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/automation/session-memory.md

@@ -0,0 +1,106 @@
+# Cross-Session Memory
+
+## Purpose
+
+Maintain context and learnings across Claude Code sessions for continuous improvement.
+
+## Memory Features
+
+### 1. Automatic State Persistence
+
+At session end, automatically saves:
+
+- Active agents and specializations
+- Task history and patterns
+- Performance metrics
+- Neural network weights
+- Knowledge base updates
+
+### 2. Session Restoration
+
+```javascript
+// Using MCP tools for memory operations
+mcp__claude -
+  flow__memory_usage({
+    action: "retrieve",
+    key: "session-state",
+    namespace: "sessions",
+  });
+
+// Restore swarm state
+mcp__claude -
+  flow__context_restore({
+    snapshotId: "sess-123",
+  });
+```
+
+**Fallback with npx:**
+
+```bash
+npx claude-flow hook session-restore --session-id "sess-123"
+```
+
+### 3. Memory Types
+
+**Project Memory:**
+
+- File relationships
+- Common edit patterns
+- Testing approaches
+- Build configurations
+
+**Agent Memory:**
+
+- Specialization levels
+- Task success rates
+- Optimization strategies
+- Error patterns
+
+**Performance Memory:**
+
+- Bottleneck history
+- Optimization results
+- Token usage patterns
+- Efficiency trends
+
+### 4. Privacy & Control
+
+```javascript
+// List memory contents
+mcp__claude -
+  flow__memory_usage({
+    action: "list",
+    namespace: "sessions",
+  });
+
+// Delete specific memory
+mcp__claude -
+  flow__memory_usage({
+    action: "delete",
+    key: "session-123",
+    namespace: "sessions",
+  });
+
+// Backup memory
+mcp__claude -
+  flow__memory_backup({
+    path: "./backups/memory-backup.json",
+  });
+```
+
+**Manual control:**
+
+```bash
+# View stored memory
+ls .claude-flow/memory/
+
+# Disable memory
+export CLAUDE_FLOW_MEMORY_PERSIST=false
+```
+
+## Benefits
+
+- 🧠 Contextual awareness
+- 📈 Cumulative learning
+- ⚡ Faster task completion
+- 🎯 Personalized optimization