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/optimization/topology-optimize.md

@@ -0,0 +1,28 @@
+# topology-optimize
+
+Optimize swarm topology for current workload.
+
+## Usage
+
+```bash
+npx claude-flow optimization topology-optimize [options]
+```
+
+## Options
+
+- `--analyze-first` - Analyze before optimizing
+- `--target <metric>` - Optimization target
+- `--apply` - Apply optimizations
+
+## Examples
+
+```bash
+# Analyze and suggest
+npx claude-flow optimization topology-optimize --analyze-first
+
+# Optimize for speed
+npx claude-flow optimization topology-optimize --target speed
+
+# Apply changes
+npx claude-flow optimization topology-optimize --target efficiency --apply
+```