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/trl-fine-tuning/references/dpo-variants.md

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+# DPO Variants
+
+Complete guide to Direct Preference Optimization loss variants in TRL.
+
+## Overview
+
+DPO optimizes models using preference data (chosen/rejected pairs). TRL supports 10+ loss variants for different scenarios.
+
+## Loss Types
+
+### 1. Sigmoid (Standard DPO)
+
+**Formula**: `-log(sigmoid(β * logits))`
+
+**When to use**: Default choice, general preference alignment
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="sigmoid",
+    beta=0.1,  # KL penalty
+    per_device_train_batch_size=64,
+    learning_rate=1e-6
+)
+```
+
+### 2. IPO (Identity Policy Optimization)
+
+**Formula**: `(logits - 1/(2β))²`
+
+**When to use**: Better theoretical foundation, reduce overfitting
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="ipo",
+    beta=0.1,
+    per_device_train_batch_size=90,
+    learning_rate=1e-2
+)
+```
+
+### 3. Hinge (SLiC)
+
+**Formula**: `ReLU(1 - β * logits)`
+
+**When to use**: Margin-based objective
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="hinge",
+    beta=0.1,
+    per_device_train_batch_size=512,
+    learning_rate=1e-4
+)
+```
+
+### 4. Robust DPO
+
+**Formula**: Sigmoid with label smoothing for noise robustness
+
+**When to use**: Noisy preference labels
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="robust",
+    beta=0.01,
+    label_smoothing=0.1,  # Noise probability
+    per_device_train_batch_size=16,
+    learning_rate=1e-3,
+    max_prompt_length=128,
+    max_length=512
+)
+```
+
+### 5. BCO Pair (Binary Classification)
+
+**Formula**: Train binary classifier (chosen=1, rejected=0)
+
+**When to use**: Pairwise preference data
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="bco_pair",
+    beta=0.01,
+    per_device_train_batch_size=128,
+    learning_rate=5e-7,
+    max_prompt_length=1536,
+    max_completion_length=512
+)
+```
+
+### 6. SPPO Hard
+
+**Formula**: Push chosen→0.5, rejected→-0.5
+
+**When to use**: Nash equilibrium, sparse data
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="sppo_hard",
+    beta=0.1
+)
+```
+
+### 7. DiscoPOP
+
+**Formula**: Log-Ratio Modulated Loss
+
+**When to use**: Automated loss discovery
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="discopop",
+    beta=0.05,
+    discopop_tau=0.05,
+    per_device_train_batch_size=64,
+    learning_rate=5e-7
+)
+```
+
+### 8. APO Zero
+
+**Formula**: Increase chosen, decrease rejected likelihood
+
+**When to use**: Model worse than winning outputs
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="apo_zero",
+    beta=0.1,
+    per_device_train_batch_size=64,
+    learning_rate=2e-7,
+    max_prompt_length=512,
+    max_completion_length=512
+)
+```
+
+### 9. APO Down
+
+**Formula**: Decrease both, emphasize rejected reduction
+
+**When to use**: Model better than winning outputs
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="apo_down",
+    beta=0.1,
+    # Same hyperparameters as apo_zero
+)
+```
+
+### 10. AOT & AOT Pair
+
+**Formula**: Distributional alignment via stochastic dominance
+
+**When to use**:
+- `aot_pair`: Paired preference data
+- `aot`: Unpaired data
+
+**Config**:
+```python
+DPOConfig(
+    loss_type="aot_pair",  # or "aot"
+    beta=0.1,
+    label_smoothing=0.0
+)
+```
+
+## Multi-Loss Training
+
+Combine multiple losses:
+
+```python
+DPOConfig(
+    loss_type=["sigmoid", "ipo"],
+    loss_weights=[0.7, 0.3],  # Weighted combination
+    beta=0.1
+)
+```
+
+## Key Parameters
+
+### Beta (β)
+
+Controls deviation from reference model:
+- **Higher** (0.5): More conservative, stays close to reference
+- **Lower** (0.01): More aggressive alignment
+- **Default**: 0.1
+
+### Label Smoothing
+
+For robust DPO:
+- **0.0**: No smoothing (default)
+- **0.1-0.3**: Moderate noise robustness
+- **0.5**: Maximum noise tolerance
+
+### Max Lengths
+
+- `max_prompt_length`: 128-1536
+- `max_completion_length`: 128-512
+- `max_length`: Total sequence (1024-2048)
+
+## Comparison Table
+
+| Loss | Speed | Stability | Best For |
+|------|-------|-----------|----------|
+| Sigmoid | Fast | Good | **General use** |
+| IPO | Fast | Better | Overfitting issues |
+| Hinge | Fast | Good | Margin objectives |
+| Robust | Fast | Best | Noisy data |
+| BCO | Medium | Good | Binary classification |
+| DiscoPOP | Fast | Good | New architectures |
+| APO | Fast | Good | Model quality matching |
+
+## References
+
+- DPO paper: https://arxiv.org/abs/2305.18290
+- IPO paper: https://arxiv.org/abs/2310.12036
+- TRL docs: https://huggingface.co/docs/trl/dpo_trainer

skills/mlops/trl-fine-tuning/references/online-rl.md

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+# Online RL Methods
+
+Guide to online reinforcement learning with PPO, GRPO, RLOO, and OnlineDPO.
+
+## Overview
+
+Online RL generates completions during training and optimizes based on rewards.
+
+## PPO (Proximal Policy Optimization)
+
+Classic RL algorithm for LLM alignment.
+
+### Basic Usage
+
+```bash
+python -m trl.scripts.ppo \
+    --model_name_or_path Qwen/Qwen2.5-0.5B-Instruct \
+    --reward_model_path reward-model \
+    --dataset_name trl-internal-testing/descriptiveness-sentiment-trl-style \
+    --output_dir model-ppo \
+    --learning_rate 3e-6 \
+    --per_device_train_batch_size 64 \
+    --total_episodes 10000 \
+    --num_ppo_epochs 4 \
+    --kl_coef 0.05
+```
+
+### Key Parameters
+
+- `kl_coef`: KL penalty (0.05-0.2)
+- `num_ppo_epochs`: Epochs per batch (2-4)
+- `cliprange`: PPO clip (0.1-0.3)
+- `vf_coef`: Value function coef (0.1)
+
+## GRPO (Group Relative Policy Optimization)
+
+Memory-efficient online RL.
+
+### Basic Usage
+
+```python
+from trl import GRPOTrainer, GRPOConfig
+from datasets import load_dataset
+
+# Define reward function
+def reward_func(completions, **kwargs):
+    return [len(set(c.split())) for c in completions]
+
+config = GRPOConfig(
+    output_dir="model-grpo",
+    num_generations=4,  # Completions per prompt
+    max_new_tokens=128
+)
+
+trainer = GRPOTrainer(
+    model="Qwen/Qwen2-0.5B-Instruct",
+    reward_funcs=reward_func,
+    args=config,
+    train_dataset=load_dataset("trl-lib/tldr", split="train")
+)
+trainer.train()
+```
+
+### Key Parameters
+
+- `num_generations`: 2-8 completions
+- `max_new_tokens`: 64-256
+- Learning rate: 1e-5 to 1e-4
+
+## Memory Comparison
+
+| Method | Memory (7B) | Speed | Use Case |
+|--------|-------------|-------|----------|
+| PPO | 40GB | Medium | Maximum control |
+| GRPO | 24GB | Fast | **Memory-constrained** |
+| OnlineDPO | 28GB | Fast | No reward model |
+
+## References
+
+- PPO paper: https://arxiv.org/abs/1707.06347
+- GRPO paper: https://arxiv.org/abs/2402.03300
+- TRL docs: https://huggingface.co/docs/trl/

skills/mlops/trl-fine-tuning/references/reward-modeling.md

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+# Reward Modeling
+
+Guide to training reward models with TRL for RLHF pipelines.
+
+## Overview
+
+Reward models score completions based on human preferences. Used in:
+- PPO training (RL feedback)
+- GRPO online RL
+- Completion ranking
+
+## Basic Training
+
+```python
+from transformers import AutoModelForSequenceClassification, AutoTokenizer
+from trl import RewardTrainer, RewardConfig
+from datasets import load_dataset
+
+# Load model (num_labels=1 for single reward score)
+model = AutoModelForSequenceClassification.from_pretrained(
+    "Qwen/Qwen2.5-0.5B-Instruct",
+    num_labels=1
+)
+tokenizer = AutoTokenizer.from_pretrained("Qwen/Qwen2.5-0.5B-Instruct")
+
+# Load preference dataset (chosen/rejected pairs)
+dataset = load_dataset("trl-lib/ultrafeedback_binarized", split="train")
+
+# Configure
+config = RewardConfig(
+    output_dir="Qwen2.5-Reward",
+    per_device_train_batch_size=2,
+    num_train_epochs=1,
+    learning_rate=1e-5
+)
+
+# Train
+trainer = RewardTrainer(
+    model=model,
+    args=config,
+    processing_class=tokenizer,
+    train_dataset=dataset
+)
+trainer.train()
+```
+
+## Dataset Format
+
+Required fields:
+```json
+{
+  "prompt": "Question or instruction",
+  "chosen": "Better response",
+  "rejected": "Worse response"
+}
+```
+
+## Bradley-Terry Loss
+
+Default loss function:
+```
+loss = -log(sigmoid(reward_chosen - reward_rejected))
+```
+
+Learns to score chosen > rejected.
+
+## Using Reward Models
+
+### Inference
+
+```python
+from transformers import pipeline
+
+# Load trained reward model
+reward_pipe = pipeline("text-classification", model="Qwen2.5-Reward")
+
+# Score completions
+texts = ["Good answer", "Bad answer"]
+scores = reward_pipe(texts)
+print(scores)  # Higher score = better
+```
+
+### In PPO
+
+```python
+from trl import PPOTrainer, PPOConfig
+
+config = PPOConfig(
+    reward_model_path="Qwen2.5-Reward"  # Use trained reward model
+)
+
+trainer = PPOTrainer(
+    model=policy_model,
+    config=config,
+    # Reward model loaded automatically
+)
+```
+
+## Hyperparameters
+
+| Model Size | Learning Rate | Batch Size | Epochs |
+|------------|---------------|------------|--------|
+| <1B | 2e-5 | 4-8 | 1-2 |
+| 1-7B | 1e-5 | 2-4 | 1 |
+| 7-13B | 5e-6 | 1-2 | 1 |
+
+## Evaluation
+
+Check reward separation:
+```python
+# Chosen should score higher than rejected
+chosen_rewards = model(**chosen_inputs).logits
+rejected_rewards = model(**rejected_inputs).logits
+
+accuracy = (chosen_rewards > rejected_rewards).float().mean()
+print(f"Accuracy: {accuracy:.2%}")  # Target: >80%
+```
+
+## References
+
+- InstructGPT paper: https://arxiv.org/abs/2203.02155
+- TRL docs: https://huggingface.co/docs/trl/reward_trainer

skills/mlops/trl-fine-tuning/references/sft-training.md

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+# SFT Training Guide
+
+Complete guide to Supervised Fine-Tuning (SFT) with TRL for instruction tuning and task-specific fine-tuning.
+
+## Overview
+
+SFT trains models on input-output pairs to minimize cross-entropy loss. Use for:
+- Instruction following
+- Task-specific fine-tuning
+- Chatbot training
+- Domain adaptation
+
+## Dataset Formats
+
+### Format 1: Prompt-Completion
+
+```json
+[
+  {
+    "prompt": "What is the capital of France?",
+    "completion": "The capital of France is Paris."
+  }
+]
+```
+
+### Format 2: Conversational (ChatML)
+
+```json
+[
+  {
+    "messages": [
+      {"role": "user", "content": "What is Python?"},
+      {"role": "assistant", "content": "Python is a programming language."}
+    ]
+  }
+]
+```
+
+### Format 3: Text-only
+
+```json
+[
+  {"text": "User: Hello\nAssistant: Hi! How can I help?"}
+]
+```
+
+## Basic Training
+
+```python
+from trl import SFTTrainer, SFTConfig
+from transformers import AutoModelForCausalLM, AutoTokenizer
+from datasets import load_dataset
+
+# Load model
+model = AutoModelForCausalLM.from_pretrained("Qwen/Qwen2.5-0.5B")
+tokenizer = AutoTokenizer.from_pretrained("Qwen/Qwen2.5-0.5B")
+
+# Load dataset
+dataset = load_dataset("trl-lib/Capybara", split="train")
+
+# Configure
+config = SFTConfig(
+    output_dir="Qwen2.5-SFT",
+    per_device_train_batch_size=4,
+    num_train_epochs=1,
+    learning_rate=2e-5,
+    save_strategy="epoch"
+)
+
+# Train
+trainer = SFTTrainer(
+    model=model,
+    args=config,
+    train_dataset=dataset,
+    tokenizer=tokenizer
+)
+trainer.train()
+```
+
+## Chat Templates
+
+Apply chat templates automatically:
+
+```python
+trainer = SFTTrainer(
+    model=model,
+    args=config,
+    train_dataset=dataset,  # Messages format
+    tokenizer=tokenizer
+    # Chat template applied automatically
+)
+```
+
+Or manually:
+```python
+def format_chat(example):
+    messages = example["messages"]
+    text = tokenizer.apply_chat_template(messages, tokenize=False)
+    return {"text": text}
+
+dataset = dataset.map(format_chat)
+```
+
+## Packing for Efficiency
+
+Pack multiple sequences into one to maximize GPU utilization:
+
+```python
+config = SFTConfig(
+    packing=True,  # Enable packing
+    max_seq_length=2048,
+    dataset_text_field="text"
+)
+```
+
+**Benefits**: 2-3× faster training
+**Trade-off**: Slightly more complex batching
+
+## Multi-GPU Training
+
+```bash
+accelerate launch --num_processes 4 train_sft.py
+```
+
+Or with config:
+```python
+config = SFTConfig(
+    output_dir="model-sft",
+    per_device_train_batch_size=4,
+    gradient_accumulation_steps=4,
+    num_train_epochs=1
+)
+```
+
+## LoRA Fine-Tuning
+
+```python
+from peft import LoraConfig
+
+lora_config = LoraConfig(
+    r=16,
+    lora_alpha=32,
+    target_modules="all-linear",
+    lora_dropout=0.05,
+    task_type="CAUSAL_LM"
+)
+
+trainer = SFTTrainer(
+    model=model,
+    args=config,
+    train_dataset=dataset,
+    peft_config=lora_config  # Add LoRA
+)
+```
+
+## Hyperparameters
+
+| Model Size | Learning Rate | Batch Size | Epochs |
+|------------|---------------|------------|--------|
+| <1B | 5e-5 | 8-16 | 1-3 |
+| 1-7B | 2e-5 | 4-8 | 1-2 |
+| 7-13B | 1e-5 | 2-4 | 1 |
+| 13B+ | 5e-6 | 1-2 | 1 |
+
+## References
+
+- TRL docs: https://huggingface.co/docs/trl/sft_trainer
+- Examples: https://github.com/huggingface/trl/tree/main/examples/scripts