gsd-antigravity-kit 2.0.1 → 2.1.0

package/.agent/skills/gsd/bin/lib/frontmatter.cjs

@@ -4,7 +4,7 @@
 
 const fs = require('fs');
 const path = require('path');
-const { safeReadFile, normalizeMd, output, error } = require('./core.cjs');
+const { safeReadFile, normalizeMd, output, error, atomicWriteFileSync } = require('./core.cjs');
 
 // ─── Parsing engine ───────────────────────────────────────────────────────────
 
@@ -42,11 +42,9 @@ function splitInlineArray(body) {
 
 function extractFrontmatter(content) {
   const frontmatter = {};
-  // Find ALL frontmatter blocks at the start of the file.
-  // If multiple blocks exist (corruption from CRLF mismatch), use the LAST one
-  // since it represents the most recent state sync.
-  const allBlocks = [...content.matchAll(/(?:^|\n)\s*---\r?\n([\s\S]+?)\r?\n---/g)];
-  const match = allBlocks.length > 0 ? allBlocks[allBlocks.length - 1] : null;
+  // Match frontmatter only at byte 0 — a `---` block later in the document
+  // body (YAML examples, horizontal rules) must never be treated as frontmatter.
+  const match = content.match(/^---\r?\n([\s\S]+?)\r?\n---/);
   if (!match) return frontmatter;
 
   const yaml = match[1];
@@ -337,7 +335,7 @@ function cmdFrontmatterSet(cwd, filePath, field, value, raw) {
   try { parsedValue = JSON.parse(value); } catch { parsedValue = value; }
   fm[field] = parsedValue;
   const newContent = spliceFrontmatter(content, fm);
-  fs.writeFileSync(fullPath, normalizeMd(newContent), 'utf-8');
+  atomicWriteFileSync(fullPath, normalizeMd(newContent));
   output({ updated: true, field, value: parsedValue }, raw, 'true');
 }
 
@@ -351,7 +349,7 @@ function cmdFrontmatterMerge(cwd, filePath, data, raw) {
   try { mergeData = JSON.parse(data); } catch { error('Invalid JSON for --data'); return; }
   Object.assign(fm, mergeData);
   const newContent = spliceFrontmatter(content, fm);
-  fs.writeFileSync(fullPath, normalizeMd(newContent), 'utf-8');
+  atomicWriteFileSync(fullPath, normalizeMd(newContent));
   output({ merged: true, fields: Object.keys(mergeData) }, raw, 'true');
 }
 

package/.agent/skills/gsd/bin/lib/graphify.cjs

@@ -0,0 +1,494 @@
+'use strict';
+
+const fs = require('fs');
+const path = require('path');
+const childProcess = require('child_process');
+const { atomicWriteFileSync } = require('./core.cjs');
+
+// ─── Config Gate ─────────────────────────────────────────────────────────────
+
+/**
+ * Check whether graphify is enabled in the project config.
+ * Reads config.json directly via fs. Returns false by default
+ * (when no config, no graphify key, or on error).
+ *
+ * @param {string} planningDir - Path to .planning directory
+ * @returns {boolean}
+ */
+function isGraphifyEnabled(planningDir) {
+  try {
+  const configPath = path.join(planningDir, 'config.json');
+  if (!fs.existsSync(configPath)) return false;
+  const config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
+  if (config && config.graphify && config.graphify.enabled === true) return true;
+  return false;
+  } catch (_e) {
+  return false;
+  }
+}
+
+/**
+ * Return the standard disabled response object.
+ * @returns {{ disabled: true, message: string }}
+ */
+function disabledResponse() {
+  return { disabled: true, message: 'graphify is not enabled. Enable with: gsd-tools config-set graphify.enabled true' };
+}
+
+// ─── Subprocess Helper ───────────────────────────────────────────────────────
+
+/**
+ * Execute graphify CLI as a subprocess with proper env and timeout handling.
+ *
+ * @param {string} cwd - Working directory for the subprocess
+ * @param {string[]} args - Arguments to pass to graphify
+ * @param {{ timeout?: number }} [options={}] - Options (timeout in ms, default 30000)
+ * @returns {{ exitCode: number, stdout: string, stderr: string }}
+ */
+function execGraphify(cwd, args, options = {}) {
+  const timeout = options.timeout ?? 30000;
+  const result = childProcess.spawnSync('graphify', args, {
+  cwd,
+  stdio: 'pipe',
+  encoding: 'utf-8',
+  timeout,
+  env: { ...process.env, PYTHONUNBUFFERED: '1' },
+  });
+
+  // ENOENT -- graphify binary not found on PATH
+  if (result.error && result.error.code === 'ENOENT') {
+  return { exitCode: 127, stdout: '', stderr: 'graphify not found on PATH' };
+  }
+
+  // Timeout -- subprocess killed via SIGTERM
+  if (result.signal === 'SIGTERM') {
+  return {
+    exitCode: 124,
+    stdout: (result.stdout ?? '').toString().trim(),
+    stderr: 'graphify timed out after ' + timeout + 'ms',
+  };
+  }
+
+  return {
+  exitCode: result.status ?? 1,
+  stdout: (result.stdout ?? '').toString().trim(),
+  stderr: (result.stderr ?? '').toString().trim(),
+  };
+}
+
+// ─── Presence & Version ──────────────────────────────────────────────────────
+
+/**
+ * Check whether the graphify CLI binary is installed and accessible on PATH.
+ * Uses --help (NOT --version, which graphify does not support).
+ *
+ * @returns {{ installed: boolean, message?: string }}
+ */
+function checkGraphifyInstalled() {
+  const result = childProcess.spawnSync('graphify', ['--help'], {
+  stdio: 'pipe',
+  encoding: 'utf-8',
+  timeout: 5000,
+  });
+
+  if (result.error) {
+  return {
+    installed: false,
+    message: 'graphify is not installed.\n\nInstall with:\n  uv pip install graphifyy && graphify install',
+  };
+  }
+
+  return { installed: true };
+}
+
+/**
+ * Detect graphify version via python3 importlib.metadata and check compatibility.
+ * Tested range: >=0.4.0,<1.0
+ *
+ * @returns {{ version: string|null, compatible: boolean|null, warning: string|null }}
+ */
+function checkGraphifyVersion() {
+  const result = childProcess.spawnSync('python3', [
+  '-c',
+  'from importlib.metadata import version; print(version("graphifyy"))',
+  ], {
+  stdio: 'pipe',
+  encoding: 'utf-8',
+  timeout: 5000,
+  });
+
+  if (result.status !== 0 || !result.stdout || !result.stdout.trim()) {
+  return { version: null, compatible: null, warning: 'Could not determine graphify version' };
+  }
+
+  const versionStr = result.stdout.trim();
+  const parts = versionStr.split('.').map(Number);
+
+  if (parts.length < 2 || parts.some(isNaN)) {
+  return { version: versionStr, compatible: null, warning: 'Could not parse version: ' + versionStr };
+  }
+
+  const compatible = parts[0] === 0 && parts[1] >= 4;
+  const warning = compatible ? null : 'graphify version ' + versionStr + ' is outside tested range >=0.4.0,<1.0';
+
+  return { version: versionStr, compatible, warning };
+}
+
+// ─── Internal Helpers ────────────────────────────────────────────────────────
+
+/**
+ * Safely read and parse a JSON file. Returns null on missing file or parse error.
+ * Prevents crashes on malformed JSON (T-02-01 mitigation).
+ *
+ * @param {string} filePath - Absolute path to JSON file
+ * @returns {object|null}
+ */
+function safeReadJson(filePath) {
+  try {
+  if (!fs.existsSync(filePath)) return null;
+  return JSON.parse(fs.readFileSync(filePath, 'utf8'));
+  } catch (_e) {
+  return null;
+  }
+}
+
+/**
+ * Build a bidirectional adjacency map from graph nodes and edges.
+ * Each node ID maps to an array of { target, edge } entries.
+ * Bidirectional: both source->target and target->source are added (Pitfall 3).
+ *
+ * @param {{ nodes: object[], edges: object[] }} graph
+ * @returns {Object.<string, Array<{ target: string, edge: object }>>}
+ */
+function buildAdjacencyMap(graph) {
+  const adj = {};
+  for (const node of (graph.nodes || [])) {
+  adj[node.id] = [];
+  }
+  for (const edge of (graph.edges || graph.links || [])) {
+  if (!adj[edge.source]) adj[edge.source] = [];
+  if (!adj[edge.target]) adj[edge.target] = [];
+  adj[edge.source].push({ target: edge.target, edge });
+  adj[edge.target].push({ target: edge.source, edge });
+  }
+  return adj;
+}
+
+/**
+ * Seed-then-expand query: find nodes matching term, then BFS-expand up to maxHops.
+ * Matches on node label and description (case-insensitive substring, D-01).
+ *
+ * @param {{ nodes: object[], edges: object[] }} graph
+ * @param {string} term - Search term
+ * @param {number} [maxHops=2] - Maximum BFS hops from seed nodes
+ * @returns {{ nodes: object[], edges: object[], seeds: Set<string> }}
+ */
+function seedAndExpand(graph, term, maxHops = 2) {
+  const lowerTerm = term.toLowerCase();
+  const nodeMap = Object.fromEntries((graph.nodes || []).map(n => [n.id, n]));
+  const adj = buildAdjacencyMap(graph);
+
+  // Seed: match on label and description (case-insensitive substring)
+  const seeds = (graph.nodes || []).filter(n =>
+  (n.label || '').toLowerCase().includes(lowerTerm) ||
+  (n.description || '').toLowerCase().includes(lowerTerm)
+  );
+
+  // BFS expand from seeds
+  const visitedNodes = new Set(seeds.map(n => n.id));
+  const collectedEdges = [];
+  const seenEdgeKeys = new Set();
+  let frontier = seeds.map(n => n.id);
+
+  for (let hop = 0; hop < maxHops && frontier.length > 0; hop++) {
+  const nextFrontier = [];
+  for (const nodeId of frontier) {
+    for (const entry of (adj[nodeId] || [])) {
+    // Deduplicate edges by source::target::label key
+    const edgeKey = `${entry.edge.source}::${entry.edge.target}::${entry.edge.label || ''}`;
+    if (!seenEdgeKeys.has(edgeKey)) {
+      seenEdgeKeys.add(edgeKey);
+      collectedEdges.push(entry.edge);
+    }
+    if (!visitedNodes.has(entry.target)) {
+      visitedNodes.add(entry.target);
+      nextFrontier.push(entry.target);
+    }
+    }
+  }
+  frontier = nextFrontier;
+  }
+
+  const resultNodes = [...visitedNodes].map(id => nodeMap[id]).filter(Boolean);
+  return { nodes: resultNodes, edges: collectedEdges, seeds: new Set(seeds.map(n => n.id)) };
+}
+
+/**
+ * Apply token budget by dropping edges by confidence tier (D-04, D-05, D-06).
+ * Token estimation: Math.ceil(JSON.stringify(obj).length / 4).
+ * Drop order: AMBIGUOUS -> INFERRED -> EXTRACTED.
+ *
+ * @param {{ nodes: object[], edges: object[], seeds: Set<string> }} result
+ * @param {number|null} budgetTokens - Max tokens, or null/falsy for unlimited
+ * @returns {{ nodes: object[], edges: object[], trimmed: string|null, total_nodes: number, total_edges: number, term?: string }}
+ */
+function applyBudget(result, budgetTokens) {
+  if (!budgetTokens) return result;
+
+  const CONFIDENCE_ORDER = ['AMBIGUOUS', 'INFERRED', 'EXTRACTED'];
+  let edges = [...result.edges];
+  let omitted = 0;
+
+  const estimateTokens = (obj) => Math.ceil(JSON.stringify(obj).length / 4);
+
+  for (const tier of CONFIDENCE_ORDER) {
+  if (estimateTokens({ nodes: result.nodes, edges }) <= budgetTokens) break;
+  const before = edges.length;
+  // Check both confidence and confidence_score field names (Open Question 1)
+  edges = edges.filter(e => (e.confidence || e.confidence_score) !== tier);
+  omitted += before - edges.length;
+  }
+
+  // Find unreachable nodes after edge removal
+  const reachableNodes = new Set();
+  for (const edge of edges) {
+  reachableNodes.add(edge.source);
+  reachableNodes.add(edge.target);
+  }
+  // Always keep seed nodes
+  const nodes = result.nodes.filter(n => reachableNodes.has(n.id) || (result.seeds && result.seeds.has(n.id)));
+  const unreachable = result.nodes.length - nodes.length;
+
+  return {
+  nodes,
+  edges,
+  trimmed: omitted > 0 ? `[${omitted} edges omitted, ${unreachable} nodes unreachable]` : null,
+  total_nodes: nodes.length,
+  total_edges: edges.length,
+  };
+}
+
+// ─── Public API ──────────────────────────────────────────────────────────────
+
+/**
+ * Query the knowledge graph for nodes matching a term, with optional budget cap.
+ * Uses seed-then-expand BFS traversal (D-01).
+ *
+ * @param {string} cwd - Working directory
+ * @param {string} term - Search term
+ * @param {{ budget?: number|null }} [options={}]
+ * @returns {object}
+ */
+function graphifyQuery(cwd, term, options = {}) {
+  const planningDir = path.join(cwd, '.planning');
+  if (!isGraphifyEnabled(planningDir)) return disabledResponse();
+
+  const graphPath = path.join(planningDir, 'graphs', 'graph.json');
+  if (!fs.existsSync(graphPath)) {
+  return { error: 'No graph built yet. Run graphify build first.' };
+  }
+
+  const graph = safeReadJson(graphPath);
+  if (!graph) {
+  return { error: 'Failed to parse graph.json' };
+  }
+
+  let result = seedAndExpand(graph, term);
+
+  if (options.budget) {
+  result = applyBudget(result, options.budget);
+  }
+
+  return {
+  term,
+  nodes: result.nodes,
+  edges: result.edges,
+  total_nodes: result.nodes.length,
+  total_edges: result.edges.length,
+  trimmed: result.trimmed || null,
+  };
+}
+
+/**
+ * Return status information about the knowledge graph (STAT-01, STAT-02).
+ *
+ * @param {string} cwd - Working directory
+ * @returns {object}
+ */
+function graphifyStatus(cwd) {
+  const planningDir = path.join(cwd, '.planning');
+  if (!isGraphifyEnabled(planningDir)) return disabledResponse();
+
+  const graphPath = path.join(planningDir, 'graphs', 'graph.json');
+  if (!fs.existsSync(graphPath)) {
+  return { exists: false, message: 'No graph built yet. Run graphify build to create one.' };
+  }
+
+  const stat = fs.statSync(graphPath);
+  const graph = safeReadJson(graphPath);
+  if (!graph) {
+  return { error: 'Failed to parse graph.json' };
+  }
+
+  const STALE_MS = 24 * 60 * 60 * 1000; // 24 hours
+  const age = Date.now() - stat.mtimeMs;
+
+  return {
+  exists: true,
+  last_build: stat.mtime.toISOString(),
+  node_count: (graph.nodes || []).length,
+  edge_count: (graph.edges || graph.links || []).length,
+  hyperedge_count: (graph.hyperedges || []).length,
+  stale: age > STALE_MS,
+  age_hours: Math.round(age / (60 * 60 * 1000)),
+  };
+}
+
+/**
+ * Compute topology-level diff between current graph and last build snapshot (D-07, D-08, D-09).
+ *
+ * @param {string} cwd - Working directory
+ * @returns {object}
+ */
+function graphifyDiff(cwd) {
+  const planningDir = path.join(cwd, '.planning');
+  if (!isGraphifyEnabled(planningDir)) return disabledResponse();
+
+  const snapshotPath = path.join(planningDir, 'graphs', '.last-build-snapshot.json');
+  const graphPath = path.join(planningDir, 'graphs', 'graph.json');
+
+  if (!fs.existsSync(snapshotPath)) {
+  return { no_baseline: true, message: 'No previous snapshot. Run graphify build first, then build again to generate a diff baseline.' };
+  }
+
+  if (!fs.existsSync(graphPath)) {
+  return { error: 'No current graph. Run graphify build first.' };
+  }
+
+  const current = safeReadJson(graphPath);
+  const snapshot = safeReadJson(snapshotPath);
+
+  if (!current || !snapshot) {
+  return { error: 'Failed to parse graph or snapshot file' };
+  }
+
+  // Diff nodes
+  const currentNodeMap = Object.fromEntries((current.nodes || []).map(n => [n.id, n]));
+  const snapshotNodeMap = Object.fromEntries((snapshot.nodes || []).map(n => [n.id, n]));
+
+  const nodesAdded = Object.keys(currentNodeMap).filter(id => !snapshotNodeMap[id]);
+  const nodesRemoved = Object.keys(snapshotNodeMap).filter(id => !currentNodeMap[id]);
+  const nodesChanged = Object.keys(currentNodeMap).filter(id =>
+  snapshotNodeMap[id] && JSON.stringify(currentNodeMap[id]) !== JSON.stringify(snapshotNodeMap[id])
+  );
+
+  // Diff edges (keyed by source+target+relation)
+  const edgeKey = (e) => `${e.source}::${e.target}::${e.relation || e.label || ''}`;
+  const currentEdgeMap = Object.fromEntries((current.edges || current.links || []).map(e => [edgeKey(e), e]));
+  const snapshotEdgeMap = Object.fromEntries((snapshot.edges || snapshot.links || []).map(e => [edgeKey(e), e]));
+
+  const edgesAdded = Object.keys(currentEdgeMap).filter(k => !snapshotEdgeMap[k]);
+  const edgesRemoved = Object.keys(snapshotEdgeMap).filter(k => !currentEdgeMap[k]);
+  const edgesChanged = Object.keys(currentEdgeMap).filter(k =>
+  snapshotEdgeMap[k] && JSON.stringify(currentEdgeMap[k]) !== JSON.stringify(snapshotEdgeMap[k])
+  );
+
+  return {
+  nodes: { added: nodesAdded.length, removed: nodesRemoved.length, changed: nodesChanged.length },
+  edges: { added: edgesAdded.length, removed: edgesRemoved.length, changed: edgesChanged.length },
+  timestamp: snapshot.timestamp || null,
+  };
+}
+
+// ─── Build Pipeline (Phase 3) ───────────────────────────────────────────────
+
+/**
+ * Pre-flight checks for graphify build (BUILD-01, BUILD-02, D-09).
+ * Does NOT invoke graphify -- returns structured JSON for the builder agent.
+ *
+ * @param {string} cwd - Working directory
+ * @returns {object}
+ */
+function graphifyBuild(cwd) {
+  const planningDir = path.join(cwd, '.planning');
+  if (!isGraphifyEnabled(planningDir)) return disabledResponse();
+
+  const installed = checkGraphifyInstalled();
+  if (!installed.installed) return { error: installed.message };
+
+  const version = checkGraphifyVersion();
+
+  // Ensure output directory exists (D-05)
+  const graphsDir = path.join(planningDir, 'graphs');
+  fs.mkdirSync(graphsDir, { recursive: true });
+
+  // Read build timeout from config -- default 300s per D-02
+  const config = safeReadJson(path.join(planningDir, 'config.json')) || {};
+  const timeoutSec = (config.graphify && config.graphify.build_timeout) || 300;
+
+  return {
+  action: 'spawn_agent',
+  graphs_dir: graphsDir,
+  graphify_out: path.join(cwd, 'graphify-out'),
+  timeout_seconds: timeoutSec,
+  version: version.version,
+  version_warning: version.warning,
+  artifacts: ['graph.json', 'graph.html', 'GRAPH_REPORT.md'],
+  };
+}
+
+/**
+ * Write a diff snapshot after successful build (D-06).
+ * Reads graph.json from .planning/graphs/ and writes .last-build-snapshot.json
+ * using atomicWriteFileSync for crash safety.
+ *
+ * @param {string} cwd - Working directory
+ * @returns {object}
+ */
+function writeSnapshot(cwd) {
+  const graphPath = path.join(cwd, '.planning', 'graphs', 'graph.json');
+  const graph = safeReadJson(graphPath);
+  if (!graph) return { error: 'Cannot write snapshot: graph.json not parseable' };
+
+  const snapshot = {
+  version: 1,
+  timestamp: new Date().toISOString(),
+  nodes: graph.nodes || [],
+  edges: graph.edges || graph.links || [],
+  };
+
+  const snapshotPath = path.join(cwd, '.planning', 'graphs', '.last-build-snapshot.json');
+  atomicWriteFileSync(snapshotPath, JSON.stringify(snapshot, null, 2));
+  return {
+  saved: true,
+  timestamp: snapshot.timestamp,
+  node_count: snapshot.nodes.length,
+  edge_count: snapshot.edges.length,
+  };
+}
+
+// ─── Exports ─────────────────────────────────────────────────────────────────
+
+module.exports = {
+  // Config gate
+  isGraphifyEnabled,
+  disabledResponse,
+  // Subprocess
+  execGraphify,
+  // Presence and version
+  checkGraphifyInstalled,
+  checkGraphifyVersion,
+  // Query (Phase 2)
+  graphifyQuery,
+  safeReadJson,
+  buildAdjacencyMap,
+  seedAndExpand,
+  applyBudget,
+  // Status (Phase 2)
+  graphifyStatus,
+  // Diff (Phase 2)
+  graphifyDiff,
+  // Build (Phase 3)
+  graphifyBuild,
+  writeSnapshot,
+};