fix: restore all removed bundled skills + fix skills sync system

- Restored 21 skills removed in commits 757d012 and 740dd92:
  accelerate, audiocraft, code-review, faiss, flash-attention, gguf,
  grpo-rl-training, guidance, llava, nemo-curator, obliteratus, peft,
  pytorch-fsdp, pytorch-lightning, simpo, slime, stable-diffusion,
  tensorrt-llm, torchtitan, trl-fine-tuning, whisper

- Rewrote sync_skills() with proper update semantics:
  * New skills (not in manifest): copied to user dir
  * Existing skills (in manifest + on disk): updated via hash comparison
  * User-deleted skills (in manifest, not on disk): respected, not re-added
  * Stale manifest entries (removed from bundled): cleaned from manifest

- Added sync_skills() to CLI startup (cmd_chat) and gateway startup
  (start_gateway) — previously only ran during 'hermes update'

- Updated cmd_update output to show new/updated/cleaned counts

- Rewrote tests: 20 tests covering manifest CRUD, dir hashing, fresh
  install, user deletion respect, update detection, stale cleanup, and
  name collision handling

75 bundled skills total. 2002 tests pass.

skills/mlops/grpo-rl-training/templates/basic_grpo_training.py

@@ -0,0 +1,228 @@
+"""
+Basic GRPO Training Template
+=============================
+
+A minimal, production-ready template for GRPO training with TRL.
+Adapt this for your specific task by modifying:
+1. Dataset loading (get_dataset function)
+2. Reward functions (reward_*_func)
+3. System prompt (SYSTEM_PROMPT)
+4. Hyperparameters (GRPOConfig)
+"""
+
+import torch
+import re
+from datasets import load_dataset, Dataset
+from transformers import AutoModelForCausalLM, AutoTokenizer
+from peft import LoraConfig
+from trl import GRPOTrainer, GRPOConfig
+
+# ==================== CONFIGURATION ====================
+
+MODEL_NAME = "Qwen/Qwen2.5-1.5B-Instruct"
+OUTPUT_DIR = "outputs/grpo-model"
+MAX_PROMPT_LENGTH = 256
+MAX_COMPLETION_LENGTH = 512
+
+SYSTEM_PROMPT = """
+Respond in the following format:
+<reasoning>
+[Your step-by-step thinking]
+</reasoning>
+<answer>
+[Final answer]
+</answer>
+"""
+
+# ==================== DATASET ====================
+
+def get_dataset(split="train"):
+    """
+    Load and prepare your dataset.
+
+    Returns: Dataset with columns:
+    - 'prompt': List[Dict] with role/content
+    - 'answer': str (ground truth, optional)
+    """
+    # Example: GSM8K math dataset
+    data = load_dataset('openai/gsm8k', 'main')[split]
+
+    def process_example(x):
+        # Extract ground truth answer
+        answer = x['answer'].split('####')[1].strip() if '####' in x['answer'] else None
+
+        return {
+            'prompt': [
+                {'role': 'system', 'content': SYSTEM_PROMPT},
+                {'role': 'user', 'content': x['question']}
+            ],
+            'answer': answer
+        }
+
+    return data.map(process_example)
+
+# ==================== HELPER FUNCTIONS ====================
+
+def extract_xml_tag(text: str, tag: str) -> str:
+    """Extract content between XML tags."""
+    pattern = f'<{tag}>(.*?)</{tag}>'
+    match = re.search(pattern, text, re.DOTALL)
+    return match.group(1).strip() if match else ""
+
+def extract_answer(text: str) -> str:
+    """Extract the final answer from structured output."""
+    return extract_xml_tag(text, 'answer')
+
+# ==================== REWARD FUNCTIONS ====================
+
+def correctness_reward_func(prompts, completions, answer, **kwargs):
+    """
+    Reward correct answers.
+    Weight: 2.0 (highest priority)
+    """
+    responses = [comp[0]['content'] for comp in completions]
+    extracted = [extract_answer(r) for r in responses]
+    return [2.0 if ans == gt else 0.0 for ans, gt in zip(extracted, answer)]
+
+def format_reward_func(completions, **kwargs):
+    """
+    Reward proper XML format.
+    Weight: 0.5
+    """
+    pattern = r'<reasoning>.*?</reasoning>\s*<answer>.*?</answer>'
+    responses = [comp[0]['content'] for comp in completions]
+    return [0.5 if re.search(pattern, r, re.DOTALL) else 0.0 for r in responses]
+
+def incremental_format_reward_func(completions, **kwargs):
+    """
+    Incremental reward for partial format compliance.
+    Weight: up to 0.5
+    """
+    responses = [comp[0]['content'] for comp in completions]
+    rewards = []
+
+    for r in responses:
+        score = 0.0
+        if '<reasoning>' in r:
+            score += 0.125
+        if '</reasoning>' in r:
+            score += 0.125
+        if '<answer>' in r:
+            score += 0.125
+        if '</answer>' in r:
+            score += 0.125
+
+        # Penalize extra content after closing tag
+        if '</answer>' in r:
+            extra = r.split('</answer>')[-1].strip()
+            score -= len(extra) * 0.001
+
+        rewards.append(score)
+
+    return rewards
+
+# ==================== MODEL SETUP ====================
+
+def setup_model_and_tokenizer():
+    """Load model and tokenizer with optimizations."""
+    model = AutoModelForCausalLM.from_pretrained(
+        MODEL_NAME,
+        torch_dtype=torch.bfloat16,
+        attn_implementation="flash_attention_2",
+        device_map="auto"
+    )
+
+    tokenizer = AutoTokenizer.from_pretrained(MODEL_NAME)
+    tokenizer.pad_token = tokenizer.eos_token
+
+    return model, tokenizer
+
+def get_peft_config():
+    """LoRA configuration for parameter-efficient training."""
+    return LoraConfig(
+        r=16,
+        lora_alpha=32,
+        target_modules=[
+            "q_proj", "k_proj", "v_proj", "o_proj",
+            "gate_proj", "up_proj", "down_proj"
+        ],
+        task_type="CAUSAL_LM",
+        lora_dropout=0.05,
+    )
+
+# ==================== TRAINING ====================
+
+def main():
+    """Main training function."""
+
+    # Load data
+    print("Loading dataset...")
+    dataset = get_dataset()
+    print(f"Dataset size: {len(dataset)}")
+
+    # Setup model
+    print("Loading model...")
+    model, tokenizer = setup_model_and_tokenizer()
+
+    # Training configuration
+    training_args = GRPOConfig(
+        output_dir=OUTPUT_DIR,
+        run_name="grpo-training",
+
+        # Learning rate
+        learning_rate=5e-6,
+        adam_beta1=0.9,
+        adam_beta2=0.99,
+        weight_decay=0.1,
+        warmup_ratio=0.1,
+        lr_scheduler_type='cosine',
+
+        # Batch settings
+        per_device_train_batch_size=1,
+        gradient_accumulation_steps=4,
+
+        # GRPO specific
+        num_generations=8,
+        max_prompt_length=MAX_PROMPT_LENGTH,
+        max_completion_length=MAX_COMPLETION_LENGTH,
+
+        # Training duration
+        num_train_epochs=1,
+
+        # Optimization
+        bf16=True,
+        optim="adamw_8bit",
+        max_grad_norm=0.1,
+
+        # Logging
+        logging_steps=1,
+        save_steps=100,
+        report_to="wandb",  # Change to "none" to disable logging
+    )
+
+    # Initialize trainer
+    trainer = GRPOTrainer(
+        model=model,
+        processing_class=tokenizer,
+        reward_funcs=[
+            incremental_format_reward_func,
+            format_reward_func,
+            correctness_reward_func,
+        ],
+        args=training_args,
+        train_dataset=dataset,
+        peft_config=get_peft_config(),
+    )
+
+    # Train
+    print("Starting training...")
+    trainer.train()
+
+    # Save final model
+    print(f"Saving model to {OUTPUT_DIR}/final")
+    trainer.save_model(f"{OUTPUT_DIR}/final")
+
+    print("Training complete!")
+
+if __name__ == "__main__":
+    main()