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/commands/hooks/overview.md

@@ -0,0 +1,68 @@
+# Claude Code Hooks for claude-flow
+
+## Purpose
+
+Automatically coordinate, format, and learn from Claude Code operations using hooks.
+
+## Available Hooks
+
+### Pre-Operation Hooks
+
+- **pre-edit**: Validate and assign agents before file modifications
+- **pre-bash**: Check command safety and resource requirements
+- **pre-task**: Auto-spawn agents for complex tasks
+
+### Post-Operation Hooks
+
+- **post-edit**: Auto-format code and train neural patterns
+- **post-bash**: Log execution and update metrics
+- **post-search**: Cache results and improve search patterns
+
+### MCP Integration Hooks
+
+- **mcp-initialized**: Persist swarm configuration
+- **agent-spawned**: Update agent roster
+- **task-orchestrated**: Monitor task progress
+- **neural-trained**: Save pattern improvements
+
+### Session Hooks
+
+- **notify**: Custom notifications with swarm status
+- **session-end**: Generate summary and save state
+- **session-restore**: Load previous session state
+
+## Configuration
+
+Hooks are configured in `.claude/settings.json`:
+
+```json
+{
+  "hooks": {
+    "PreToolUse": [
+      {
+        "matcher": "^(Write|Edit|MultiEdit)$",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "npx claude-flow hook pre-edit --file '${tool.params.file_path}'"
+          }
+        ]
+      }
+    ]
+  }
+}
+```
+
+## Benefits
+
+- 🤖 Automatic agent assignment based on file type
+- 🎨 Consistent code formatting
+- 🧠 Continuous neural pattern improvement
+- 💾 Cross-session memory persistence
+- 📊 Performance metrics tracking
+
+## See Also
+
+- [Pre-Edit Hook](./pre-edit.md)
+- [Post-Edit Hook](./post-edit.md)
+- [Session End Hook](./session-end.md)