@duytransipher/gitnexus 1.0.0

package/hooks/claude/gitnexus-hook.cjs

@@ -0,0 +1,238 @@
+#!/usr/bin/env node
+/**
+ * GitNexus Claude Code Hook
+ *
+ * PreToolUse  — intercepts Grep/Glob/Bash searches and augments
+ *               with graph context from the GitNexus index.
+ * PostToolUse — detects stale index after git mutations and notifies
+ *               the agent to reindex.
+ *
+ * NOTE: SessionStart hooks are broken on Windows (Claude Code bug).
+ * Session context is injected via CLAUDE.md / skills instead.
+ */
+
+const fs = require('fs');
+const path = require('path');
+const { spawnSync } = require('child_process');
+
+/**
+ * Read JSON input from stdin synchronously.
+ */
+function readInput() {
+  try {
+    const data = fs.readFileSync(0, 'utf-8');
+    return JSON.parse(data);
+  } catch {
+    return {};
+  }
+}
+
+/**
+ * Find the .gitnexus directory by walking up from startDir.
+ * Returns the path to .gitnexus/ or null if not found.
+ */
+function findGitNexusDir(startDir) {
+  let dir = startDir || process.cwd();
+  for (let i = 0; i < 5; i++) {
+    const candidate = path.join(dir, '.gitnexus');
+    if (fs.existsSync(candidate)) return candidate;
+    const parent = path.dirname(dir);
+    if (parent === dir) break;
+    dir = parent;
+  }
+  return null;
+}
+
+/**
+ * Extract search pattern from tool input.
+ */
+function extractPattern(toolName, toolInput) {
+  if (toolName === 'Grep') {
+    return toolInput.pattern || null;
+  }
+
+  if (toolName === 'Glob') {
+    const raw = toolInput.pattern || '';
+    const match = raw.match(/[*\/]([a-zA-Z][a-zA-Z0-9_-]{2,})/);
+    return match ? match[1] : null;
+  }
+
+  if (toolName === 'Bash') {
+    const cmd = toolInput.command || '';
+    if (!/\brg\b|\bgrep\b/.test(cmd)) return null;
+
+    const tokens = cmd.split(/\s+/);
+    let foundCmd = false;
+    let skipNext = false;
+    const flagsWithValues = new Set(['-e', '-f', '-m', '-A', '-B', '-C', '-g', '--glob', '-t', '--type', '--include', '--exclude']);
+
+    for (const token of tokens) {
+      if (skipNext) { skipNext = false; continue; }
+      if (!foundCmd) {
+        if (/\brg$|\bgrep$/.test(token)) foundCmd = true;
+        continue;
+      }
+      if (token.startsWith('-')) {
+        if (flagsWithValues.has(token)) skipNext = true;
+        continue;
+      }
+      const cleaned = token.replace(/['"]/g, '');
+      return cleaned.length >= 3 ? cleaned : null;
+    }
+    return null;
+  }
+
+  return null;
+}
+
+/**
+ * Resolve the gitnexus CLI path.
+ * 1. Relative path (works when script is inside npm package)
+ * 2. require.resolve (works when gitnexus is globally installed)
+ * 3. Fall back to npx (returns empty string)
+ */
+function resolveCliPath() {
+  let cliPath = path.resolve(__dirname, '..', '..', 'dist', 'cli', 'index.js');
+  if (!fs.existsSync(cliPath)) {
+    try {
+      cliPath = require.resolve('gitnexus/dist/cli/index.js');
+    } catch {
+      cliPath = '';
+    }
+  }
+  return cliPath;
+}
+
+/**
+ * Spawn a gitnexus CLI command synchronously.
+ * Returns the stderr output (KuzuDB captures stdout at OS level).
+ */
+function runGitNexusCli(cliPath, args, cwd, timeout) {
+  const isWin = process.platform === 'win32';
+  if (cliPath) {
+    return spawnSync(
+      process.execPath,
+      [cliPath, ...args],
+      { encoding: 'utf-8', timeout, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+    );
+  }
+  // On Windows, invoke npx.cmd directly (no shell needed)
+  return spawnSync(
+    isWin ? 'npx.cmd' : 'npx',
+    ['-y', 'gitnexus', ...args],
+    { encoding: 'utf-8', timeout: timeout + 5000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+  );
+}
+
+/**
+ * PreToolUse handler — augment searches with graph context.
+ */
+function handlePreToolUse(input) {
+  const cwd = input.cwd || process.cwd();
+  if (!path.isAbsolute(cwd)) return;
+  if (!findGitNexusDir(cwd)) return;
+
+  const toolName = input.tool_name || '';
+  const toolInput = input.tool_input || {};
+
+  if (toolName !== 'Grep' && toolName !== 'Glob' && toolName !== 'Bash') return;
+
+  const pattern = extractPattern(toolName, toolInput);
+  if (!pattern || pattern.length < 3) return;
+
+  const cliPath = resolveCliPath();
+  let result = '';
+  try {
+    const child = runGitNexusCli(cliPath, ['augment', '--', pattern], cwd, 7000);
+    if (!child.error && child.status === 0) {
+      result = child.stderr || '';
+    }
+  } catch { /* graceful failure */ }
+
+  if (result && result.trim()) {
+    sendHookResponse('PreToolUse', result.trim());
+  }
+}
+
+/**
+ * Emit a PostToolUse hook response with additional context for the agent.
+ */
+function sendHookResponse(hookEventName, message) {
+  console.log(JSON.stringify({
+    hookSpecificOutput: { hookEventName, additionalContext: message }
+  }));
+}
+
+/**
+ * PostToolUse handler — detect index staleness after git mutations.
+ *
+ * Instead of spawning a full `gitnexus analyze` synchronously (which blocks
+ * the agent for up to 120s and risks KuzuDB corruption on timeout), we do a
+ * lightweight staleness check: compare `git rev-parse HEAD` against the
+ * lastCommit stored in `.gitnexus/meta.json`. If they differ, notify the
+ * agent so it can decide when to reindex.
+ */
+function handlePostToolUse(input) {
+  const toolName = input.tool_name || '';
+  if (toolName !== 'Bash') return;
+
+  const command = (input.tool_input || {}).command || '';
+  if (!/\bgit\s+(commit|merge|rebase|cherry-pick|pull)(\s|$)/.test(command)) return;
+
+  // Only proceed if the command succeeded
+  const toolOutput = input.tool_output || {};
+  if (toolOutput.exit_code !== undefined && toolOutput.exit_code !== 0) return;
+
+  const cwd = input.cwd || process.cwd();
+  if (!path.isAbsolute(cwd)) return;
+  const gitNexusDir = findGitNexusDir(cwd);
+  if (!gitNexusDir) return;
+
+  // Compare HEAD against last indexed commit — skip if unchanged
+  let currentHead = '';
+  try {
+    const headResult = spawnSync('git', ['rev-parse', 'HEAD'], {
+      encoding: 'utf-8', timeout: 3000, cwd, stdio: ['pipe', 'pipe', 'pipe'],
+    });
+    currentHead = (headResult.stdout || '').trim();
+  } catch { return; }
+
+  if (!currentHead) return;
+
+  let lastCommit = '';
+  let hadEmbeddings = false;
+  try {
+    const meta = JSON.parse(fs.readFileSync(path.join(gitNexusDir, 'meta.json'), 'utf-8'));
+    lastCommit = meta.lastCommit || '';
+    hadEmbeddings = (meta.stats && meta.stats.embeddings > 0);
+  } catch { /* no meta — treat as stale */ }
+
+  // If HEAD matches last indexed commit, no reindex needed
+  if (currentHead && currentHead === lastCommit) return;
+
+  const analyzeCmd = `npx gitnexus analyze${hadEmbeddings ? ' --embeddings' : ''}`;
+  sendHookResponse('PostToolUse',
+    `GitNexus index is stale (last indexed: ${lastCommit ? lastCommit.slice(0, 7) : 'never'}). ` +
+    `Run \`${analyzeCmd}\` to update the knowledge graph.`
+  );
+}
+
+// Dispatch map for hook events
+const handlers = {
+  PreToolUse: handlePreToolUse,
+  PostToolUse: handlePostToolUse,
+};
+
+function main() {
+  try {
+    const input = readInput();
+    const handler = handlers[input.hook_event_name || ''];
+    if (handler) handler(input);
+  } catch (err) {
+    if (process.env.GITNEXUS_DEBUG) {
+      console.error('GitNexus hook error:', (err.message || '').slice(0, 200));
+    }
+  }
+}
+
+main();

package/hooks/claude/pre-tool-use.sh

@@ -0,0 +1,79 @@
+#!/bin/bash
+# GitNexus PreToolUse hook for Claude Code
+# Intercepts Grep/Glob/Bash searches and augments with graph context.
+# Receives JSON on stdin with { tool_name, tool_input, cwd, ... }
+# Returns JSON with additionalContext for graph-enriched results.
+
+INPUT=$(cat)
+
+TOOL_NAME=$(echo "$INPUT" | jq -r '.tool_name // empty' 2>/dev/null)
+CWD=$(echo "$INPUT" | jq -r '.cwd // empty' 2>/dev/null)
+
+# Extract search pattern based on tool type
+PATTERN=""
+
+case "$TOOL_NAME" in
+  Grep)
+    PATTERN=$(echo "$INPUT" | jq -r '.tool_input.pattern // empty' 2>/dev/null)
+    ;;
+  Glob)
+    # Glob patterns are file paths, not search terms — extract meaningful part
+    RAW=$(echo "$INPUT" | jq -r '.tool_input.pattern // empty' 2>/dev/null)
+    # Strip glob syntax to get the meaningful name (e.g., "**/*.ts" → skip, "auth*.ts" → "auth")
+    PATTERN=$(echo "$RAW" | sed -n 's/.*[*\/]\([a-zA-Z][a-zA-Z0-9_-]*\).*/\1/p')
+    ;;
+  Bash)
+    CMD=$(echo "$INPUT" | jq -r '.tool_input.command // empty' 2>/dev/null)
+    # Only augment grep/rg commands
+    if echo "$CMD" | grep -qE '\brg\b|\bgrep\b'; then
+      # Extract pattern from rg/grep
+      if echo "$CMD" | grep -qE '\brg\b'; then
+        PATTERN=$(echo "$CMD" | sed -n "s/.*\brg\s\+\(--[^ ]*\s\+\)*['\"]\\?\([^'\";\| >]*\\).*/\2/p")
+      elif echo "$CMD" | grep -qE '\bgrep\b'; then
+        PATTERN=$(echo "$CMD" | sed -n "s/.*\bgrep\s\+\(-[^ ]*\s\+\)*['\"]\\?\([^'\";\| >]*\\).*/\2/p")
+      fi
+    fi
+    ;;
+  *)
+    # Not a search tool — skip
+    exit 0
+    ;;
+esac
+
+# Skip if pattern too short or empty
+if [ -z "$PATTERN" ] || [ ${#PATTERN} -lt 3 ]; then
+  exit 0
+fi
+
+# Check if we're in a GitNexus-indexed repo
+dir="${CWD:-$PWD}"
+found=false
+for i in 1 2 3 4 5; do
+  if [ -d "$dir/.gitnexus" ]; then
+    found=true
+    break
+  fi
+  parent="$(dirname "$dir")"
+  [ "$parent" = "$dir" ] && break
+  dir="$parent"
+done
+
+if [ "$found" = false ]; then
+  exit 0
+fi
+
+# Run gitnexus augment — must be fast (<500ms target)
+# augment writes to stderr (KuzuDB captures stdout at OS level), so capture stderr and discard stdout
+RESULT=$(cd "$CWD" && npx -y gitnexus augment "$PATTERN" 2>&1 1>/dev/null)
+
+if [ -n "$RESULT" ]; then
+  ESCAPED=$(echo "$RESULT" | jq -Rs .)
+  jq -n --argjson ctx "$ESCAPED" '{
+    hookSpecificOutput: {
+      hookEventName: "PreToolUse",
+      additionalContext: $ctx
+    }
+  }'
+else
+  exit 0
+fi

package/hooks/claude/session-start.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+# GitNexus SessionStart hook for Claude Code
+# Fires on session startup. Stdout is injected into Claude's context.
+# Checks if the current directory has a GitNexus index.
+
+dir="$PWD"
+found=false
+for i in 1 2 3 4 5; do
+  if [ -d "$dir/.gitnexus" ]; then
+    found=true
+    break
+  fi
+  parent="$(dirname "$dir")"
+  [ "$parent" = "$dir" ] && break
+  dir="$parent"
+done
+
+if [ "$found" = false ]; then
+  exit 0
+fi
+
+# Inject GitNexus context — this stdout goes directly into Claude's context
+cat << 'EOF'
+## GitNexus Code Intelligence
+
+This codebase is indexed by GitNexus, providing a knowledge graph with execution flows, relationships, and semantic search.
+
+**Available MCP Tools:**
+- `query` — Process-grouped code intelligence (execution flows related to a concept)
+- `context` — 360-degree symbol view (categorized refs, process participation)
+- `impact` — Blast radius analysis (what breaks if you change a symbol)
+- `detect_changes` — Git-diff impact analysis (what do your changes affect)
+- `rename` — Multi-file coordinated rename with confidence tags
+- `cypher` — Raw graph queries
+- `list_repos` — Discover indexed repos
+
+**Quick Start:** READ `gitnexus://repo/{name}/context` for codebase overview, then use `query` to find execution flows.
+
+**Resources:** `gitnexus://repo/{name}/context` (overview), `/processes` (execution flows), `/schema` (for Cypher)
+EOF
+
+exit 0

package/package.json

@@ -0,0 +1,100 @@
+{
+  "name": "@duytransipher/gitnexus",
+  "version": "1.0.0",
+  "description": "Sipher-maintained fork of GitNexus for graph-powered code intelligence via MCP and CLI.",
+  "author": "DuyTranSipher",
+  "license": "PolyForm-Noncommercial-1.0.0",
+  "homepage": "https://github.com/DuyTranSipher/sipher-git-nexus#readme",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/DuyTranSipher/sipher-git-nexus.git",
+    "directory": "gitnexus"
+  },
+  "bugs": {
+    "url": "https://github.com/DuyTranSipher/sipher-git-nexus/issues"
+  },
+  "keywords": [
+    "mcp",
+    "model-context-protocol",
+    "code-intelligence",
+    "knowledge-graph",
+    "cursor",
+    "claude",
+    "ai-agent",
+    "gitnexus",
+    "static-analysis",
+    "codebase-indexing"
+  ],
+  "type": "module",
+  "bin": {
+    "gitnexus": "dist/cli/index.js"
+  },
+  "files": [
+    "dist",
+    "hooks",
+    "scripts",
+    "skills",
+    "vendor"
+  ],
+  "scripts": {
+    "build": "tsc",
+    "dev": "tsx watch src/cli/index.ts",
+    "pack:dry-run": "npm pack --dry-run",
+    "test": "vitest run",
+    "test:unit": "vitest run test/unit",
+    "test:integration": "vitest run test/integration",
+    "test:watch": "vitest",
+    "test:coverage": "vitest run --coverage",
+    "prepare": "npm run build",
+    "postinstall": "node scripts/patch-tree-sitter-swift.cjs",
+    "prepack": "npm run build && node scripts/ensure-cli-executable.cjs"
+  },
+  "dependencies": {
+    "@huggingface/transformers": "^3.0.0",
+    "@modelcontextprotocol/sdk": "^1.0.0",
+    "cli-progress": "^3.12.0",
+    "commander": "^12.0.0",
+    "cors": "^2.8.5",
+    "express": "^4.19.2",
+    "glob": "^11.0.0",
+    "graphology": "^0.25.4",
+    "graphology-indices": "^0.17.0",
+    "graphology-utils": "^2.3.0",
+    "@ladybugdb/core": "^0.15.2",
+    "ignore": "^7.0.5",
+    "lru-cache": "^11.0.0",
+    "mnemonist": "^0.39.0",
+    "pandemonium": "^2.4.0",
+    "tree-sitter": "^0.21.0",
+    "tree-sitter-c": "^0.21.0",
+    "tree-sitter-c-sharp": "^0.21.0",
+    "tree-sitter-cpp": "^0.22.0",
+    "tree-sitter-go": "^0.21.0",
+    "tree-sitter-java": "^0.21.0",
+    "tree-sitter-javascript": "^0.21.0",
+    "tree-sitter-php": "^0.23.12",
+    "tree-sitter-python": "^0.21.0",
+    "tree-sitter-ruby": "^0.23.1",
+    "tree-sitter-rust": "^0.21.0",
+    "tree-sitter-typescript": "^0.21.0",
+    "uuid": "^13.0.0"
+  },
+  "optionalDependencies": {
+    "tree-sitter-kotlin": "^0.3.8",
+    "tree-sitter-swift": "^0.6.0"
+  },
+  "devDependencies": {
+    "@types/cli-progress": "^3.11.6",
+    "@types/cors": "^2.8.17",
+    "@types/express": "^4.17.21",
+    "@types/node": "^20.0.0",
+    "@types/uuid": "^10.0.0",
+    "@vitest/coverage-v8": "^4.0.18",
+    "tsx": "^4.0.0",
+    "typescript": "^5.4.5",
+    "vitest": "^4.0.18"
+  },
+  "engines": {
+    "node": ">=18.0.0"
+  }
+}

package/scripts/ensure-cli-executable.cjs

@@ -0,0 +1,21 @@
+const fs = require('node:fs');
+const path = require('node:path');
+
+const cliPath = path.join(__dirname, '..', 'dist', 'cli', 'index.js');
+
+if (!fs.existsSync(cliPath)) {
+  console.warn(`[prepack] Skipping executable bit because ${cliPath} does not exist.`);
+  process.exit(0);
+}
+
+try {
+  fs.chmodSync(cliPath, 0o755);
+} catch (error) {
+  if (process.platform === 'win32') {
+    const message = error instanceof Error ? error.message : String(error);
+    console.warn(`[prepack] Continuing without chmod on Windows: ${message}`);
+    process.exit(0);
+  }
+
+  throw error;
+}

package/scripts/patch-tree-sitter-swift.cjs

@@ -0,0 +1,74 @@
+#!/usr/bin/env node
+/**
+ * WORKAROUND: tree-sitter-swift@0.6.0 binding.gyp build failure
+ *
+ * Background:
+ *   tree-sitter-swift@0.6.0's binding.gyp contains an "actions" array that
+ *   invokes `tree-sitter generate` to regenerate parser.c from grammar.js.
+ *   This is intended for grammar developers, but the published npm package
+ *   already ships pre-generated parser files (parser.c, scanner.c), so the
+ *   actions are unnecessary for consumers. Since consumers don't have
+ *   tree-sitter-cli installed, the actions always fail during `npm install`.
+ *
+ * Why we can't just upgrade:
+ *   tree-sitter-swift@0.7.1 fixes this (removes postinstall, ships prebuilds),
+ *   but it requires tree-sitter@^0.22.1. The upstream project pins tree-sitter
+ *   to ^0.21.0 and all other grammar packages depend on that version.
+ *   Upgrading tree-sitter would be a separate breaking change.
+ *
+ * How this workaround works:
+ *   1. tree-sitter-swift's own postinstall fails (npm warns but continues)
+ *   2. This script runs as gitnexus's postinstall
+ *   3. It removes the "actions" array from binding.gyp
+ *   4. It rebuilds the native binding with the cleaned binding.gyp
+ *
+ * TODO: Remove this script when tree-sitter is upgraded to ^0.22.x,
+ *       which allows using tree-sitter-swift@0.7.1+ directly.
+ */
+const fs = require('fs');
+const path = require('path');
+const { execSync } = require('child_process');
+
+const swiftDir = path.join(__dirname, '..', 'node_modules', 'tree-sitter-swift');
+const bindingPath = path.join(swiftDir, 'binding.gyp');
+
+try {
+  if (!fs.existsSync(bindingPath)) {
+    process.exit(0);
+  }
+
+  const content = fs.readFileSync(bindingPath, 'utf8');
+  let needsRebuild = false;
+
+  if (content.includes('"actions"')) {
+    // Strip Python-style comments (#) before JSON parsing
+    const cleaned = content.replace(/#[^\n]*/g, '');
+    const gyp = JSON.parse(cleaned);
+
+    if (gyp.targets && gyp.targets[0] && gyp.targets[0].actions) {
+      delete gyp.targets[0].actions;
+      fs.writeFileSync(bindingPath, JSON.stringify(gyp, null, 2) + '\n');
+      console.log('[tree-sitter-swift] Patched binding.gyp (removed actions array)');
+      needsRebuild = true;
+    }
+  }
+
+  // Check if native binding exists
+  const bindingNode = path.join(swiftDir, 'build', 'Release', 'tree_sitter_swift_binding.node');
+  if (!fs.existsSync(bindingNode)) {
+    needsRebuild = true;
+  }
+
+  if (needsRebuild) {
+    console.log('[tree-sitter-swift] Rebuilding native binding...');
+    execSync('npx node-gyp rebuild', {
+      cwd: swiftDir,
+      stdio: 'pipe',
+      timeout: 120000,
+    });
+    console.log('[tree-sitter-swift] Native binding built successfully');
+  }
+} catch (err) {
+  console.warn('[tree-sitter-swift] Could not build native binding:', err.message);
+  console.warn('[tree-sitter-swift] You may need to manually run: cd node_modules/tree-sitter-swift && npx node-gyp rebuild');
+}