@assistkick/create 1.10.0 → 1.11.0

package/templates/assistkick-product-system/packages/shared/lib/workflow_orchestrator.ts

@@ -55,7 +55,7 @@ export class WorkflowOrchestrator {
 
     // Fire-and-forget — loop runs in the background
     this.runLoop().catch(err => {
-      this.log('ORCHESTRATOR', `Play All UNCAUGHT ERROR: ${err.message}`);
+      this.log('ORCHESTRATOR', `Play All UNCAUGHT ERROR:`, err.stack || err.message);
     }).finally(() => {
       this.active = false;
       this.currentFeatureId = null;
@@ -100,7 +100,7 @@ export class WorkflowOrchestrator {
         kanbanData = await this.loadKanban(this.projectId);
         graphData = await this.readGraph(this.projectId);
       } catch (err: any) {
-        this.log('ORCHESTRATOR', `Failed to fetch data: ${err.message}`);
+        this.log('ORCHESTRATOR', `Failed to fetch data:`, err.stack || err.message);
         break;
       }
 
@@ -167,7 +167,7 @@ export class WorkflowOrchestrator {
         try {
           await this.workflowEngine.start(card.id, defaultWorkflow.id, this.projectId);
         } catch (err: any) {
-          this.log('ORCHESTRATOR', `Failed to start workflow for ${card.id}: ${err.message}`);
+          this.log('ORCHESTRATOR', `Failed to start workflow for ${card.id}:`, err.stack || err.message);
           continue;
         }
 
@@ -201,7 +201,7 @@ export class WorkflowOrchestrator {
           return;
         }
       } catch (err: any) {
-        this.log('ORCHESTRATOR', `Error polling status for ${featureId}: ${err.message}`);
+        this.log('ORCHESTRATOR', `Error polling status for ${featureId}:`, err.stack || err.message);
         return;
       }
 

package/templates/assistkick-product-system/packages/shared/package.json

@@ -19,7 +19,8 @@
     "dotenv": "^17.3.1",
     "drizzle-orm": "^0.45.1",
     "glob": "11.1.0",
-    "gray-matter": "^4.0.3"
+    "gray-matter": "^4.0.3",
+    "isolated-vm": "^6.1.0"
   },
   "devDependencies": {
     "@types/node": "^25.3.3",

package/templates/assistkick-product-system/packages/shared/test_fixtures/hanging_stream.mjs

@@ -0,0 +1,46 @@
+/**
+ * Test fixture: simulates a Claude CLI process in stream-json mode
+ * that emits a result event but never exits (hangs).
+ * Used by claude-service tests to verify the post-result timeout.
+ *
+ * Usage: node hanging_stream.mjs [--exit-after-ms <ms>]
+ *   No args: emits result event and hangs indefinitely
+ *   --exit-after-ms <ms>: emits result event and exits normally after <ms> milliseconds
+ */
+
+// Read stdin (prompt) to avoid broken pipe
+process.stdin.resume();
+process.stdin.on('data', () => {});
+process.stdin.on('end', () => {});
+
+// Emit an assistant event
+const assistantEvent = JSON.stringify({
+  type: 'assistant',
+  message: {
+    content: [{ type: 'text', text: 'Implementation complete.' }],
+    usage: { input_tokens: 100, output_tokens: 50 },
+  },
+});
+process.stdout.write(assistantEvent + '\n');
+
+// Emit a result event (this signals the conversation is complete)
+const resultEvent = JSON.stringify({
+  type: 'result',
+  result: 'Test result output from the agent.',
+  cost_usd: 0.01,
+  duration_ms: 1234,
+  num_turns: 1,
+  stop_reason: 'end_turn',
+  model: 'claude-test',
+});
+process.stdout.write(resultEvent + '\n');
+
+// Parse args
+const exitAfterIdx = process.argv.indexOf('--exit-after-ms');
+if (exitAfterIdx !== -1) {
+  const ms = parseInt(process.argv[exitAfterIdx + 1], 10);
+  setTimeout(() => process.exit(0), ms);
+} else {
+  // Hang indefinitely — keep the event loop alive with a long timer
+  setInterval(() => {}, 60_000);
+}

package/templates/assistkick-product-system/packages/shared/tools/add_node.test.ts

@@ -16,6 +16,25 @@ const deriveFeatureType = (
   return null;
 };
 
+/**
+ * Determines whether a new node should be auto-added to the kanban backlog.
+ * Mirrors the logic in add_node.ts.
+ */
+const shouldAutoAddToKanban = (nodeType: string): boolean => {
+  return nodeType === 'feature';
+};
+
+/**
+ * Builds the initial kanban entry for a newly created feature.
+ * Mirrors the entry shape passed to saveKanbanEntry in add_node.ts.
+ */
+const buildInitialKanbanEntry = () => ({
+  column: 'backlog',
+  rejection_count: 0,
+  notes: [],
+  reviews: [],
+});
+
 describe('deriveFeatureType', () => {
   it('returns "video" for feature nodes in video projects', () => {
     assert.equal(deriveFeatureType('feature', 'video'), 'video');
@@ -41,3 +60,28 @@ describe('deriveFeatureType', () => {
     assert.equal(deriveFeatureType('decision', 'software'), null);
   });
 });
+
+describe('shouldAutoAddToKanban', () => {
+  it('returns true for feature nodes', () => {
+    assert.equal(shouldAutoAddToKanban('feature'), true);
+  });
+
+  it('returns false for non-feature node types', () => {
+    assert.equal(shouldAutoAddToKanban('component'), false);
+    assert.equal(shouldAutoAddToKanban('decision'), false);
+    assert.equal(shouldAutoAddToKanban('epic'), false);
+    assert.equal(shouldAutoAddToKanban('data_entity'), false);
+    assert.equal(shouldAutoAddToKanban('tech_choice'), false);
+    assert.equal(shouldAutoAddToKanban('non_functional_requirement'), false);
+  });
+});
+
+describe('buildInitialKanbanEntry', () => {
+  it('creates a backlog entry with zeroed counters', () => {
+    const entry = buildInitialKanbanEntry();
+    assert.equal(entry.column, 'backlog');
+    assert.equal(entry.rejection_count, 0);
+    assert.deepEqual(entry.notes, []);
+    assert.deepEqual(entry.reviews, []);
+  });
+});

package/templates/assistkick-product-system/packages/shared/tools/add_node.ts

@@ -14,6 +14,7 @@ import { getDb } from '../lib/db.js';
 import { nodes, projects } from '../db/schema.js';
 import { deriveMetadata, templateSections } from '../lib/markdown.js';
 import { assertValidType, assertUniqueName } from '../lib/validator.js';
+import { saveKanbanEntry } from '../lib/kanban.js';
 
 program
   .requiredOption('--type <type>', 'Node type (e.g., feature, component, decision)')
@@ -96,6 +97,12 @@ const opts = program.opts();
       projectId: opts.projectId,
     });
 
+    // Auto-add features to the kanban backlog
+    if (opts.type === 'feature') {
+      await saveKanbanEntry(id, { column: 'backlog', rejection_count: 0, notes: [], reviews: [] }, opts.projectId);
+      console.log(chalk.green(`✓ Added ${id} to kanban backlog`));
+    }
+
     console.log(chalk.green(`✓ Created ${opts.type} node: ${id}`));
     console.log(JSON.stringify({ id, type: opts.type, name: opts.name }));
   } catch (err) {

package/templates/assistkick-product-system/packages/shared/tools/remove_node.ts

@@ -10,7 +10,7 @@ import { eq, or } from 'drizzle-orm';
 import { createInterface } from 'node:readline';
 import { getDb } from '../lib/db.js';
 import { getNode } from '../lib/graph.js';
-import { assertNodeExists } from '../lib/validator.js';
+import { assertNodeExists, assertNotDone } from '../lib/validator.js';
 import { nodes, edges, kanban, reviewMeta } from '../db/schema.js';
 
 program
@@ -35,6 +35,7 @@ const confirm = async (message: string): Promise<boolean> => {
 (async () => {
   try {
     await assertNodeExists(id);
+    await assertNotDone(id);
 
     const node = await getNode(id);
     const db = getDb();

package/templates/assistkick-product-system/packages/shared/tools/resolve_question.ts

@@ -8,7 +8,7 @@ import { program } from 'commander';
 import chalk from 'chalk';
 import { readGraph, patchNode } from '../lib/graph.js';
 import { readNode, writeNode, deriveMetadata } from '../lib/markdown.js';
-import { assertNodeExists } from '../lib/validator.js';
+import { assertNodeExists, assertNotDone } from '../lib/validator.js';
 
 program
   .argument('<id>', 'Node ID containing the question')
@@ -23,6 +23,7 @@ const opts = program.opts();
 (async () => {
   try {
     await assertNodeExists(id);
+    await assertNotDone(id);
 
     const graph = await readGraph();
     const nodeMeta = graph.nodes.find(n => n.id === id);

package/templates/assistkick-product-system/packages/shared/tools/update_node.ts

@@ -8,7 +8,7 @@ import { program } from 'commander';
 import chalk from 'chalk';
 import { readGraph, patchNode } from '../lib/graph.js';
 import { readNode, writeNode, appendToSection, setSection, deriveMetadata } from '../lib/markdown.js';
-import { assertNodeExists } from '../lib/validator.js';
+import { assertNodeExists, assertNotDone } from '../lib/validator.js';
 import { VALID_STATUSES, VALID_PRIORITIES, VALID_FEATURE_KINDS } from '../lib/constants.js';
 import { getKanbanEntry, saveKanbanEntry } from '../lib/kanban.js';
 
@@ -32,6 +32,7 @@ const opts = program.opts();
 (async () => {
   try {
     await assertNodeExists(id);
+    await assertNotDone(id);
 
     const graph = await readGraph();
     const nodeMeta = graph.nodes.find(n => n.id === id);

package/templates/assistkick-product-system/tests/message_queue.test.ts

@@ -0,0 +1,178 @@
+/**
+ * Tests for the Chat v2 Message Queue.
+ * Validates enqueue, remove, clear, drainAll, and mergeTexts operations.
+ * Uses node:test built-in runner.
+ */
+import { describe, it, beforeEach } from 'node:test';
+import assert from 'node:assert/strict';
+import { MessageQueue } from '../packages/frontend/src/lib/message_queue.ts';
+
+describe('MessageQueue', () => {
+  let queue: MessageQueue;
+
+  beforeEach(() => {
+    queue = new MessageQueue();
+  });
+
+  describe('enqueue', () => {
+    it('adds a message to an empty queue', () => {
+      queue.enqueue('Hello');
+
+      assert.equal(queue.getLength(), 1);
+      assert.equal(queue.getQueue()[0].text, 'Hello');
+    });
+
+    it('appends multiple messages in order', () => {
+      queue.enqueue('First');
+      queue.enqueue('Second');
+      queue.enqueue('Third');
+
+      const items = queue.getQueue();
+      assert.equal(items.length, 3);
+      assert.equal(items[0].text, 'First');
+      assert.equal(items[1].text, 'Second');
+      assert.equal(items[2].text, 'Third');
+    });
+
+    it('generates unique IDs for each message', () => {
+      queue.enqueue('A');
+      queue.enqueue('B');
+
+      const items = queue.getQueue();
+      assert.notEqual(items[0].id, items[1].id);
+    });
+
+    it('sets createdAt timestamp', () => {
+      const before = Date.now();
+      queue.enqueue('Test');
+      const after = Date.now();
+
+      const msg = queue.getQueue()[0];
+      assert.ok(msg.createdAt >= before);
+      assert.ok(msg.createdAt <= after);
+    });
+
+    it('returns the enqueued message', () => {
+      const msg = queue.enqueue('Return me');
+
+      assert.equal(msg.text, 'Return me');
+      assert.ok(msg.id.startsWith('q_'));
+    });
+  });
+
+  describe('remove', () => {
+    it('removes a specific message by id', () => {
+      queue.enqueue('Keep');
+      queue.enqueue('Remove me');
+      queue.enqueue('Also keep');
+
+      const removeId = queue.getQueue()[1].id;
+      const removed = queue.remove(removeId);
+
+      assert.equal(removed, true);
+      assert.equal(queue.getLength(), 2);
+      assert.equal(queue.getQueue()[0].text, 'Keep');
+      assert.equal(queue.getQueue()[1].text, 'Also keep');
+    });
+
+    it('returns false when id does not exist', () => {
+      queue.enqueue('Only one');
+
+      const removed = queue.remove('nonexistent_id');
+
+      assert.equal(removed, false);
+      assert.equal(queue.getLength(), 1);
+    });
+  });
+
+  describe('clear', () => {
+    it('removes all messages from the queue', () => {
+      queue.enqueue('One');
+      queue.enqueue('Two');
+      queue.enqueue('Three');
+
+      queue.clear();
+
+      assert.equal(queue.getLength(), 0);
+    });
+
+    it('is safe to call on an empty queue', () => {
+      queue.clear();
+
+      assert.equal(queue.getLength(), 0);
+    });
+  });
+
+  describe('drainAll', () => {
+    it('returns all messages and empties the queue', () => {
+      queue.enqueue('First');
+      queue.enqueue('Second');
+
+      const drained = queue.drainAll();
+
+      assert.equal(drained.length, 2);
+      assert.equal(drained[0].text, 'First');
+      assert.equal(drained[1].text, 'Second');
+      assert.equal(queue.getLength(), 0);
+    });
+
+    it('returns empty array when queue is empty', () => {
+      const drained = queue.drainAll();
+
+      assert.equal(drained.length, 0);
+    });
+
+    it('subsequent drain returns empty after first drain', () => {
+      queue.enqueue('Once');
+
+      const first = queue.drainAll();
+      const second = queue.drainAll();
+
+      assert.equal(first.length, 1);
+      assert.equal(second.length, 0);
+    });
+  });
+
+  describe('mergeTexts', () => {
+    it('merges messages with double newline separator', () => {
+      queue.enqueue('Fix the bug in auth');
+      queue.enqueue('Also update the docs');
+      queue.enqueue('Run the tests when done');
+
+      const drained = queue.drainAll();
+      const merged = MessageQueue.mergeTexts(drained);
+
+      assert.equal(
+        merged,
+        'Fix the bug in auth\n\nAlso update the docs\n\nRun the tests when done',
+      );
+    });
+
+    it('returns single message text without separator', () => {
+      queue.enqueue('Only one message');
+
+      const drained = queue.drainAll();
+      const merged = MessageQueue.mergeTexts(drained);
+
+      assert.equal(merged, 'Only one message');
+    });
+
+    it('returns empty string for empty array', () => {
+      const merged = MessageQueue.mergeTexts([]);
+
+      assert.equal(merged, '');
+    });
+  });
+
+  describe('getQueue immutability', () => {
+    it('returns a readonly snapshot that is not affected by later enqueues', () => {
+      queue.enqueue('Original');
+      const snapshot = queue.getQueue();
+
+      queue.enqueue('New');
+
+      assert.equal(snapshot.length, 1);
+      assert.equal(queue.getLength(), 2);
+    });
+  });
+});

package/templates/assistkick-product-system/tests/message_queue_per_session.test.ts

@@ -0,0 +1,143 @@
+/**
+ * Tests for per-session message queue scoping.
+ *
+ * Validates that the MessageQueue class correctly isolates queues when used
+ * in a per-session Map pattern (as useMessageQueueStore does internally).
+ * Uses node:test built-in runner.
+ */
+import { describe, it, beforeEach } from 'node:test';
+import assert from 'node:assert/strict';
+import { MessageQueue } from '../packages/frontend/src/lib/message_queue.ts';
+
+describe('Per-session MessageQueue isolation', () => {
+  let sessionQueues: Map<string, MessageQueue>;
+
+  const getOrCreateQueue = (sessionId: string): MessageQueue => {
+    let mq = sessionQueues.get(sessionId);
+    if (!mq) {
+      mq = new MessageQueue();
+      sessionQueues.set(sessionId, mq);
+    }
+    return mq;
+  };
+
+  beforeEach(() => {
+    sessionQueues = new Map();
+  });
+
+  it('enqueues messages to separate sessions independently', () => {
+    const queueA = getOrCreateQueue('session_a');
+    const queueB = getOrCreateQueue('session_b');
+
+    queueA.enqueue('Message for A');
+    queueB.enqueue('Message for B');
+    queueA.enqueue('Second message for A');
+
+    assert.equal(queueA.getLength(), 2);
+    assert.equal(queueB.getLength(), 1);
+    assert.equal(queueA.getQueue()[0].text, 'Message for A');
+    assert.equal(queueB.getQueue()[0].text, 'Message for B');
+  });
+
+  it('draining one session does not affect another', () => {
+    const queueA = getOrCreateQueue('session_a');
+    const queueB = getOrCreateQueue('session_b');
+
+    queueA.enqueue('A1');
+    queueA.enqueue('A2');
+    queueB.enqueue('B1');
+
+    const drained = queueA.drainAll();
+
+    assert.equal(drained.length, 2);
+    assert.equal(queueA.getLength(), 0);
+    assert.equal(queueB.getLength(), 1);
+    assert.equal(queueB.getQueue()[0].text, 'B1');
+  });
+
+  it('clearing one session preserves the other', () => {
+    const queueA = getOrCreateQueue('session_a');
+    const queueB = getOrCreateQueue('session_b');
+
+    queueA.enqueue('A1');
+    queueB.enqueue('B1');
+    queueB.enqueue('B2');
+
+    queueA.clear();
+
+    assert.equal(queueA.getLength(), 0);
+    assert.equal(queueB.getLength(), 2);
+  });
+
+  it('removing a message from one session does not affect another', () => {
+    const queueA = getOrCreateQueue('session_a');
+    const queueB = getOrCreateQueue('session_b');
+
+    const msgA = queueA.enqueue('A1');
+    queueB.enqueue('B1');
+
+    queueA.remove(msgA.id);
+
+    assert.equal(queueA.getLength(), 0);
+    assert.equal(queueB.getLength(), 1);
+  });
+
+  it('switching active session shows correct queue', () => {
+    const queueA = getOrCreateQueue('session_a');
+    const queueB = getOrCreateQueue('session_b');
+
+    queueA.enqueue('A1');
+    queueA.enqueue('A2');
+    queueB.enqueue('B1');
+
+    // Simulate switching to session_b — visible queue is session_b's
+    let activeSessionId = 'session_b';
+    let visibleQueue = [...getOrCreateQueue(activeSessionId).getQueue()];
+    assert.equal(visibleQueue.length, 1);
+    assert.equal(visibleQueue[0].text, 'B1');
+
+    // Switch back to session_a
+    activeSessionId = 'session_a';
+    visibleQueue = [...getOrCreateQueue(activeSessionId).getQueue()];
+    assert.equal(visibleQueue.length, 2);
+    assert.equal(visibleQueue[0].text, 'A1');
+  });
+
+  it('draining a specific session while viewing another returns correct messages', () => {
+    const queueA = getOrCreateQueue('session_a');
+    const queueB = getOrCreateQueue('session_b');
+
+    queueA.enqueue('A1');
+    queueA.enqueue('A2');
+    queueB.enqueue('B1');
+
+    // Active session is B, but we drain A (onStreamEnd scenario)
+    const drained = queueA.drainAll();
+
+    assert.equal(drained.length, 2);
+    assert.equal(drained[0].text, 'A1');
+    assert.equal(drained[1].text, 'A2');
+    // Session B still has its message
+    assert.equal(queueB.getLength(), 1);
+  });
+
+  it('creating a new session starts with empty queue', () => {
+    getOrCreateQueue('session_a').enqueue('A1');
+
+    const queueNew = getOrCreateQueue('session_new');
+
+    assert.equal(queueNew.getLength(), 0);
+  });
+
+  it('merged texts from drained session are correct', () => {
+    const queueA = getOrCreateQueue('session_a');
+
+    queueA.enqueue('Fix the bug');
+    queueA.enqueue('Also update docs');
+
+    const drained = queueA.drainAll();
+    const merged = MessageQueue.mergeTexts(drained);
+
+    assert.equal(merged, 'Fix the bug\n\nAlso update docs');
+  });
+});

package/templates/skills/assistkick-bootstrap/SKILL.md

@@ -13,7 +13,7 @@ priorities, and preferences**. You interact with the graph exclusively
 through the tools below.
 
 All tools live in `assistkick-product-system/packages/shared/tools/` and
-are run with `npx tsx`.
+are run with `pnpm tsx`.
 
 ## Bootstrap Philosophy
 Unlike a greenfield interview, the project already exists. The codebase is
@@ -205,33 +205,33 @@ Use the same `<project_id>` on **every** tool call in this session.
 
 ### start_session
 ```
-npx tsx packages/shared/tools/start_session.ts --project-id <project_id>
+pnpm tsx packages/shared/tools/start_session.ts --project-id <project_id>
 ```
 
 ### end_session
 ```
-npx tsx packages/shared/tools/end_session.ts --project-id <project_id> --summary "..." --nodes-touched "feat_001,dec_001" --questions-resolved 3
+pnpm tsx packages/shared/tools/end_session.ts --project-id <project_id> --summary "..." --nodes-touched "feat_001,dec_001" --questions-resolved 3
 ```
 
 ### search_nodes
 ```
-npx tsx packages/shared/tools/search_nodes.ts --project-id <project_id> --query "keyword"
-npx tsx packages/shared/tools/search_nodes.ts --project-id <project_id> --type feature
-npx tsx packages/shared/tools/search_nodes.ts --project-id <project_id> --has-open-questions
-npx tsx packages/shared/tools/search_nodes.ts --project-id <project_id> --completeness-below 0.5
+pnpm tsx packages/shared/tools/search_nodes.ts --project-id <project_id> --query "keyword"
+pnpm tsx packages/shared/tools/search_nodes.ts --project-id <project_id> --type feature
+pnpm tsx packages/shared/tools/search_nodes.ts --project-id <project_id> --has-open-questions
+pnpm tsx packages/shared/tools/search_nodes.ts --project-id <project_id> --completeness-below 0.5
 ```
 
 ### get_node
 ```
-npx tsx packages/shared/tools/get_node.ts <node_id> --project-id <project_id>
-npx tsx packages/shared/tools/get_node.ts --name "Node Name" --project-id <project_id>
+pnpm tsx packages/shared/tools/get_node.ts <node_id> --project-id <project_id>
+pnpm tsx packages/shared/tools/get_node.ts --name "Node Name" --project-id <project_id>
 ```
 Returns the node content (formatted as markdown) plus a Relations section listing
 all connected nodes with direction, relation type, name, type, and status.
 
 ### add_node
 ```
-npx tsx packages/shared/tools/add_node.ts --project-id <project_id> --type <type> --name "Name" --description "..."
+pnpm tsx packages/shared/tools/add_node.ts --project-id <project_id> --type <type> --name "Name" --description "..."
 ```
 Valid types: feature, component, data_entity, decision, tech_choice,
 non_functional_requirement, design_token, design_pattern, user_role,
@@ -239,23 +239,23 @@ flow, assumption, open_question
 
 ### update_node
 ```
-npx tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --add-acceptance-criteria "..."
-npx tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --add-open-question "..."
-npx tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --add-note "Session N: ..."
-npx tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --set-status <draft|partially_defined|defined>
-npx tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --set-priority <low|medium|high|blocking>
-npx tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --set-description "..."
-npx tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --set-section "SectionName=content"
+pnpm tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --add-acceptance-criteria "..."
+pnpm tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --add-open-question "..."
+pnpm tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --add-note "Session N: ..."
+pnpm tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --set-status <draft|partially_defined|defined>
+pnpm tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --set-priority <low|medium|high|blocking>
+pnpm tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --set-description "..."
+pnpm tsx packages/shared/tools/update_node.ts <id> --project-id <project_id> --set-section "SectionName=content"
 ```
 
 ### resolve_question
 ```
-npx tsx packages/shared/tools/resolve_question.ts <id> --project-id <project_id> --question "..." --answer "..."
+pnpm tsx packages/shared/tools/resolve_question.ts <id> --project-id <project_id> --question "..." --answer "..."
 ```
 
 ### add_edge
 ```
-npx tsx packages/shared/tools/add_edge.ts <from_id> <relation> <to_id> --project-id <project_id>
+pnpm tsx packages/shared/tools/add_edge.ts <from_id> <relation> <to_id> --project-id <project_id>
 ```
 Valid relations: contains, depends_on, governed_by, constrained_by,
 implemented_with, reads_writes, exposes, consumes, performed_by,
@@ -263,25 +263,25 @@ escalates_to, relates_to
 
 ### remove_edge
 ```
-npx tsx packages/shared/tools/remove_edge.ts <from_id> <relation> <to_id> --project-id <project_id>
+pnpm tsx packages/shared/tools/remove_edge.ts <from_id> <relation> <to_id> --project-id <project_id>
 ```
 
 ### get_gaps
 ```
-npx tsx packages/shared/tools/get_gaps.ts --project-id <project_id>
-npx tsx packages/shared/tools/get_gaps.ts --project-id <project_id> --blocking-only
-npx tsx packages/shared/tools/get_gaps.ts --project-id <project_id> --type feature
+pnpm tsx packages/shared/tools/get_gaps.ts --project-id <project_id>
+pnpm tsx packages/shared/tools/get_gaps.ts --project-id <project_id> --blocking-only
+pnpm tsx packages/shared/tools/get_gaps.ts --project-id <project_id> --type feature
 ```
 
 ### get_status
 ```
-npx tsx packages/shared/tools/get_status.ts --project-id <project_id>
+pnpm tsx packages/shared/tools/get_status.ts --project-id <project_id>
 ```
 
 ### rebuild_index
 ```
-npx tsx packages/shared/tools/rebuild_index.ts --project-id <project_id>
-npx tsx packages/shared/tools/rebuild_index.ts --project-id <project_id> --dry-run
+pnpm tsx packages/shared/tools/rebuild_index.ts --project-id <project_id>
+pnpm tsx packages/shared/tools/rebuild_index.ts --project-id <project_id> --dry-run
 ```
 
 ## Search Strategy