[docs] Update CLAUDE.md.

CLAUDE.md

@@ -20,6 +20,80 @@ For sparse attention related content (block sparse attention, MInference, FlexPr
 - **BlockManager** (`block_manager.py`): Paged attention with prefix caching (xxhash), default block size 4096
 - **Attention** (`layers/attention.py`): FlashAttention with chunked methods for CPU offload
 
+## PyTorch Hooks for Debugging
+
+### Hook Positions in Qwen3
+
+```
+decoder_layer
+├── input_layernorm (RMSNorm)
+├── self_attn (Qwen3Attention)          ← Hook here for attention I/O after o_proj
+│   ├── q_proj → q_norm → RoPE
+│   ├── k_proj → k_norm → RoPE
+│   ├── v_proj
+│   ├── attn (Attention)                ← Hook here for Q/K/V tensors
+│   │   └── FlashAttention / SDPA
+│   └── o_proj
+├── post_attention_layernorm (RMSNorm)
+└── mlp (Qwen3MLP)
+```
+
+### Hook Types & Data Shapes
+
+| Hook Position | Type | Captured Data |
+|---------------|------|---------------|
+| `self_attn` | post | `[batch, seq_len, hidden_size]` - after o_proj |
+| `self_attn.attn` | pre | Q,K,V: `[seq_len, num_heads, head_dim]` - after RoPE |
+| `self_attn.attn` | post | `[seq_len, num_heads, head_dim]` - before o_proj |
+
+### Example: Capture Attention Outputs
+
+```python
+storage = {}
+
+def make_hook(layer_id: int, storage: dict):
+    def hook(module, inputs, output):
+        if isinstance(output, tuple):
+            attn_output = output[0]
+        else:
+            attn_output = output
+        # nanovllm shape: [num_tokens, hidden_size] -> add batch dim
+        if attn_output.dim() == 2:
+            attn_output = attn_output.unsqueeze(0)
+        storage[layer_id] = attn_output.detach().clone()
+    return hook
+
+# Register hooks
+hooks = []
+for layer_idx, layer in enumerate(model.model.layers):
+    hooks.append(layer.self_attn.register_forward_hook(make_hook(layer_idx, storage)))
+
+# Run inference...
+
+# Cleanup
+for hook in hooks:
+    hook.remove()
+```
+
+### Alignment Testing
+
+Use `tests/test_align.py` to compare nanovllm with reference torch implementation:
+
+```bash
+python tests/test_align.py
+```
+
+Key files:
+- `tests/modeling_qwen3.py`: Reference Qwen3 implementation (torch + transformers only)
+- `tests/test_align.py`: Compares attention outputs between nanovllm and reference
+- `tests/test_needle_ref.py`: Reference needle test using custom Qwen3
+
+### Common Pitfalls
+
+1. **Shape mismatch**: nanovllm uses `[num_tokens, ...]` while torch uses `[batch, seq_len, ...]`
+2. **Hook position**: `self_attn` captures after o_proj, `self_attn.attn` captures before o_proj
+3. **Output format**: nanovllm returns tuple `(attn_output, None)`, handle with `output[0]`
+
 ## CPU Offload System
 
 ### Ring Buffer Design