — fall through to the basename\n  }\n  return path.basename(root);\n}\n\nexport async function runGlobalAdd(target: string = '.'): Promise<void> {\n  const root = path.resolve(target);\n  const graphJson = path.join(root, 'graphify-out', 'graph.json');\n  try {\n    await fs.access(graphJson);\n  } catch {\n    throw new Error(`${root} has no graphify-out/graph.json — run \\`graphify ${target}\\` first, then add it.`);\n  }\n\n  const name = await projectNameFor(root);\n  const registry = await readRegistry();\n\n  const existing = registry.projects.find((p) => p.name === name);\n  if (existing) {\n    if (existing.root === root) {\n      console.log(`${name} is already registered (${root}).`);\n      return;\n    }\n    throw new Error(\n      `A different project is already registered as \"${name}\" (${existing.root}). ` +\n        'Remove it first with `graphify global remove`.',\n    );\n  }\n\n  registry.projects.push({ name, root });\n  registry.projects.sort((a, b) => a.name.localeCompare(b.name));\n  await writeRegistry(registry);\n  console.log(`Registered ${name} (${root}). ${registry.projects.length} project(s) in the global graph.`);\n}\n\nexport async function runGlobalRemove(name: string): Promise<void> {\n  const registry = await readRegistry();\n  const before = registry.projects.length;\n  registry.projects = registry.projects.filter((p) => p.name !== name);\n  if (registry.projects.length === before) {\n    throw new Error(`No project named \"${name}\" is registered. See \\`graphify global list\\`.`);\n  }\n  await writeRegistry(registry);\n  console.log(`Removed ${name}. ${registry.projects.length} project(s) remain.`);\n}\n\nexport async function runGlobalList(): Promise<void> {\n  const registry = await readRegistry();\n  if (registry.projects.length === 0) {\n    console.log('No projects registered. Add one with `graphify global add <path>`.');\n    return;\n  }\n  for (const project of registry.projects) {\n    console.log(`${project.name}  ${project.root}`);\n  }\n}\n\n/** Load every entry's graph, skipping (with a warning) the ones that fail — one broken project must not sink the merge. */\nasync function loadEntries(sources: Array<{ name: string; outDir: string }>): Promise<MergeEntry[]> {\n  const entries: MergeEntry[] = [];\n  for (const source of sources) {\n    try {\n      entries.push({ name: source.name, graph: await loadGraph(source.outDir) });\n    } catch (error) {\n      console.warn(`Skipping ${source.name}: ${(error as Error).message}`);\n    }\n  }\n  return entries;\n}\n\nasync function mergeAndExport(entries: MergeEntry[], outDir: string): Promise<void> {\n  if (entries.length === 0) {\n    throw new Error('Nothing to merge — no project graphs could be loaded.');\n  }\n\n  const merged = mergeGraphs(entries);\n  cluster(merged);\n  const analysis = analyze(merged);\n  const report = renderReport(merged, analysis);\n  await exportGraph(merged, { outDir }, report);\n\n  console.log(\n    `Merged ${entries.length} project(s) into ${outDir} — ` +\n      `${merged.order} node(s), ${merged.size} edge(s).`,\n  );\n}\n\nexport async function runGlobalBuild(options: { out?: string } = {}): Promise<void> {\n  const registry = await readRegistry();\n  if (registry.projects.length === 0) {\n    throw new Error('No projects registered. Add some with `graphify global add <path>` first.');\n  }\n\n  const entries = await loadEntries(\n    registry.projects.map((p) => ({ name: p.name, outDir: path.join(p.root, 'graphify-out') })),\n  );\n  await mergeAndExport(entries, path.resolve(options.out ?? path.join(registryDir(), 'global-out')));\n}\n\n/** One-shot merge of two or more project directories, no registry involved. */\nexport async function runMerge(targets: string[], options: { out?: string } = {}): Promise<void> {\n  if (targets.length < 2) {\n    throw new Error('Provide at least two project directories to merge.');\n  }\n\n  const sources: Array<{ name: string; outDir: string }> = [];\n  for (const target of targets) {\n    const root = path.resolve(target);\n    sources.push({ name: await projectNameFor(root), outDir: path.join(root, 'graphify-out') });\n  }\n\n  const names = sources.map((s) => s.name);\n  const duplicate = names.find((name, i) => names.indexOf(name) !== i);\n  if (duplicate !== undefined) {\n    throw new Error(`Two of the given projects resolve to the same name (\"${duplicate}\") — rename one.`);\n  }\n\n  const entries = await loadEntries(sources);\n  await mergeAndExport(entries, path.resolve(options.out ?? 'graphify-merged'));\n}\n","import * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\n\n/**\n * `graphify hook install` / `graphify hook uninstall` — auto-rebuild the\n * graph after commits and pulls, mirroring the Python original's\n * `hook install`. The hook body lives inside a marked block so we can\n * coexist with (and later cleanly remove ourselves from) hooks the user\n * already has; we never overwrite or delete anything outside our markers.\n */\n\nconst MARKER_BEGIN = '# >>> graphify >>>';\nconst MARKER_END = '# <<< graphify <<<';\n\n/** post-commit: rebuild after each commit. post-merge: rebuild after pull/merge. */\nconst HOOK_NAMES = ['post-commit', 'post-merge'] as const;\n\nconst HOOK_BLOCK = `${MARKER_BEGIN}\n# Rebuild the graphify knowledge graph in the background so the hook never\n# slows down the commit. Errors are silenced — a failed rebuild should never\n# break a git operation. Installed by \\`graphify hook install\\`.\n(graphify . --update --no-viz >/dev/null 2>&1 &)\n${MARKER_END}`;\n\nexport interface HookResult {\n  hook: string;\n  path: string;\n  action: 'created' | 'appended' | 'already-installed' | 'removed' | 'not-installed';\n}\n\nasync function hooksDir(cwd: string): Promise<string> {\n  const gitDir = path.join(cwd, '.git');\n  let stats;\n  try {\n    stats = await fs.stat(gitDir);\n  } catch {\n    throw new Error(`${cwd} is not a git repository (no .git directory) — run this from the repo root.`);\n  }\n  if (!stats.isDirectory()) {\n    // .git can be a file in worktrees/submodules (\"gitdir: <path>\") — follow it.\n    const content = (await fs.readFile(gitDir, 'utf-8')).trim();\n    const match = /^gitdir:\\s*(.+)$/.exec(content);\n    if (!match) throw new Error(`${gitDir} exists but is neither a directory nor a gitdir pointer.`);\n    return path.resolve(cwd, match[1] as string, 'hooks');\n  }\n  return path.join(gitDir, 'hooks');\n}\n\n/** Install the marked graphify block into post-commit and post-merge, preserving any existing hook content. */\nexport async function runHookInstall(cwd: string = process.cwd()): Promise<HookResult[]> {\n  const dir = await hooksDir(cwd);\n  await fs.mkdir(dir, { recursive: true });\n\n  const results: HookResult[] = [];\n  for (const hook of HOOK_NAMES) {\n    const hookPath = path.join(dir, hook);\n    let existing: string | null = null;\n    try {\n      existing = await fs.readFile(hookPath, 'utf-8');\n    } catch {\n      // no existing hook — we'll create it\n    }\n\n    if (existing === null) {\n      await fs.writeFile(hookPath, `#!/bin/sh\\n${HOOK_BLOCK}\\n`, { mode: 0o755 });\n      results.push({ hook, path: hookPath, action: 'created' });\n    } else if (existing.includes(MARKER_BEGIN)) {\n      results.push({ hook, path: hookPath, action: 'already-installed' });\n    } else {\n      const separator = existing.endsWith('\\n') ? 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Try different keywords, or run \\`graphify explain <node>\\` ` +\n        'if you already know the name.',\n    );\n    return;\n  }\n\n  console.log(`Matched ${result.seeds.length} seed node(s):`);\n  for (const seed of result.seeds) {\n    console.log(`  - ${seed.label} (${seed.id})`);\n  }\n\n  console.log('');\n  console.log(`Context — ${result.visited.length} node(s), ${options.dfs ? 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+{"version":3,"sources":["../../src/cli/index.ts","../../src/cli/commands/affected.ts","../../src/cli/commands/benchmark.ts","../../src/cli/commands/check.ts","../../src/cli/commands/context.ts","../../src/cli/commands/explain.ts","../../src/cli/commands/review.ts","../../src/cli/commands/tests.ts","../../src/cli/commands/global.ts","../../src/cli/commands/hook.ts","../../src/cli/commands/install.ts","../../src/cli/commands/path.ts","../../src/cli/commands/query.ts"],"sourcesContent":["#!/usr/bin/env node\nimport { execFile } from 'node:child_process';\nimport * as fs from 'node:fs/promises';\nimport * as os from 'node:os';\nimport * as path from 'node:path';\nimport { promisify } from 'node:util';\nimport { watch as watchFiles } from 'chokidar';\nimport { Command } from 'commander';\nimport { analyze } from '../analyze.js';\nimport { cluster } from '../cluster.js';\nimport { exportGraph } from '../export.js';\nimport { loadGraph } from '../graphStore.js';\nimport { runPipeline } from '../pipeline.js';\nimport { renderReport } from '../report.js';\nimport { validateDsn, validateUrl } from '../security.js';\nimport type { ExtractionResult } from '../types.js';\nimport { runAffected } from './commands/affected.js';\nimport { runBenchmark } from './commands/benchmark.js';\nimport { runCheck } from './commands/check.js';\nimport { runContext } from './commands/context.js';\nimport { runExplain } from './commands/explain.js';\nimport { runReview } from './commands/review.js';\nimport { runTests } from './commands/tests.js';\nimport { runGlobalAdd, runGlobalBuild, runGlobalList, runGlobalRemove, runMerge } from './commands/global.js';\nimport { runHookInstall, runHookUninstall } from './commands/hook.js';\nimport { loadResults, renderLessons, saveResult, type ResultOutcome, type ResultType } from '../memory.js';\nimport { detectPlatforms, runInstall } from './commands/install.js';\nimport { runPath } from './commands/path.js';\nimport { runQuery } from './commands/query.js';\n\nconst execFileAsync = promisify(execFile);\n\ninterface DefaultCommandOptions {\n  mode?: string;\n  update?: boolean;\n  watch?: boolean;\n  clusterOnly?: boolean;\n  viz: boolean; // commander negatable --no-viz -> options.viz\n  svg?: boolean;\n  graphml?: boolean;\n  neo4j?: boolean;\n  mcp?: boolean;\n  install: boolean; // commander negatable --no-install -> options.install\n  leiden?: boolean;\n  maxIterations?: number;\n  mysql?: string;\n}\n\nfunction looksLikeGitUrl(value: string): boolean {\n  if (!/^https?:\\/\\//i.test(value)) return false;\n  return /github\\.com|gitlab\\.com|bitbucket\\.org/i.test(value) || value.endsWith('.git');\n}\n\n/** Clone `url` into a fresh temp directory using an argv-array child_process call (never shell: true, never a shell string built from input). */\nasync function cloneRepo(url: string): Promise<string> {\n  const validated = validateUrl(url);\n  const dest = await fs.mkdtemp(path.join(os.tmpdir(), 'graphify-clone-'));\n  await execFileAsync('git', ['clone', '--depth', '1', validated, dest]);\n  return dest;\n}\n\nfunction exportOptionsFrom(options: DefaultCommandOptions) {\n  return { html: options.viz, svg: options.svg, graphml: options.graphml, neo4j: options.neo4j };\n}\n\nfunction clusterOptionsFrom(options: DefaultCommandOptions) {\n  return {\n    algorithm: options.leiden ? ('leiden' as const) : ('louvain' as const),\n    maxIterations: options.maxIterations,\n  };\n}\n\nasync function runClusterOnly(root: string, options: DefaultCommandOptions): Promise<void> {\n  const outDir = path.join(root, 'graphify-out');\n  const graph = await loadGraph(outDir);\n  cluster(graph, clusterOptionsFrom(options));\n  const analysis = analyze(graph);\n  const report = renderReport(graph, analysis);\n  await exportGraph(graph, { outDir, ...exportOptionsFrom(options) }, report);\n  console.error(`Re-clustered the existing graph (${clusterOptionsFrom(options).algorithm}).`);\n}\n\n/** Watch `root` (ignoring graphify-out/, node_modules/, .git/) and re-run `runOnce` on any change, debounced. Never resolves — the process stays alive until interrupted, matching normal watch-mode CLI behavior. */\nasync function watchAndRebuild(root: string, runOnce: () => Promise<unknown>): Promise<void> {\n  const watcher = watchFiles(root, {\n    ignored: (filePath: string) => /(^|[/\\\\])(node_modules|\\.git|graphify-out)([/\\\\]|$)/.test(filePath),\n    ignoreInitial: true,\n  });\n\n  let timer: ReturnType<typeof setTimeout> | null = null;\n  let running = false;\n  const schedule = (): void => {\n    if (timer) clearTimeout(timer);\n    timer = setTimeout(() => {\n      if (running) return;\n      running = true;\n      console.error('Change detected, rebuilding...');\n      runOnce()\n        .catch((error: unknown) => console.error(`graphify --watch: rebuild failed: ${(error as Error).message}`))\n        .finally(() => {\n          running = false;\n        });\n    }, 300);\n  };\n\n  watcher.on('add', schedule).on('change', schedule).on('unlink', schedule);\n\n  await new Promise<never>(() => {\n    /* keep the process alive until the user interrupts it (Ctrl+C) */\n  });\n}\n\nconst program = new Command();\n\nprogram\n  .name('graphify')\n  .description('Turn a folder of code/docs/papers into a queryable knowledge graph.')\n  .argument('[path]', 'path to scan, or a GitHub URL', '.')\n  .option('--mode <mode>', 'extraction mode (deep for richer INFERRED edges — reserved, no-op in v1)')\n  .option('--update', 'incremental rebuild — reuse cached extractions for unchanged files')\n  .option('--watch', 'rebuild on file change')\n  .option('--cluster-only', 'rerun clustering on an existing graph')\n  .option('--leiden', 'use Leiden instead of Louvain for community detection (v2 — better community quality)')\n  .option('--max-iterations <n>', 'Leiden only: cap on outer iterations for very large graphs', Number)\n  .option('--no-viz', 'skip graph.html')\n  .option('--svg', 'also export graph.svg (not implemented in v1)')\n  .option('--graphml', 'also export graph.graphml (not implemented in v1)')\n  .option('--neo4j', 'generate graphify-out/cypher.txt for Neo4j (not implemented in v1)')\n  .option('--mcp', 'start MCP stdio server instead of running the pipeline')\n  .option('--no-install', 'skip auto-installing the agent skill + MCP config after the build')\n  .option('--mysql <dsn>', 'also extract a MySQL schema (mysql://user:pass@host:port/db) into the graph')\n  .action(async (targetArg: string, options: DefaultCommandOptions) => {\n    try {\n      if (options.mcp) {\n        const outDir = path.resolve(targetArg === '.' ? process.cwd() : targetArg, 'graphify-out');\n        const { startServer } = await import('../mcp/server.js');\n        await startServer(path.join(outDir, 'graph.json'));\n        return;\n      }\n\n      let root = targetArg;\n      const cloned = looksLikeGitUrl(targetArg);\n      if (cloned) {\n        console.error(`Cloning ${targetArg} ...`);\n        root = await cloneRepo(targetArg);\n      }\n      root = path.resolve(root);\n\n      if (options.mode) {\n        console.error(`--mode ${options.mode} is reserved for a future richer-INFERRED-edges pass — currently a no-op.`);\n      }\n\n      if (options.clusterOnly) {\n        await runClusterOnly(root, options);\n        return;\n      }\n\n      let extraExtractions: ExtractionResult[] | undefined;\n      if (options.mysql) {\n        const { extractMysql } = await import('../extractors/mysql.js');\n        console.error(`Extracting MySQL schema from ${validateDsn(options.mysql).safeDisplay} ...`);\n        extraExtractions = [await extractMysql(options.mysql)];\n      }\n\n      const runOnce = () =>\n        runPipeline(root, {\n          ...exportOptionsFrom(options),\n          ...clusterOptionsFrom(options),\n          extraExtractions,\n          update: options.update,\n          onProgress: (m) => console.error(m),\n        });\n      await runOnce();\n\n      // Make the graph instantly usable by AI agents: install the skill and\n      // register the project-scoped MCP server for whichever hosts this\n      // project uses. Skipped for cloned URLs (the clone lives in a temp\n      // dir) and with --no-install; a failure here never fails the build.\n      if (options.install && !cloned) {\n        try {\n          await runInstall(await detectPlatforms(root), root);\n        } catch (error) {\n          console.error(`graphify: agent skill/MCP install skipped: ${(error as Error).message}`);\n        }\n      }\n\n      if (options.watch) {\n        console.error(`Watching ${root} for changes (Ctrl+C to stop) ...`);\n        await watchAndRebuild(root, runOnce);\n      }\n    } catch (error) {\n      console.error(`graphify: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('query <question>')\n  .description('BFS (default) or DFS traversal answering a question against the existing graph')\n  .option('--dfs', 'depth-first traversal (trace a specific path)')\n  .option('--budget <tokens>', 'cap answer at N tokens', Number)\n  .action(async (question: string, options: { dfs?: boolean; budget?: number }) => {\n    try {\n      await runQuery(question, options);\n    } catch (error) {\n      console.error(`graphify query: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('path <from> <to>')\n  .description('shortest path between two named nodes')\n  .action(async (from: string, to: string) => {\n    try {\n      await runPath(from, to);\n    } catch (error) {\n      console.error(`graphify path: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('explain <node>')\n  .description('plain-language explanation of a node')\n  .action(async (node: string) => {\n    try {\n      await runExplain(node);\n    } catch (error) {\n      console.error(`graphify explain: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('affected <node>')\n  .description('reverse impact analysis — everything that (transitively) depends on a node')\n  .option('--depth <n>', 'how many reverse hops to follow (default 3)', Number)\n  .option('--limit <n>', 'cap on affected nodes reported (default 200)', Number)\n  .action(async (node: string, options: { depth?: number; limit?: number }) => {\n    try {\n      await runAffected(node, options);\n    } catch (error) {\n      console.error(`graphify affected: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('context <task>')\n  .description('token-budgeted working-set pack — the actual code for a task, in one call')\n  .option('--budget <tokens>', 'approximate token cap for the pack (default 4000)', Number)\n  .action(async (task: string, options: { budget?: number }) => {\n    try {\n      await runContext(task, options);\n    } catch (error) {\n      console.error(`graphify context: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('tests [node]')\n  .description('structural test selection — the minimal test files worth running for a change')\n  .option('--changed [rev]', 'select for the working-tree diff (optionally vs a revision) instead of a node')\n  .action(async (node: string | undefined, options: { changed?: string | boolean }) => {\n    try {\n      await runTests(node, options);\n    } catch (error) {\n      console.error(`graphify tests: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('review <base> [head]')\n  .description('structural review between two git revisions: added/removed/rewired symbols with blast radius + tests')\n  .action(async (base: string, head?: string) => {\n    try {\n      await runReview(base, head);\n    } catch (error) {\n      console.error(`graphify review: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('check')\n  .description('check the graph against dependency rules (graphify.rules.json) — exits 1 on violations')\n  .option('--rules <file>', 'rules file (default ./graphify.rules.json)')\n  .action(async (options: { rules?: string }) => {\n    try {\n      await runCheck(options);\n    } catch (error) {\n      console.error(`graphify check: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('benchmark [questions...]')\n  .description('measure token savings of graph answers vs reading the files they touch')\n  .action(async (questions: string[]) => {\n    try {\n      await runBenchmark(questions);\n    } catch (error) {\n      console.error(`graphify benchmark: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('install')\n  .description('install the skill/rules files + project MCP config into local agents (claude, cursor, windsurf, cline, agents, gemini, all)')\n  .option('--platform <names...>', 'platform(s) to install for', ['claude'])\n  .action(async (options: { platform: string[] }) => {\n    try {\n      await runInstall(options.platform);\n    } catch (error) {\n      console.error(`graphify install: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nconst globalCommand = program\n  .command('global')\n  .description('manage the cross-project global graph (registry at ~/.graphify/global.json)');\n\nglobalCommand\n  .command('add [path]')\n  .description('register a project (must already have graphify-out/graph.json)')\n  .action(async (target?: string) => {\n    try {\n      await runGlobalAdd(target);\n    } catch (error) {\n      console.error(`graphify global add: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nglobalCommand\n  .command('remove <name>')\n  .description('unregister a project by name')\n  .action(async (name: string) => {\n    try {\n      await runGlobalRemove(name);\n    } catch (error) {\n      console.error(`graphify global remove: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nglobalCommand\n  .command('list')\n  .description('list registered projects')\n  .action(async () => {\n    try {\n      await runGlobalList();\n    } catch (error) {\n      console.error(`graphify global list: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nglobalCommand\n  .command('build')\n  .description('merge every registered project into one global graph')\n  .option('--out <dir>', 'output directory (default ~/.graphify/global-out)')\n  .action(async (options: { out?: string }) => {\n    try {\n      await runGlobalBuild(options);\n    } catch (error) {\n      console.error(`graphify global build: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('merge <dirs...>')\n  .description('one-shot merge of two or more built project graphs into one')\n  .option('--out <dir>', 'output directory (default ./graphify-merged)')\n  .action(async (dirs: string[], options: { out?: string }) => {\n    try {\n      await runMerge(dirs, options);\n    } catch (error) {\n      console.error(`graphify merge: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('save-result')\n  .description('save a Q&A result to graphify-out/memory/ for the graph feedback loop')\n  .requiredOption('--question <q>', 'the question that was asked')\n  .requiredOption('--answer <a>', 'the answer that was given')\n  .option('--nodes <ids...>', 'node ids/labels cited in the answer', [])\n  .option('--type <t>', 'query|path|explain|affected', 'query')\n  .option('--outcome <o>', 'useful|dead_end|corrected', 'useful')\n  .option('--correction <text>', 'what the right answer was (pairs with --outcome corrected)')\n  .action(async (options: {\n    question: string;\n    answer: string;\n    nodes: string[];\n    type: string;\n    outcome: string;\n    correction?: string;\n  }) => {\n    try {\n      const memoryDir = path.join(process.cwd(), 'graphify-out', 'memory');\n      const file = await saveResult(\n        {\n          question: options.question,\n          answer: options.answer,\n          nodes: options.nodes,\n          type: options.type as ResultType,\n          outcome: options.outcome as ResultOutcome,\n          correction: options.correction,\n        },\n        memoryDir,\n      );\n      console.log(`Saved -> ${file}`);\n    } catch (error) {\n      console.error(`graphify save-result: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('reflect')\n  .description('aggregate graphify-out/memory/ into a recency-weighted lessons doc')\n  .option('--half-life-days <n>', 'a result loses half its weight every N days (default 30)', Number)\n  .option('--out <file>', 'output path (default graphify-out/reflections/LESSONS.md)')\n  .action(async (options: { halfLifeDays?: number; out?: string }) => {\n    try {\n      const memoryDir = path.join(process.cwd(), 'graphify-out', 'memory');\n      const results = await loadResults(memoryDir);\n      const lessons = renderLessons(results, { halfLifeDays: options.halfLifeDays });\n      const outPath = path.resolve(options.out ?? path.join(process.cwd(), 'graphify-out', 'reflections', 'LESSONS.md'));\n      await fs.mkdir(path.dirname(outPath), { recursive: true });\n      await fs.writeFile(outPath, lessons, 'utf-8');\n      console.log(`Reflected ${results.length} result(s) -> ${outPath}`);\n    } catch (error) {\n      console.error(`graphify reflect: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nconst hookCommand = program\n  .command('hook')\n  .description('manage the git hooks that auto-rebuild the graph on commit/pull');\n\nhookCommand\n  .command('install')\n  .description('install post-commit and post-merge hooks (preserves existing hook content)')\n  .action(async () => {\n    try {\n      await runHookInstall();\n    } catch (error) {\n      console.error(`graphify hook install: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nhookCommand\n  .command('uninstall')\n  .description('remove the graphify block from the git hooks')\n  .action(async () => {\n    try {\n      await runHookUninstall();\n    } catch (error) {\n      console.error(`graphify hook uninstall: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram.parseAsync(process.argv);\n","import { loadGraph } from '../../graphStore.js';\nimport { affectedBy } from '../../impact.js';\n\nexport interface AffectedOptions {\n  depth?: number;\n  limit?: number;\n}\n\n/** Reverse impact analysis: everything that (transitively) depends on the named node. */\nexport async function runAffected(nodeName: string, options: AffectedOptions = {}): Promise<void> {\n  const graph = await loadGraph();\n  const result = affectedBy(graph, nodeName, { maxDepth: options.depth, limit: options.limit });\n\n  if (!result) {\n    console.log(`No node matched \"${nodeName}\".`);\n    return;\n  }\n\n  console.log(`Impact of changing ${result.target.label} (${result.target.id}):`);\n\n  if (result.affected.length === 0) {\n    console.log('  Nothing in the graph depends on it — no incoming dependency edges.');\n    return;\n  }\n\n  let currentDepth = 0;\n  for (const node of result.affected) {\n    if (node.depth !== currentDepth) {\n      currentDepth = node.depth;\n      console.log('');\n      console.log(currentDepth === 1 ? 'Directly affected:' : `Affected at depth ${currentDepth}:`);\n    }\n    const isPlaceholder =\n      node.sourceFile === '<unknown>' || node.sourceFile === '<external>' || node.sourceFile === '';\n    const where = isPlaceholder\n      ? '(reference only)'\n      : `${node.sourceFile}${node.sourceLocation ? `:${node.sourceLocation}` : ''}`;\n    console.log(\n      `  ${node.label} — ${where} ` +\n        `(--${node.via.relation}--> ${node.via.dependsOn}, ${node.via.confidence})`,\n    );\n  }\n\n  console.log('');\n  const { EXTRACTED, INFERRED, AMBIGUOUS } = result.byConfidence;\n  console.log(\n    `Blast radius: ${result.affected.length} node(s) within ${result.maxDepth} hop(s) — ` +\n      `${EXTRACTED} certain (EXTRACTED), ${INFERRED} likely (INFERRED), ${AMBIGUOUS} uncertain (AMBIGUOUS).`,\n  );\n  if (result.truncated) {\n    console.log('(List truncated — raise --limit to see more.)');\n  }\n}\n","import * as fs from 'node:fs/promises';\nimport type Graph from 'graphology';\nimport { loadGraph } from '../../graphStore.js';\nimport { queryGraph } from '../../query.js';\nimport { isTestFile } from '../../testmap.js';\n\n/**\n * `graphify benchmark` — measure the token savings of answering through the\n * graph instead of reading source files. For each question it compares the\n * serialized size of the graph answer against the size of every source file\n * that answer's nodes live in (the \"just read the relevant files\" baseline\n * an agent without the graph would pay). Chars/4 is the usual token\n * approximation, applied to both sides so the ratio is fair.\n */\n\nexport interface BenchmarkRow {\n  question: string;\n  graphTokens: number;\n  naiveTokens: number;\n  /** naive / graph — how many times cheaper the graph answer is. */\n  reduction: number;\n  filesRead: number;\n  filesMissing: number;\n}\n\nexport type FileReader = (path: string) => Promise<string>;\n\nconst tokensOf = (text: string): number => Math.ceil(text.length / 4);\n\nexport async function benchmarkQuestion(\n  graph: Graph,\n  question: string,\n  readFile: FileReader,\n): Promise<BenchmarkRow> {\n  const result = queryGraph(graph, question);\n  // Compact JSON, matching how queryGraph's own token budget measures itself.\n  const graphTokens = tokensOf(JSON.stringify(result));\n\n  const sourceFiles = new Set<string>();\n  for (const node of result.visited) {\n    if (node.sourceFile && !node.sourceFile.startsWith('<') && !node.sourceFile.includes('://')) {\n      sourceFiles.add(node.sourceFile);\n    }\n  }\n\n  let naiveTokens = 0;\n  let filesRead = 0;\n  let filesMissing = 0;\n  for (const file of [...sourceFiles].sort((a, b) => a.localeCompare(b))) {\n    try {\n      naiveTokens += tokensOf(await readFile(file));\n      filesRead++;\n    } catch {\n      filesMissing++;\n    }\n  }\n\n  return {\n    question,\n    graphTokens,\n    naiveTokens,\n    reduction: graphTokens > 0 && naiveTokens > 0 ? naiveTokens / graphTokens : 0,\n    filesRead,\n    filesMissing,\n  };\n}\n\n/** Files no agent would ask a \"how does X work\" question about — build config, examples, scripts, docs. */\nconst NON_QUESTION_FILE =\n  /(^|\\/)(examples?|scripts?|bench(?:mark)?s?|fixtures?|docs?|\\.github)\\/|\\.(config|conf)\\.[^/]+$|(^|\\/)(rollup|webpack|vite|vitest|jest|babel|tsup|eslint|prettier)\\.[^/]*$/i;\n\n/**\n * Default questions when none are given: the labels of the highest-degree\n * (most load-bearing) SOURCE entities. Tests, build config, and examples\n * are excluded — they score high on degree but are questions no agent\n * would ask, and they drag the measured reduction down unfairly.\n */\nexport function defaultQuestions(graph: Graph, count = 5): string[] {\n  const entries = [...graph.nodes()]\n    .map((id) => ({\n      id,\n      degree: graph.degree(id),\n      label: (graph.getNodeAttribute(id, 'label') as string | undefined) ?? id,\n      file: (graph.getNodeAttribute(id, 'sourceFile') as string | undefined) ?? '',\n    }))\n    // File nodes score high on degree but make poor questions — prefer entities.\n    .filter((e) => e.id.includes('::'))\n    .filter((e) => !isTestFile(e.file) && !NON_QUESTION_FILE.test(e.file))\n    .sort((a, b) => b.degree - a.degree || a.id.localeCompare(b.id));\n  return entries.slice(0, count).map((e) => `how does ${e.label} work`);\n}\n\nexport async function runBenchmark(questions: string[]): Promise<BenchmarkRow[]> {\n  const graph = await loadGraph();\n  const effective = questions.length > 0 ? questions : defaultQuestions(graph);\n  if (effective.length === 0) {\n    console.log('The graph has no entity nodes to benchmark against — build it first.');\n    return [];\n  }\n\n  const rows: BenchmarkRow[] = [];\n  for (const question of effective) {\n    rows.push(await benchmarkQuestion(graph, question, (p) => fs.readFile(p, 'utf-8')));\n  }\n\n  console.log('Token cost per question — graph answer vs reading the files it touches:\\n');\n  for (const row of rows) {\n    const reduction = row.reduction > 0 ? `${row.reduction.toFixed(1)}x` : 'n/a';\n    console.log(`  \"${row.question}\"`);\n    console.log(\n      `    graph: ~${row.graphTokens} tokens | files: ~${row.naiveTokens} tokens ` +\n        `(${row.filesRead} file(s)${row.filesMissing ? `, ${row.filesMissing} unreadable` : ''}) | reduction: ${reduction}`,\n    );\n  }\n\n  const scored = rows.filter((r) => r.reduction > 0);\n  if (scored.length > 0) {\n    const avg = scored.reduce((s, r) => s + r.reduction, 0) / scored.length;\n    console.log(`\\nAverage reduction: ${avg.toFixed(1)}x across ${scored.length} question(s).`);\n  } else {\n    console.log('\\nNo reduction could be measured — run from the project root so source files are readable.');\n  }\n  return rows;\n}\n","import * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport { checkRules, validateRules } from '../../check.js';\nimport { loadGraph } from '../../graphStore.js';\n\nexport interface CheckCommandOptions {\n  rules?: string;\n}\n\n/**\n * Check the graph against declared dependency rules. Exits non-zero on\n * violations so CI (and agents verifying their own edits) can gate on it.\n */\nexport async function runCheck(options: CheckCommandOptions = {}): Promise<void> {\n  const rulesPath = path.resolve(options.rules ?? 'graphify.rules.json');\n  let raw: string;\n  try {\n    raw = await fs.readFile(rulesPath, 'utf-8');\n  } catch {\n    throw new Error(\n      `No rules file at ${rulesPath} — create graphify.rules.json with ` +\n        '{ \"rules\": [{ \"name\": \"...\", \"from\": \"src/a/**\", \"disallow\": [\"src/b/**\"] }] }.',\n    );\n  }\n  const config = validateRules(JSON.parse(raw));\n\n  const graph = await loadGraph();\n  const violations = checkRules(graph, config);\n\n  if (violations.length === 0) {\n    console.log(`OK — ${config.rules.length} rule(s), no violations.`);\n    return;\n  }\n\n  console.log(`${violations.length} violation(s):`);\n  for (const v of violations) {\n    console.log(`  [${v.rule}] ${v.fromNode} --${v.relation}--> ${v.toNode}`);\n    console.log(`    ${v.fromFile} must not depend on ${v.toFile}${v.reason ? ` — ${v.reason}` : ''}`);\n  }\n  process.exitCode = 1;\n}\n","import * as fs from 'node:fs/promises';\nimport { buildContextPack, renderContextPack } from '../../context.js';\nimport { loadGraph } from '../../graphStore.js';\n\nexport interface ContextCommandOptions {\n  budget?: number;\n}\n\n/** Token-budgeted working-set pack: the actual code an agent needs for a task, in one call. */\nexport async function runContext(task: string, options: ContextCommandOptions = {}): Promise<void> {\n  const graph = await loadGraph();\n  const pack = await buildContextPack(graph, task, (p) => fs.readFile(p, 'utf-8'), {\n    tokenBudget: options.budget,\n  });\n  console.log(renderContextPack(pack));\n}\n","import { loadGraph } from '../../graphStore.js';\nimport { explainNode } from '../../query.js';\n\n/** Plain-language explanation of a single node. */\nexport async function runExplain(nodeName: string): Promise<void> {\n  const graph = await loadGraph();\n  const result = explainNode(graph, nodeName);\n\n  if (!result) {\n    console.log(`No node matched \"${nodeName}\".`);\n    return;\n  }\n\n  console.log(result.label);\n  if (result.sourceFile === '<unknown>' || result.sourceFile === '<external>' || result.sourceFile === '') {\n    // Auto-vivified endpoint (re-export alias / unresolved reference) — it\n    // has no source of its own, so \"<unknown>:L0\" would read like a bug.\n    console.log('  location: (reference only — no declaration seen; check its outgoing edges for the real definition)');\n  } else {\n    const location = result.sourceLocation ? `:${result.sourceLocation}` : '';\n    console.log(`  location: ${result.sourceFile}${location}`);\n  }\n  if (result.communityLabel) {\n    console.log(`  community: ${result.communityLabel}`);\n  }\n\n  console.log('');\n  console.log(`Calls / references out (${result.outgoing.length}):`);\n  if (result.outgoing.length === 0) {\n    console.log('  (none)');\n  } else {\n    for (const edge of result.outgoing) {\n      console.log(`  --${edge.relation}--> ${edge.target} (${edge.confidence})`);\n    }\n  }\n\n  console.log('');\n  console.log(`Referenced by (${result.incoming.length}):`);\n  if (result.incoming.length === 0) {\n    console.log('  (none)');\n  } else {\n    for (const edge of result.incoming) {\n      console.log(`  ${edge.source} --${edge.relation}--> (${edge.confidence})`);\n    }\n  }\n}\n","import { renderReview, reviewRevisions } from '../../diff.js';\n\n/** Structural review between two git revisions (head defaults to HEAD). */\nexport async function runReview(base: string, head?: string): Promise<void> {\n  const diff = await reviewRevisions(process.cwd(), base, head ?? 'HEAD');\n  console.log(renderReview(diff));\n}\n","import { execFile } from 'node:child_process';\nimport { promisify } from 'node:util';\nimport { loadGraph } from '../../graphStore.js';\nimport { testsForChangedFiles, testsForNode } from '../../testmap.js';\n\nconst execFileAsync = promisify(execFile);\n\nexport interface TestsCommandOptions {\n  /** Select tests for the working-tree diff (optionally against a rev) instead of a named node. */\n  changed?: string | boolean;\n}\n\n/** Structural test selection: the minimal test files worth running for a change. */\nexport async function runTests(nodeQuery: string | undefined, options: TestsCommandOptions = {}): Promise<void> {\n  const graph = await loadGraph();\n\n  let selection;\n  if (options.changed !== undefined && options.changed !== false) {\n    const args = ['diff', '--name-only'];\n    if (typeof options.changed === 'string') args.push(options.changed);\n    const { stdout } = await execFileAsync('git', args);\n    const changedFiles = stdout.split('\\n').map((l) => l.trim()).filter(Boolean);\n    if (changedFiles.length === 0) {\n      console.log('No changed files in the diff.');\n      return;\n    }\n    selection = testsForChangedFiles(graph, changedFiles);\n  } else if (nodeQuery) {\n    selection = testsForNode(graph, nodeQuery);\n    if (!selection) {\n      console.log(`No node matched \"${nodeQuery}\".`);\n      return;\n    }\n  } else {\n    console.log('Provide a node to select tests for, or --changed for the working-tree diff.');\n    return;\n  }\n\n  if (selection.testFiles.length === 0) {\n    console.log(\n      `No test files found in the blast radius of ${selection.target} ` +\n        `(${selection.affectedNodeCount} affected node(s) checked) — either it's untested or the tests ` +\n        'reach it through a path the graph does not capture.',\n    );\n    return;\n  }\n\n  const how =\n    selection.precision === 'usage'\n      ? 'selected by actual usage (calls/inheritance)'\n      : 'selected by import reachability — may over-include files sharing an entry point';\n  console.log(`Test files for ${selection.target} (${how}; most direct first):`);\n  for (const test of selection.testFiles) {\n    const via = test.depth === 0 ? test.via : `depth ${test.depth}, via ${test.via}`;\n    console.log(`  ${test.file}  (${via})`);\n  }\n}\n","import * as fs from 'node:fs/promises';\nimport * as os from 'node:os';\nimport * as path from 'node:path';\nimport { analyze } from '../../analyze.js';\nimport { cluster } from '../../cluster.js';\nimport { exportGraph } from '../../export.js';\nimport { loadGraph } from '../../graphStore.js';\nimport { mergeGraphs, type MergeEntry } from '../../merge.js';\nimport { renderReport } from '../../report.js';\n\n/**\n * `graphify global add|remove|list|build` — a registry of projects whose\n * built graphs get merged into one global cross-project graph, plus the\n * one-shot `graphify merge <dir...>` for merging without a registry.\n * The registry lives at ~/.graphify/global.json; the merged output defaults\n * to ~/.graphify/global-out/.\n */\n\nexport interface GlobalRegistry {\n  projects: Array<{ name: string; root: string }>;\n}\n\nfunction registryDir(): string {\n  return path.join(os.homedir(), '.graphify');\n}\n\nfunction registryPath(): string {\n  return path.join(registryDir(), 'global.json');\n}\n\nasync function readRegistry(): Promise<GlobalRegistry> {\n  try {\n    const raw = await fs.readFile(registryPath(), 'utf-8');\n    const parsed: unknown = JSON.parse(raw);\n    const projects = (parsed as GlobalRegistry).projects;\n    if (!Array.isArray(projects)) return { projects: [] };\n    return { projects: projects.filter((p) => typeof p?.name === 'string' && typeof p?.root === 'string') };\n  } catch {\n    return { projects: [] };\n  }\n}\n\nasync function writeRegistry(registry: GlobalRegistry): Promise<void> {\n  await fs.mkdir(registryDir(), { recursive: true });\n  await fs.writeFile(registryPath(), JSON.stringify(registry, null, 2), 'utf-8');\n}\n\n/** Project name for a root: its package.json \"name\" if present, else the directory basename. */\nasync function projectNameFor(root: string): Promise<string> {\n  try {\n    const raw = await fs.readFile(path.join(root, 'package.json'), 'utf-8');\n    const name = (JSON.parse(raw) as { name?: unknown }).name;\n    if (typeof name === 'string' && name.length > 0) return name;\n  } catch {\n    // no package.json — fall through to the basename\n  }\n  return path.basename(root);\n}\n\nexport async function runGlobalAdd(target: string = '.'): Promise<void> {\n  const root = path.resolve(target);\n  const graphJson = path.join(root, 'graphify-out', 'graph.json');\n  try {\n    await fs.access(graphJson);\n  } catch {\n    throw new Error(`${root} has no graphify-out/graph.json — run \\`graphify ${target}\\` first, then add it.`);\n  }\n\n  const name = await projectNameFor(root);\n  const registry = await readRegistry();\n\n  const existing = registry.projects.find((p) => p.name === name);\n  if (existing) {\n    if (existing.root === root) {\n      console.log(`${name} is already registered (${root}).`);\n      return;\n    }\n    throw new Error(\n      `A different project is already registered as \"${name}\" (${existing.root}). ` +\n        'Remove it first with `graphify global remove`.',\n    );\n  }\n\n  registry.projects.push({ name, root });\n  registry.projects.sort((a, b) => a.name.localeCompare(b.name));\n  await writeRegistry(registry);\n  console.log(`Registered ${name} (${root}). ${registry.projects.length} project(s) in the global graph.`);\n}\n\nexport async function runGlobalRemove(name: string): Promise<void> {\n  const registry = await readRegistry();\n  const before = registry.projects.length;\n  registry.projects = registry.projects.filter((p) => p.name !== name);\n  if (registry.projects.length === before) {\n    throw new Error(`No project named \"${name}\" is registered. See \\`graphify global list\\`.`);\n  }\n  await writeRegistry(registry);\n  console.log(`Removed ${name}. ${registry.projects.length} project(s) remain.`);\n}\n\nexport async function runGlobalList(): Promise<void> {\n  const registry = await readRegistry();\n  if (registry.projects.length === 0) {\n    console.log('No projects registered. Add one with `graphify global add <path>`.');\n    return;\n  }\n  for (const project of registry.projects) {\n    console.log(`${project.name}  ${project.root}`);\n  }\n}\n\n/** Load every entry's graph, skipping (with a warning) the ones that fail — one broken project must not sink the merge. */\nasync function loadEntries(sources: Array<{ name: string; outDir: string }>): Promise<MergeEntry[]> {\n  const entries: MergeEntry[] = [];\n  for (const source of sources) {\n    try {\n      entries.push({ name: source.name, graph: await loadGraph(source.outDir) });\n    } catch (error) {\n      console.warn(`Skipping ${source.name}: ${(error as Error).message}`);\n    }\n  }\n  return entries;\n}\n\nasync function mergeAndExport(entries: MergeEntry[], outDir: string): Promise<void> {\n  if (entries.length === 0) {\n    throw new Error('Nothing to merge — no project graphs could be loaded.');\n  }\n\n  const merged = mergeGraphs(entries);\n  cluster(merged);\n  const analysis = analyze(merged);\n  const report = renderReport(merged, analysis);\n  await exportGraph(merged, { outDir }, report);\n\n  console.log(\n    `Merged ${entries.length} project(s) into ${outDir} — ` +\n      `${merged.order} node(s), ${merged.size} edge(s).`,\n  );\n}\n\nexport async function runGlobalBuild(options: { out?: string } = {}): Promise<void> {\n  const registry = await readRegistry();\n  if (registry.projects.length === 0) {\n    throw new Error('No projects registered. Add some with `graphify global add <path>` first.');\n  }\n\n  const entries = await loadEntries(\n    registry.projects.map((p) => ({ name: p.name, outDir: path.join(p.root, 'graphify-out') })),\n  );\n  await mergeAndExport(entries, path.resolve(options.out ?? path.join(registryDir(), 'global-out')));\n}\n\n/** One-shot merge of two or more project directories, no registry involved. */\nexport async function runMerge(targets: string[], options: { out?: string } = {}): Promise<void> {\n  if (targets.length < 2) {\n    throw new Error('Provide at least two project directories to merge.');\n  }\n\n  const sources: Array<{ name: string; outDir: string }> = [];\n  for (const target of targets) {\n    const root = path.resolve(target);\n    sources.push({ name: await projectNameFor(root), outDir: path.join(root, 'graphify-out') });\n  }\n\n  const names = sources.map((s) => s.name);\n  const duplicate = names.find((name, i) => names.indexOf(name) !== i);\n  if (duplicate !== undefined) {\n    throw new Error(`Two of the given projects resolve to the same name (\"${duplicate}\") — rename one.`);\n  }\n\n  const entries = await loadEntries(sources);\n  await mergeAndExport(entries, path.resolve(options.out ?? 'graphify-merged'));\n}\n","import * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\n\n/**\n * `graphify hook install` / `graphify hook uninstall` — auto-rebuild the\n * graph after commits and pulls, mirroring the Python original's\n * `hook install`. The hook body lives inside a marked block so we can\n * coexist with (and later cleanly remove ourselves from) hooks the user\n * already has; we never overwrite or delete anything outside our markers.\n */\n\nconst MARKER_BEGIN = '# >>> graphify >>>';\nconst MARKER_END = '# <<< graphify <<<';\n\n/** post-commit: rebuild after each commit. post-merge: rebuild after pull/merge. */\nconst HOOK_NAMES = ['post-commit', 'post-merge'] as const;\n\nconst HOOK_BLOCK = `${MARKER_BEGIN}\n# Rebuild the graphify knowledge graph in the background so the hook never\n# slows down the commit. Errors are silenced — a failed rebuild should never\n# break a git operation. Installed by \\`graphify hook install\\`.\n(graphify . --update --no-viz >/dev/null 2>&1 &)\n${MARKER_END}`;\n\nexport interface HookResult {\n  hook: string;\n  path: string;\n  action: 'created' | 'appended' | 'already-installed' | 'removed' | 'not-installed';\n}\n\nasync function hooksDir(cwd: string): Promise<string> {\n  const gitDir = path.join(cwd, '.git');\n  let stats;\n  try {\n    stats = await fs.stat(gitDir);\n  } catch {\n    throw new Error(`${cwd} is not a git repository (no .git directory) — run this from the repo root.`);\n  }\n  if (!stats.isDirectory()) {\n    // .git can be a file in worktrees/submodules (\"gitdir: <path>\") — follow it.\n    const content = (await fs.readFile(gitDir, 'utf-8')).trim();\n    const match = /^gitdir:\\s*(.+)$/.exec(content);\n    if (!match) throw new Error(`${gitDir} exists but is neither a directory nor a gitdir pointer.`);\n    return path.resolve(cwd, match[1] as string, 'hooks');\n  }\n  return path.join(gitDir, 'hooks');\n}\n\n/** Install the marked graphify block into post-commit and post-merge, preserving any existing hook content. */\nexport async function runHookInstall(cwd: string = process.cwd()): Promise<HookResult[]> {\n  const dir = await hooksDir(cwd);\n  await fs.mkdir(dir, { recursive: true });\n\n  const results: HookResult[] = [];\n  for (const hook of HOOK_NAMES) {\n    const hookPath = path.join(dir, hook);\n    let existing: string | null = null;\n    try {\n      existing = await fs.readFile(hookPath, 'utf-8');\n    } catch {\n      // no existing hook — we'll create it\n    }\n\n    if (existing === null) {\n      await fs.writeFile(hookPath, `#!/bin/sh\\n${HOOK_BLOCK}\\n`, { mode: 0o755 });\n      results.push({ hook, path: hookPath, action: 'created' });\n    } else if (existing.includes(MARKER_BEGIN)) {\n      results.push({ hook, path: hookPath, action: 'already-installed' });\n    } else {\n      const separator = existing.endsWith('\\n') ? '' : '\\n';\n      await fs.writeFile(hookPath, `${existing}${separator}${HOOK_BLOCK}\\n`, 'utf-8');\n      await fs.chmod(hookPath, 0o755);\n      results.push({ hook, path: hookPath, action: 'appended' });\n    }\n  }\n\n  for (const result of results) {\n    console.log(`${result.hook}: ${result.action} (${result.path})`);\n  }\n  console.log('');\n  console.log('The graph will rebuild in the background after each commit and pull.');\n  console.log('Remove with `graphify hook uninstall`.');\n  return results;\n}\n\n/** Remove only the marked graphify block; delete the hook file if nothing else is left in it. */\nexport async function runHookUninstall(cwd: string = process.cwd()): Promise<HookResult[]> {\n  const dir = await hooksDir(cwd);\n\n  const results: HookResult[] = [];\n  for (const hook of HOOK_NAMES) {\n    const hookPath = path.join(dir, hook);\n    let existing: string | null = null;\n    try {\n      existing = await fs.readFile(hookPath, 'utf-8');\n    } catch {\n      // nothing installed\n    }\n\n    if (existing === null || !existing.includes(MARKER_BEGIN)) {\n      results.push({ hook, path: hookPath, action: 'not-installed' });\n      continue;\n    }\n\n    const blockPattern = new RegExp(`\\\\n?${MARKER_BEGIN}[\\\\s\\\\S]*?${MARKER_END}\\\\n?`);\n    const remaining = existing.replace(blockPattern, '\\n').trim();\n\n    if (remaining === '' || remaining === '#!/bin/sh') {\n      await fs.unlink(hookPath);\n    } else {\n      await fs.writeFile(hookPath, `${remaining}\\n`, 'utf-8');\n    }\n    results.push({ hook, path: hookPath, action: 'removed' });\n  }\n\n  for (const result of results) {\n    console.log(`${result.hook}: ${result.action}`);\n  }\n  return results;\n}\n","import { createRequire } from 'node:module';\nimport * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\n\nconst require = createRequire(import.meta.url);\n\n/**\n * Resolve this package's own root directory, whether we're running from\n * source (tests/dev), the built dist/ bundle, or installed as a real\n * dependency elsewhere. Uses Node's self-reference resolution (walking up\n * from this module's location to the nearest package.json named\n * \"@dreamtree-org/graphify\") rather than a hardcoded relative path, since\n * the number of directories between this file and the package root\n * differs between src/ and the bundled dist/ output.\n */\nfunction packageRoot(): string {\n  const packageJsonPath = require.resolve('@dreamtree-org/graphify/package.json');\n  return path.dirname(packageJsonPath);\n}\n\nexport interface InstallResult {\n  host: string;\n  path: string;\n  /** Project-scoped MCP config file this install registered the graphify server in, if the host supports one. */\n  mcpPath?: string;\n}\n\n/**\n * The MCP server entry written into project-scoped MCP configs. `npx -y`\n * resolves a locally installed @dreamtree-org/graphify first and falls back\n * to fetching it, so the config works both for the person who ran the\n * install and for teammates who check the file in without installing\n * anything. MCP hosts launch project servers with cwd = project root, so\n * the default graph path (./graphify-out/graph.json) resolves correctly.\n */\nconst MCP_SERVER_ENTRY = {\n  command: 'npx',\n  args: ['-y', '@dreamtree-org/graphify', '--mcp'],\n};\n\n/**\n * Register the graphify MCP server under `serversKey` in a JSON config\n * file, creating the file if needed and preserving every existing key\n * (other servers, unrelated settings). Idempotent: re-running replaces the\n * graphify entry only. Refuses to touch a file it cannot parse rather than\n * clobbering user config.\n */\nasync function upsertMcpServer(filePath: string, serversKey = 'mcpServers'): Promise<string> {\n  let config: Record<string, unknown> = {};\n  try {\n    config = JSON.parse(await fs.readFile(filePath, 'utf-8')) as Record<string, unknown>;\n  } catch (error) {\n    if ((error as NodeJS.ErrnoException).code !== 'ENOENT') {\n      throw new Error(`cannot update ${filePath} — it exists but is not valid JSON; fix or remove it and re-run.`, {\n        cause: error,\n      });\n    }\n  }\n\n  const servers = (config[serversKey] ?? {}) as Record<string, unknown>;\n  servers['graphify'] = MCP_SERVER_ENTRY;\n  config[serversKey] = servers;\n\n  await fs.mkdir(path.dirname(filePath), { recursive: true });\n  await fs.writeFile(filePath, `${JSON.stringify(config, null, 2)}\\n`, 'utf-8');\n  return filePath;\n}\n\n/** Markers for hosts where we append into a shared file (AGENTS.md / GEMINI.md) instead of owning one. */\nconst MD_MARKER_BEGIN = '<!-- >>> graphify >>> -->';\nconst MD_MARKER_END = '<!-- <<< graphify <<< -->';\n\nasync function writeOwnedFile(filePath: string, content: string): Promise<void> {\n  await fs.mkdir(path.dirname(filePath), { recursive: true });\n  await fs.writeFile(filePath, content, 'utf-8');\n}\n\n/** Create `filePath` with the marked block, or replace/append the block in an existing file — user content is never touched. */\nasync function upsertMarkedBlock(filePath: string, content: string): Promise<void> {\n  const block = `${MD_MARKER_BEGIN}\\n${content.trim()}\\n${MD_MARKER_END}`;\n  let existing: string | null = null;\n  try {\n    existing = await fs.readFile(filePath, 'utf-8');\n  } catch {\n    // file doesn't exist yet\n  }\n\n  if (existing === null) {\n    await fs.mkdir(path.dirname(filePath), { recursive: true });\n    await fs.writeFile(filePath, `${block}\\n`, 'utf-8');\n    return;\n  }\n  if (existing.includes(MD_MARKER_BEGIN)) {\n    const pattern = new RegExp(`${MD_MARKER_BEGIN}[\\\\s\\\\S]*?${MD_MARKER_END}`);\n    await fs.writeFile(filePath, existing.replace(pattern, block), 'utf-8');\n    return;\n  }\n  const separator = existing.endsWith('\\n') ? 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Claude Code is always included — it picks\n * up `.claude/skills/` and `.mcp.json` from any project with zero prior\n * setup, so installing it is what makes `npx @dreamtree-org/graphify .`\n * work \"instantly\"; the other hosts are added only when their config\n * dir/file already exists.\n */\nexport async function detectPlatforms(cwd: string = process.cwd()): Promise<string[]> {\n  const platforms = ['claude'];\n  for (const [platform, markers] of Object.entries(PLATFORM_MARKERS)) {\n    for (const marker of markers) {\n      try {\n        await fs.access(path.join(cwd, marker));\n        platforms.push(platform);\n        break;\n      } catch {\n        // marker absent — not this host\n      }\n    }\n  }\n  return platforms;\n}\n\n/**\n * Install the graphify skill/rules for the requested platforms (default:\n * claude). `all` installs every supported platform.\n */\nexport async function runInstall(\n  platforms: string[] = ['claude'],\n  cwd: string = process.cwd(),\n): Promise<InstallResult[]> {\n  const sourcePath = path.join(packageRoot(), 'src', 'skill', 'SKILL.md');\n  const content = await fs.readFile(sourcePath, 'utf-8');\n\n  const requested = platforms.includes('all') ? SUPPORTED_PLATFORMS : platforms;\n  const results: InstallResult[] = [];\n  for (const platform of requested) {\n    const installer = PLATFORMS[platform];\n    if (!installer) {\n      throw new Error(\n        `Unknown platform \"${platform}\" — supported: ${SUPPORTED_PLATFORMS.join(', ')}, or \"all\".`,\n      );\n    }\n    results.push(await installer(cwd, content));\n  }\n\n  for (const result of results) {\n    const mcpNote = result.mcpPath ? ` (MCP server registered in ${result.mcpPath})` : '';\n    console.log(`Installed graphify for ${result.host} -> ${result.path}${mcpNote}`);\n  }\n  return results;\n}\n","import { loadGraph } from '../../graphStore.js';\nimport { shortestPath } from '../../query.js';\n\n/** Shortest path between two named nodes. */\nexport async function runPath(fromNode: string, toNode: string): Promise<void> {\n  const graph = await loadGraph();\n  const result = shortestPath(graph, fromNode, toNode);\n\n  if (!result) {\n    console.log(`Could not resolve \"${fromNode}\" and/or \"${toNode}\" to a node in the graph.`);\n    return;\n  }\n\n  if (!result.found) {\n    console.log(\n      `No path found between \"${result.from.label}\" and \"${result.to.label}\" — they may be in ` +\n        'disconnected parts of the graph (see GRAPH_REPORT.md § Open Questions).',\n    );\n    return;\n  }\n\n  console.log(`${result.from.label} -> ${result.to.label} (${result.path.length} node(s)):`);\n  console.log(`  ${result.path.join(' -> ')}`);\n  if (result.edges.length > 0) {\n    console.log('');\n    console.log('Edges along the path:');\n    for (const edge of result.edges) {\n      console.log(`  ${edge.source} --${edge.relation}--> ${edge.target} (${edge.confidence})`);\n    }\n  }\n}\n","import { loadGraph } from '../../graphStore.js';\nimport { queryGraph } from '../../query.js';\n\nexport interface QueryOptions {\n  dfs?: boolean;\n  /** Approximate token cap for the printed context (default 2000). */\n  budget?: number;\n}\n\n/** BFS (default) or DFS traversal answering a natural-language question against the graph. */\nexport async function runQuery(question: string, options: QueryOptions = {}): Promise<void> {\n  const graph = await loadGraph();\n  const result = queryGraph(graph, question, { dfs: options.dfs, tokenBudget: options.budget });\n\n  if (result.seeds.length === 0) {\n    console.log(\n      `No nodes matched \"${question}\". Try different keywords, or run \\`graphify explain <node>\\` ` +\n        'if you already know the name.',\n    );\n    return;\n  }\n\n  console.log(`Matched ${result.seeds.length} seed node(s):`);\n  for (const seed of result.seeds) {\n    console.log(`  - ${seed.label} (${seed.id})`);\n  }\n\n  console.log('');\n  console.log(`Context — ${result.visited.length} node(s), ${options.dfs ? 'DFS' : 'BFS'} traversal:`);\n  for (const node of result.visited) {\n    const location = node.sourceLocation ? `:${node.sourceLocation}` : '';\n    console.log(`  [depth ${node.depth}] ${node.label} — ${node.sourceFile}${location}`);\n  }\n\n  console.log('');\n  console.log(`Edges within this context (${result.edges.length}):`);\n  for (const edge of result.edges) {\n    console.log(`  ${edge.source} --${edge.relation}--> ${edge.target} (${edge.confidence})`);\n  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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@dreamtree-org/graphify",
-  "version": "1.1.3",
+  "version": "1.2.0",
   "description": "Turn a folder of code/docs/papers into a queryable, persistent knowledge graph for AI coding assistants.",
   "type": "module",
   "license": "MIT",

package/src/skill/SKILL.md

@@ -59,7 +59,10 @@ graphify benchmark [q...]         # measure token savings of graph answers vs re
 graphify save-result --question Q --answer A --nodes id... --outcome useful|dead_end|corrected
                                   # log which nodes answered — feeds the graph feedback loop
 graphify reflect                  # aggregate saved results into graphify-out/reflections/LESSONS.md
-graphify install [--platform p]   # (re-)install this skill (claude|cursor|windsurf|cline|agents|gemini|all)
+graphify install [--platform p]   # (re-)install this skill + project MCP config
+                                  #   (claude|cursor|windsurf|cline|agents|gemini|all); a plain
+                                  #   `graphify .` run already does this for detected hosts
+                                  #   (opt out with --no-install)
 
 graphify hook install|uninstall   # auto-rebuild the graph after each commit/pull
 graphify global add|remove|list|build   # cross-project global graph (registry in ~/.graphify)
@@ -104,6 +107,8 @@ graphify merge <dirA> <dirB> ...  # one-shot merge of built project graphs (--ou
   based and deterministic. You (the agent) are the semantic layer on top of its output.
 - `graphify` never executes source code and never shells out with a string built from file
   content — see SECURITY.md if you need to reason about its threat model.
-- If an MCP server is preferred over shelling out, run `graphify <path> --mcp` and use its
-  `query`/`path`/`explain`/`affected` tools instead of the CLI subcommands above — same
-  underlying logic, tool-call interface instead of stdout.
+- If an MCP server is preferred over shelling out, check the project MCP config first — the
+  pipeline run registers a `graphify` stdio server (in `.mcp.json` / `.cursor/mcp.json` /
+  `.gemini/settings.json`), so its `context`/`query`/`path`/`explain`/`affected`/`tests` tools
+  may already be available. Otherwise run `graphify <path> --mcp` — same underlying logic,
+  tool-call interface instead of stdout.