ma-agents 3.4.9 → 3.5.1

package/.opencode/skills/ml-experiment/assets/template_gnn_module.py

@@ -1,341 +0,0 @@
-"""
-template_gnn_module.py — BMAD DL Lifecycle
-(Inspired by K-Dense claude-scientific-skills/pytorch-geometric/)
-
-PyTorch Geometric (PyG) template for Graph Neural Network tasks.
-Covers GCN, GAT, GraphSAGE, and GIN architectures for:
-  - Node classification  (predicting labels for each node in a graph)
-  - Graph classification (predicting a label for an entire graph)
-
-Use this for defect detection on circuit graphs, molecular property prediction,
-social network analysis, or any graph-structured data.
-
-Requires: pip install torch-geometric
-
-Usage:
-    Copy this file to src/models/your_gnn.py and:
-    1. Choose an architecture (GCN / GAT / GraphSAGE / GIN)
-    2. Set in_channels to your node feature dimension
-    3. Set out_channels to number of classes
-    4. Wrap with your LightningModule or use train/test helpers directly
-"""
-
-from __future__ import annotations
-
-from typing import Optional
-
-try:
-    import torch
-    import torch.nn as nn
-    import torch.nn.functional as F
-    HAS_TORCH = True
-except ImportError:
-    HAS_TORCH = False
-    raise ImportError("Install PyTorch: pip install torch")
-
-try:
-    from torch_geometric.nn import (
-        GCNConv, GATConv, SAGEConv, GINConv,
-        global_mean_pool, global_max_pool, global_add_pool,
-    )
-    from torch_geometric.data import Data, DataLoader
-    HAS_PYG = True
-except ImportError:
-    HAS_PYG = False
-    raise ImportError(
-        "Install PyTorch Geometric: pip install torch-geometric\n"
-        "See: https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html"
-    )
-
-
-# ══════════════════════════════════════════════════════════════════════════════
-# Architecture 1: GCN — Graph Convolutional Network
-# Best for: Homophilic graphs (connected nodes tend to share labels)
-# ══════════════════════════════════════════════════════════════════════════════
-
-class GCN(nn.Module):
-    """
-    Graph Convolutional Network (Kipf & Welling, 2017).
-
-    Args:
-        in_channels:   Dimension of input node features.
-        hidden_channels: Hidden layer dimension.
-        out_channels:  Number of output classes.
-        num_layers:    Number of GCN layers (2-4 recommended).
-        dropout:       Dropout rate.
-        task:          'node' or 'graph' classification.
-    """
-    def __init__(
-        self, in_channels: int, hidden_channels: int, out_channels: int,
-        num_layers: int = 3, dropout: float = 0.5, task: str = "node",
-    ):
-        super().__init__()
-        self.task = task
-        self.dropout = dropout
-
-        self.convs = nn.ModuleList()
-        self.bns = nn.ModuleList()
-
-        for i in range(num_layers):
-            in_ch = in_channels if i == 0 else hidden_channels
-            self.convs.append(GCNConv(in_ch, hidden_channels))
-            self.bns.append(nn.BatchNorm1d(hidden_channels))
-
-        self.classifier = nn.Linear(hidden_channels, out_channels)
-
-    def forward(self, x: torch.Tensor, edge_index: torch.Tensor,
-                batch: Optional[torch.Tensor] = None) -> torch.Tensor:
-        for conv, bn in zip(self.convs[:-1], self.bns[:-1]):
-            x = F.relu(bn(conv(x, edge_index)))
-            x = F.dropout(x, p=self.dropout, training=self.training)
-
-        x = self.convs[-1](x, edge_index)
-
-        if self.task == "graph":
-            x = global_mean_pool(x, batch)
-
-        return self.classifier(x)
-
-
-# ══════════════════════════════════════════════════════════════════════════════
-# Architecture 2: GAT — Graph Attention Network
-# Best for: Graphs where some neighbors are more important than others
-# ══════════════════════════════════════════════════════════════════════════════
-
-class GAT(nn.Module):
-    """
-    Graph Attention Network (Veličković et al., 2018).
-    Multi-head attention assigns different importance to each neighbor.
-
-    Args:
-        in_channels:     Dimension of input node features.
-        hidden_channels: Hidden layer dimension per head.
-        out_channels:    Number of output classes.
-        heads:           Number of attention heads (4-8 recommended).
-        dropout:         Dropout rate (applied to attention weights too).
-        task:            'node' or 'graph' classification.
-    """
-    def __init__(
-        self, in_channels: int, hidden_channels: int, out_channels: int,
-        heads: int = 4, dropout: float = 0.5, task: str = "node",
-    ):
-        super().__init__()
-        self.task = task
-        self.dropout = dropout
-
-        self.conv1 = GATConv(in_channels, hidden_channels, heads=heads, dropout=dropout)
-        self.conv2 = GATConv(hidden_channels * heads, out_channels, heads=1,
-                             concat=False, dropout=dropout)
-        self.bn1 = nn.BatchNorm1d(hidden_channels * heads)
-
-    def forward(self, x: torch.Tensor, edge_index: torch.Tensor,
-                batch: Optional[torch.Tensor] = None) -> torch.Tensor:
-        x = F.dropout(x, p=self.dropout, training=self.training)
-        x = F.elu(self.bn1(self.conv1(x, edge_index)))
-        x = F.dropout(x, p=self.dropout, training=self.training)
-        x = self.conv2(x, edge_index)
-
-        if self.task == "graph":
-            x = global_mean_pool(x, batch)
-
-        return x  # Raw logits — apply softmax/sigmoid in loss
-
-
-# ══════════════════════════════════════════════════════════════════════════════
-# Architecture 3: GraphSAGE — Inductive / large-graph friendly
-# Best for: Large graphs, inductive settings (unseen nodes at test time)
-# ══════════════════════════════════════════════════════════════════════════════
-
-class GraphSAGE(nn.Module):
-    """
-    GraphSAGE (Hamilton et al., 2017).
-    Aggregates neighbor features via mean/max/LSTM — scales to large graphs.
-    Inductive: can generalize to unseen nodes not in the training graph.
-
-    Args:
-        in_channels:     Dimension of input node features.
-        hidden_channels: Hidden layer dimension.
-        out_channels:    Number of output classes.
-        num_layers:      Number of SAGE layers.
-        dropout:         Dropout rate.
-        task:            'node' or 'graph' classification.
-    """
-    def __init__(
-        self, in_channels: int, hidden_channels: int, out_channels: int,
-        num_layers: int = 3, dropout: float = 0.5, task: str = "node",
-    ):
-        super().__init__()
-        self.task = task
-        self.dropout = dropout
-
-        self.convs = nn.ModuleList()
-        self.bns = nn.ModuleList()
-
-        for i in range(num_layers):
-            in_ch = in_channels if i == 0 else hidden_channels
-            self.convs.append(SAGEConv(in_ch, hidden_channels))
-            self.bns.append(nn.BatchNorm1d(hidden_channels))
-
-        self.classifier = nn.Linear(hidden_channels, out_channels)
-
-    def forward(self, x: torch.Tensor, edge_index: torch.Tensor,
-                batch: Optional[torch.Tensor] = None) -> torch.Tensor:
-        for conv, bn in zip(self.convs, self.bns):
-            x = F.relu(bn(conv(x, edge_index)))
-            x = F.dropout(x, p=self.dropout, training=self.training)
-
-        if self.task == "graph":
-            x = global_mean_pool(x, batch)
-
-        return self.classifier(x)
-
-
-# ══════════════════════════════════════════════════════════════════════════════
-# Architecture 4: GIN — Graph Isomorphism Network
-# Best for: Graph classification, maximally expressive (Weisfeiler-Leman equiv.)
-# ══════════════════════════════════════════════════════════════════════════════
-
-class GIN(nn.Module):
-    """
-    Graph Isomorphism Network (Xu et al., 2019).
-    Most expressive GNN for graph-level tasks in the WL hierarchy.
-    Aggregates by: h_v = MLP((1 + eps) * h_v + sum(neighbors))
-
-    Args:
-        in_channels:     Dimension of input node features.
-        hidden_channels: Hidden dimension for each MLP layer.
-        out_channels:    Number of output classes.
-        num_layers:      Number of GIN layers (3-5 for graph classification).
-        dropout:         Dropout rate.
-    """
-    def __init__(
-        self, in_channels: int, hidden_channels: int, out_channels: int,
-        num_layers: int = 4, dropout: float = 0.5,
-    ):
-        super().__init__()
-        self.dropout = dropout
-        self.convs = nn.ModuleList()
-        self.bns = nn.ModuleList()
-
-        for i in range(num_layers):
-            in_ch = in_channels if i == 0 else hidden_channels
-            mlp = nn.Sequential(
-                nn.Linear(in_ch, hidden_channels),
-                nn.BatchNorm1d(hidden_channels),
-                nn.ReLU(),
-                nn.Linear(hidden_channels, hidden_channels),
-            )
-            self.convs.append(GINConv(mlp, train_eps=True))
-            self.bns.append(nn.BatchNorm1d(hidden_channels))
-
-        # Jumping Knowledge: concat all layer outputs before classifier
-        self.classifier = nn.Sequential(
-            nn.Linear(hidden_channels * num_layers, hidden_channels),
-            nn.ReLU(),
-            nn.Dropout(dropout),
-            nn.Linear(hidden_channels, out_channels),
-        )
-
-    def forward(self, x: torch.Tensor, edge_index: torch.Tensor,
-                batch: torch.Tensor) -> torch.Tensor:
-        layer_outputs: list[torch.Tensor] = []
-        for conv, bn in zip(self.convs, self.bns):
-            x = F.relu(bn(conv(x, edge_index)))
-            x = F.dropout(x, p=self.dropout, training=self.training)
-            # Global pooling at each layer (Jumping Knowledge)
-            layer_outputs.append(global_add_pool(x, batch))
-
-        # Concatenate all layers' pooled outputs
-        x = torch.cat(layer_outputs, dim=1)
-        return self.classifier(x)
-
-
-# ══════════════════════════════════════════════════════════════════════════════
-# Training helpers
-# ══════════════════════════════════════════════════════════════════════════════
-
-def train_epoch(model: nn.Module, loader: "DataLoader",
-                optimizer: "torch.optim.Optimizer",
-                criterion: nn.Module, device: str) -> float:
-    model.train()
-    total_loss = 0.0
-    for data in loader:
-        data = data.to(device)
-        optimizer.zero_grad()
-        if model.__class__.__name__ == "GIN" or getattr(model, "task", "") == "graph":
-            out = model(data.x, data.edge_index, data.batch)
-        else:
-            out = model(data.x, data.edge_index)
-            if hasattr(data, "train_mask"):
-                out = out[data.train_mask]
-                target = data.y[data.train_mask]
-            else:
-                target = data.y
-            loss = criterion(out, target)
-            loss.backward()
-            optimizer.step()
-            total_loss += float(loss)
-            continue
-        loss = criterion(out, data.y)
-        loss.backward()
-        optimizer.step()
-        total_loss += float(loss)
-    return total_loss / len(loader)
-
-
-@torch.no_grad()
-def evaluate(model: nn.Module, loader: "DataLoader", device: str) -> float:
-    model.eval()
-    correct = total = 0
-    for data in loader:
-        data = data.to(device)
-        if model.__class__.__name__ == "GIN" or getattr(model, "task", "") == "graph":
-            out = model(data.x, data.edge_index, data.batch)
-            pred = out.argmax(dim=1)
-            correct += int((pred == data.y).sum())
-            total += data.y.size(0)
-        else:
-            out = model(data.x, data.edge_index)
-            if hasattr(data, "test_mask"):
-                pred = out[data.test_mask].argmax(dim=1)
-                correct += int((pred == data.y[data.test_mask]).sum())
-                total += int(data.test_mask.sum())
-            else:
-                pred = out.argmax(dim=1)
-                correct += int((pred == data.y).sum())
-                total += data.y.size(0)
-    return correct / total if total > 0 else 0.0
-
-
-# ══════════════════════════════════════════════════════════════════════════════
-# Architecture selection guide
-# ══════════════════════════════════════════════════════════════════════════════
-
-ARCHITECTURE_GUIDE = """
-GNN Architecture Selection Guide — BMAD DL Lifecycle
-─────────────────────────────────────────────────────
-Task: Node classification
-  Homophilic graph (similar nodes connected)  → GCN
-  Attention needed (noisy neighbors)          → GAT
-  Large / dynamic / inductive graph           → GraphSAGE
-
-Task: Graph classification
-  Standard accuracy                           → GraphSAGE or GCN + global pool
-  Maximum expressiveness                      → GIN (recommended)
-  Edge features matter                        → GAT with edge_attr
-
-Quick model size guide:
-  Small dataset  (<1K graphs)  → 2 layers, hidden=64
-  Medium dataset (1K–50K)      → 3 layers, hidden=128
-  Large dataset  (50K+)        → 4-5 layers, hidden=256, mini-batch DataLoader
-
-Typical hyperparameter ranges:
-  hidden_channels: 64, 128, 256
-  num_layers:      2, 3, 4
-  dropout:         0.3 – 0.6
-  heads (GAT):     4, 8
-  learning_rate:   0.001 – 0.01
-"""
-
-if __name__ == "__main__":
-    print(ARCHITECTURE_GUIDE)

package/.opencode/skills/ml-experiment/assets/template_lightning_module.py

@@ -1,158 +0,0 @@
-"""
-template_lightning_module.py — BMAD DL Lifecycle
-PyTorch Lightning LightningModule template for supervised classification/regression.
-
-Drop this file into your project and fill in the TODO sections.
-
-Usage:
-    Copy to src/models/your_model.py and implement:
-      - __init__: define layers
-      - forward: define forward pass
-      - _shared_step: compute loss + metrics for any split
-    The training/validation/test steps call _shared_step automatically.
-"""
-
-from __future__ import annotations
-
-from typing import Any
-
-import torch
-import torch.nn as nn
-import torch.nn.functional as F
-
-try:
-    import lightning as L
-    LightningModule = L.LightningModule
-except ImportError:
-    try:
-        import pytorch_lightning as pl
-        LightningModule = pl.LightningModule
-    except ImportError:
-        raise ImportError(
-            "Install PyTorch Lightning: pip install lightning\n"
-            "  or: pip install pytorch-lightning"
-        )
-
-
-class YourModel(LightningModule):
-    """
-    Template LightningModule for image/tabular classification or regression.
-
-    Replace 'YourModel' with a descriptive name (e.g. DefectClassifier, FruitNet).
-
-    Args:
-        num_classes: Number of output classes (use 1 for binary/regression).
-        learning_rate: Initial learning rate for the optimizer.
-        weight_decay: L2 regularization weight.
-    """
-
-    def __init__(
-        self,
-        num_classes: int = 2,
-        learning_rate: float = 1e-3,
-        weight_decay: float = 1e-4,
-    ):
-        super().__init__()
-        # Saves all __init__ args to self.hparams (enables checkpointing)
-        self.save_hyperparameters()
-
-        # ── TODO: Define your model architecture ──────────────────────────────
-        # Example: simple two-layer MLP for tabular data
-        self.encoder = nn.Sequential(
-            nn.Linear(128, 64),   # TODO: replace 128 with your input dim
-            nn.BatchNorm1d(64),
-            nn.ReLU(),
-            nn.Dropout(0.3),
-        )
-        self.classifier = nn.Linear(64, num_classes)
-        # ── END TODO ──────────────────────────────────────────────────────────
-
-        # Loss function
-        if num_classes == 1:
-            self.loss_fn = nn.BCEWithLogitsLoss()
-        else:
-            self.loss_fn = nn.CrossEntropyLoss()
-
-    def forward(self, x: torch.Tensor) -> torch.Tensor:
-        """
-        Forward pass.
-
-        Args:
-            x: Input tensor, shape depends on your architecture.
-        Returns:
-            Logits tensor of shape (batch, num_classes) or (batch, 1).
-        """
-        # ── TODO: Implement forward pass ──────────────────────────────────────
-        features = self.encoder(x)
-        logits = self.classifier(features)
-        return logits
-        # ── END TODO ──────────────────────────────────────────────────────────
-
-    def _shared_step(self, batch: Any, stage: str) -> torch.Tensor:
-        """
-        Common logic for train/val/test.
-
-        Args:
-            batch: Tuple of (inputs, labels) from your DataLoader.
-            stage: One of "train", "val", "test".
-        Returns:
-            Loss tensor.
-        """
-        # ── TODO: Unpack batch to match your DataLoader output ────────────────
-        x, y = batch  # e.g. (images, labels) or (features, targets)
-        # ── END TODO ──────────────────────────────────────────────────────────
-
-        logits = self(x)
-
-        if self.hparams.num_classes == 1:
-            loss = self.loss_fn(logits.squeeze(1), y.float())
-            preds = (torch.sigmoid(logits.squeeze(1)) > 0.5).long()
-        else:
-            loss = self.loss_fn(logits, y.long())
-            preds = logits.argmax(dim=1)
-
-        acc = (preds == y).float().mean()
-
-        # Log metrics — appears in TensorBoard / W&B / CSV logger
-        self.log(f"{stage}/loss", loss, prog_bar=(stage == "val"), on_step=False, on_epoch=True)
-        self.log(f"{stage}/acc", acc, prog_bar=True, on_step=False, on_epoch=True)
-
-        return loss
-
-    # ── Lightning hooks (do not rename these) ─────────────────────────────────
-
-    def training_step(self, batch: Any, batch_idx: int) -> torch.Tensor:
-        loss = self._shared_step(batch, "train")
-        if torch.cuda.is_available():
-            self.log("gpu/memory_allocated_gb", torch.cuda.memory_allocated() / 1e9,
-                     on_step=True, on_epoch=False, prog_bar=False)
-        return loss
-
-    def validation_step(self, batch: Any, batch_idx: int) -> None:
-        self._shared_step(batch, "val")
-
-    def test_step(self, batch: Any, batch_idx: int) -> None:
-        self._shared_step(batch, "test")
-
-    def configure_optimizers(self) -> dict:
-        """
-        Set up optimizer and learning rate scheduler.
-        Swap optimizer or scheduler as needed.
-        """
-        optimizer = torch.optim.AdamW(
-            self.parameters(),
-            lr=self.hparams.learning_rate,
-            weight_decay=self.hparams.weight_decay,
-        )
-        scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(
-            optimizer,
-            T_max=10,   # TODO: set to your total_epochs
-            eta_min=1e-6,
-        )
-        return {
-            "optimizer": optimizer,
-            "lr_scheduler": {
-                "scheduler": scheduler,
-                "monitor": "val/loss",
-            },
-        }

package/.opencode/skills/ml-experiment/bmad-skill-manifest.yaml

@@ -1,3 +0,0 @@
-type: skill
-name: ml-experiment
-module: ma-skills

package/.opencode/skills/ml-experiment/skill.json

@@ -1,7 +0,0 @@
-{
-  "name": "ML Experiment Execution",
-  "description": "Executes training runs against a locked TECHSPEC and logs metrics to W&B/MLflow/ClearML.",
-  "version": "1.0.0",
-  "author": "Demerzel (ML Scientist)",
-  "tags": ["Machine Learning", "Experiment", "Training", "Logging", "Demerzel"]
-}

package/.opencode/skills/ml-hparam/SKILL.md

@@ -1,81 +0,0 @@
----
-
-name: ml-hparam
-
-description: Acts as Demerzel (Machine Learning Scientist) to run structured hyperparameter optimization after a baseline architecture is confirmed to work. Uses Optuna, W&B Sweeps, or Ray Tune. Produces a validated best-parameter configuration for the next tuned experiment run.
-
----
-
-# Machine Learning Workflow: Hyperparameter Optimization (Conditional) — Demerzel
-
-## 1. Operating Instructions
-
-You are **Demerzel**, an expert Machine Learning Scientist running structured hyperparameter search. **This stage is conditional.** Run it only after `ml-analysis` confirms the baseline architecture meets at least the "Worst case (alive)" tier in the TECHSPEC.
-
-Your goal is to find the optimal parameter configuration within the search space defined in the TECHSPEC, then hand off validated parameters to the next `ml-experiment` run.
-
-1. **Verify the prerequisite:** Read the latest `ml-analysis-exp-[id].md`. Confirm: "Worst case (alive)" tier or better was reached. If not, recommend running `ml-revision` instead.
-
-2. **Read the TECHSPEC:** `_bmad-output/planning-artifacts/techspecs/ml-techspec-exp-[id].md` — use Section C as the HPO search space.
-
-3. **Run the advisor:** `/ml-advise` — check if any past HPO runs exist.
-
-4. **Run the HPO search:** (Optuna, W&B Sweeps, or Ray Tune).
-   - Define objective: Maximize the primary metric from the PRD.
-   - Use early stopping to save budget.
-   - Example (Optuna):
-   ```python
-   import optuna
-   def objective(trial):
-       lr = trial.suggest_float("lr", 1e-5, 1e-2, log=True)
-       # train and return f1
-       return f1
-   study = optuna.create_study(direction="maximize")
-   study.optimize(objective, n_trials=50)
-   ```
-
-5. **CRITICAL:** Do not write the HPO report yet. Present the top-5 parameter configurations to the user and ask for sign-off. Halt and wait.
-
-6. Upon confirmation, write `_bmad-output/planning-artifacts/techspecs/ml-hparam-exp-[id].md` with the validated best configuration and update the original TECHSPEC.
-
-7. **Commit the HPO artifact:**
-   ```bash
-   git add _bmad-output/planning-artifacts/techspecs/ml-hparam-exp-[id].md
-   git commit -m "docs(ml-hparam): validated best config for EXP-[id] val/f1=[score]"
-   ```
-
-## 2. Expected Output Template
-
-### Template A: `_bmad-output/planning-artifacts/techspecs/ml-hparam-exp-[id].md`
-
-```markdown
-# HPO Results: EXP-[ID]
-
-## A. Search Summary
-* **Linked Experiment:** EXP-[ID]
-* **HPO Tool:** [Optuna / W&B Sweeps / Ray Tune]
-* **Sweep URL:** [link]
-
-## B. Top Configurations
-| Rank | lr | batch_size | dropout | val/f1 | Run URL |
-| :--- | :--- | :--- | :--- | :--- | :--- |
-| 1 (best) | 2.3e-4 | 1024 | 0.22 | 0.94 | [link] |
-
-## C. Parameter Importance
-* [Which params had highest impact from study analysis.]
-
-## D. Validated Best Configuration (copy-paste ready)
-```yaml
-learning_rate: 2.3e-4
-batch_size: 1024
-dropout: 0.22
-```
-
-## E. Scientist Sign-off
-* [ ] Best params are within real-world acceptable ranges.
-* [ ] No anomalous values.
-* **Signed off by:** [Demerzel / Date]
-
-## F. Next Step
-* Run `/ml-experiment` with run_type="tuned" using the above config.
-```

package/.opencode/skills/ml-hparam/bmad-skill-manifest.yaml

@@ -1,3 +0,0 @@
-type: skill
-name: ml-hparam
-module: ma-skills

package/.opencode/skills/ml-hparam/skill.json

@@ -1,7 +0,0 @@
-{
-  "name": "ML Hyperparameter Optimization",
-  "description": "Runs structured HPO using Optuna, W&B Sweeps, or Ray Tune after a baseline is confirmed.",
-  "version": "1.0.0",
-  "author": "Demerzel (ML Scientist)",
-  "tags": ["Machine Learning", "HPO", "Optimization", "Optuna", "Sweeps", "Demerzel"]
-}

package/.opencode/skills/ml-ideation/SKILL.md

@@ -1,50 +0,0 @@
----
-name: ml-ideation
-description: ML Ideation — Frame the research problem, define success criteria, and produce a Machine Learning PRD
----
-
-# ML Stage 1 — Ideation & PRD
-
-Frame the ML problem rigorously before any data or modelling work begins.
-
-## Instructions
-
-### 1. Elicit Problem Context
-Ask the user for (or extract from context):
-- **Business problem**: What decision or process will the model improve?
-- **Target variable**: What are we predicting? (classification / regression / ranking / generation)
-- **Failure cost asymmetry**: What is the cost of a false negative vs a false positive in this domain?
-- **Success definition**: What metric threshold constitutes a production-ready model?
-- **Data availability**: What raw datasets exist and where are they located?
-
-### 2. Produce Research Thesis
-Write `_bmad-output/planning-artifacts/research-thesis.md` with:
-- **Hypothesis**: A single falsifiable statement (e.g. "We can predict X with >Y recall using features A, B, C")
-- **Assumptions**: List all assumptions that must hold for the hypothesis to be testable
-- **Risks**: Top 3 risks that could invalidate the hypothesis (data quality, label noise, distribution shift)
-- **Null Hypothesis**: The baseline we must beat (random, heuristic, or existing system)
-
-### 3. Produce ML PRD
-Write `_bmad-output/planning-artifacts/ml-prd.md` with sections:
-- **Problem Statement** (1 paragraph)
-- **Stakeholders & Users**
-- **Success Metrics** (primary metric, secondary metrics, guardrail metrics)
-- **Failure Cost Matrix** (FP cost vs FN cost with domain justification)
-- **Data Requirements** (source, volume, freshness, labelling)
-- **Out of Scope** (explicit non-goals)
-- **Dependencies** (upstream data pipelines, external APIs)
-
-### 4. Surface Dilemmas & Commit Gate
-
-Before presenting and **before any git commit**:
-
-- Identify every framing choice where two or more reasonable options existed (metric threshold, failure cost ratio, scope boundary, two-stage vs single-stage, etc.)
-- Format each as: **Dilemma [Letter] — Title** / **Context** / **Options (a/b)** / **Recommendation** / **Your decision:** [blank]
-- If all choices were unambiguous, state explicitly: "No open dilemmas."
-- **Do NOT commit any artifact until the user has responded and given explicit approval.**
-
-### 5. Confirm & Advance
-- Present both documents to the user for review
-- Ask: "Do you approve this framing, or would you like to adjust the hypothesis or success criteria?"
-- On approval: commit artifacts, then say "Stage 1 complete. When ready, proceed to **Stage 2 — /ml-eda** to analyze the raw data."
-- STOP and WAIT for user confirmation before advancing

package/.opencode/skills/ml-ideation/bmad-skill-manifest.yaml

@@ -1,3 +0,0 @@
-type: skill
-name: ml-ideation
-module: ma-skills