chore: restore .claude commands, agents, helpers & skills (lost in 1df208d)

Restores the entire .claude/ infrastructure that was accidentally deleted
in commit 1df208d ('feat(timeline): add pulse animation for in-flight drag
mutations'). Recovered via git checkout 1df208d^.

Restored:
- .claude/commands/ (gitlooper, sparc/, github/, automation/, monitoring/,
  optimization/, hooks/, plan, implement, research, review, perf, visualaudit)
- .claude/agents/ (core/, github/, sparc/, v3/, swarm/, templates/, ...)
- .claude/helpers/ (41 scripts incl. hook-handler.cjs, statusline.cjs)
- .claude/skills/ (20 skills incl. sparc-methodology, github-*, v3-*)
- .claude/settings.json (hooks configuration)

Also updated all CapaKraken → Nexus references in affected command files.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

.claude/helpers/github-setup.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+# Setup GitHub integration for Claude Flow
+
+echo "🔗 Setting up GitHub integration..."
+
+# Check for gh CLI
+if ! command -v gh &> /dev/null; then
+    echo "⚠️  GitHub CLI (gh) not found"
+    echo "Install from: https://cli.github.com/"
+    echo "Continuing without GitHub features..."
+else
+    echo "✅ GitHub CLI found"
+    
+    # Check auth status
+    if gh auth status &> /dev/null; then
+        echo "✅ GitHub authentication active"
+    else
+        echo "⚠️  Not authenticated with GitHub"
+        echo "Run: gh auth login"
+    fi
+fi
+
+echo ""
+echo "📦 GitHub swarm commands available:"
+echo "  - npx claude-flow github swarm"
+echo "  - npx claude-flow repo analyze"
+echo "  - npx claude-flow pr enhance"
+echo "  - npx claude-flow issue triage"