@proflandrigan/shards 1.1.0

package/src/agents/specific_instructions/deep_learning_engineer/phases/phase-2.md

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+> **Previous:** phase-1.md confirmed
+> **Next:** phase-3.md (read only after this phase's gate is confirmed)
+
+---
+
+## Create Mode — Phase 2: Training Protocol (Gated)
+
+Goal: Fully specify training before writing a line of code.
+
+Define:
+
+1. **Loss function:** Formula + justification. Why this loss for this task?
+   Known failure modes?
+
+2. **Optimizer:** AdamW is the default. State the reason explicitly if
+   deviating. Include:
+   - Weight decay value and rationale (decoupled from LR per Loshchilov &
+     Hutter, 2019)
+   - β₁, β₂, ε values if non-default, with rationale
+
+3. **Learning rate schedule:**
+   - Warmup: number of steps and rationale
+   - Decay strategy: cosine, linear, polynomial — with rationale
+   - Peak LR: concrete value with concrete justification (not "tune it")
+   - Minimum LR (if applicable)
+
+4. **Regularization:**
+   - Dropout: rate and placement (attention dropout vs residual dropout vs
+     classifier dropout — these are different)
+   - Label smoothing (if classification): value and rationale
+   - Stochastic depth (if applicable): survival probability
+   - Weight decay already specified in optimizer
+
+5. **Data augmentation table:**
+
+   | Transform | Parameters | Invariance Encoded | Apply to Val? |
+   |-----------|-----------|-------------------|---------------|
+   | <name>   | <params>  | <what it teaches> | <yes | no>   |
+
+6. **Batch configuration:**
+   - Effective batch size (global)
+   - Per-GPU batch size
+   - Gradient accumulation steps (if VRAM-constrained)
+
+7. **Checkpoint strategy:** best validation metric, every N epochs, or both.
+
+### Document Phase 2
+
+Append to `project-specs.md`:
+
+```markdown
+## Phase 2: Training Protocol
+
+### Loss Function
+- **Formula:** <L = ...>
+- **Justification:** <why this loss for this task>
+- **Known failure modes:** <class imbalance, optimization landscape issues, etc.>
+
+### Optimizer
+- **Optimizer:** <AdamW | other>
+- **Deviation rationale:** <if not AdamW, why>
+- **Weight decay:** <value> — <rationale>
+- **β₁, β₂, ε:** <values if non-default>
+
+### Learning Rate Schedule
+- **Warmup:** <N steps> — <rationale>
+- **Decay:** <cosine | linear | polynomial> — <rationale>
+- **Peak LR:** <value> — <justification>
+- **Minimum LR:** <value or "none">
+
+### Regularization
+- **Dropout:** rate=<X>, placement=<where>
+- **Label smoothing:** <value | N/A>
+- **Stochastic depth:** survival_prob=<X | N/A>
+
+### Augmentation
+| Transform | Parameters | Invariance | Val? |
+|-----------|-----------|-----------|------|
+| <name> | <params> | <invariance> | <yes/no> |
+
+### Batch Configuration
+- **Effective batch size:** <N>
+- **Per-GPU batch size:** <N>
+- **Gradient accumulation:** <N steps | none>
+
+### Checkpoint Strategy
+<best val metric | every N epochs | both — rationale>
+```
+
+::GATE:: id=deep-learning-engineer-phase-2 phase=2 kind=phase
+Read this section back to the user. Stop here — do not begin the next phase or output any further content. Wait for the user to explicitly confirm before proceeding. Do not interpret silence or partial agreement as confirmation.
+::ENDGATE::
+
+---
+
+## When this gate is confirmed
+
+Read `.claude/agents/specific_instructions/deep_learning_engineer/phases/phase-3.md` in full and follow its instructions starting from Phase 3. Do not pre-read further phase files.

package/src/agents/specific_instructions/deep_learning_engineer/phases/phase-3.md

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+> **Previous:** phase-2.md confirmed
+> **Next:** phase-4.md (read only after this phase's gate is confirmed)
+
+---
+
+## Create Mode — Phase 3: Implementation Specification (Gated)
+
+Goal: Translate architecture and training protocol into an engineering plan.
+
+Define:
+
+1. **Framework:** PyTorch vs JAX with rationale. Not a preference — a reason
+   tied to the training procedure (custom CUDA, vmap, multi-host TPU, etc.).
+
+2. **Code structure:** What each `src/` file contains, `forward()` signature
+   with input and output shapes, module interfaces.
+
+3. **Hardware config:**
+   - fp16 vs bf16: bf16 preferred for most modern GPUs (A100, H100, RTX 30xx+);
+     fp16 for older hardware — state the reason
+   - Gradient checkpointing: yes if VRAM is constrained; quantify the compute
+     overhead
+   - `torch.compile`: compatible with the architecture? Expected speedup?
+
+4. **Experiment tracking:** tool (wandb / tensorboard / MLflow), key metrics
+   logged per step and per epoch, visualization plan.
+
+5. **Inference plan:** serving format, quantization (int8 / int4 / GPTQ if
+   applicable), expected latency delta from quantization.
+
+### Document Phase 3
+
+Append to `project-specs.md`:
+
+```markdown
+## Phase 3: Implementation Specification
+
+### Framework
+- **Framework:** <PyTorch | JAX>
+- **Rationale:** <concrete reason tied to training procedure>
+
+### Code Structure
+- **model.py:** <what it contains, forward() signature with shapes>
+- **dataset.py:** <Dataset class, transforms, get_dataloaders() fn>
+- **train.py:** <training loop, optimizer/scheduler construction, checkpoint logic>
+- **evaluate.py:** <evaluation loop, metric computation, predict() fn>
+- **configs/config.yaml:** <all hyperparameters from Phases 1-2>
+
+### Hardware Config
+- **Precision:** <bf16 | fp16> — <rationale>
+- **Gradient checkpointing:** <yes — ~X% compute overhead | no>
+- **torch.compile:** <yes — expected ~X% speedup | no — incompatible because>
+
+### Experiment Tracking
+- **Tool:** <wandb | tensorboard | MLflow>
+- **Metrics per step:** <loss, grad norm, LR>
+- **Metrics per epoch:** <val loss, primary metric, secondary metrics>
+- **Visualizations:** <loss curves, confusion matrix, attention maps, etc.>
+
+### Inference Plan
+- **Serving format:** <ONNX | TorchScript | TensorRT | HuggingFace | none>
+- **Quantization:** <int8 | int4 | none> — <latency delta estimate>
+- **Expected inference latency:** ~<X>ms per sample on <hardware>
+```
+
+**DIVERGE check:** If you identified 2-3 mutually exclusive neural architectures (e.g., different backbone families, fundamentally different training paradigms) that are genuinely equally viable, you MAY propose a DIVERGE fork. Read `.claude/agents/specific_instructions/shared/diverge_protocol.md` and follow its DIVERGE Proposal Gate. If confirmed, branches execute autonomously through the remaining phases. After convergence and promotion, resume at Phase 4. If declined or not applicable, continue normally.
+
+::GATE:: id=deep-learning-engineer-phase-3 phase=3 kind=phase
+Read this section back to the user. Stop here — do not begin the next phase or output any further content. Wait for the user to explicitly confirm before proceeding. Do not interpret silence or partial agreement as confirmation.
+::ENDGATE::
+
+---
+
+## When this gate is confirmed
+
+Read `.claude/agents/specific_instructions/deep_learning_engineer/phases/phase-4.md` in full and follow its instructions starting from Phase 4. Do not pre-read further phase files.

package/src/agents/specific_instructions/deep_learning_engineer/phases/phase-4.md

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+> **Previous:** phase-3.md confirmed
+> **Next:** phase-5.md (read only after this phase's gate is confirmed)
+
+---
+
+## Create Mode — Phase 4: Execute (Gated)
+
+Goal: Build the model implementation.
+
+**Context checkpoint:** Before building, prompt the user:
+
+"Planning's locked — good moment to run `/compact` or `/clear` before we start
+executing. I'll be working from project-specs.md from here. Say the word when
+you're ready."
+
+Wait for any signal from the user before beginning build steps.
+
+**Knowledge re-check:** Follow `.claude/agents/specific_instructions/shared/knowledge_checkpoint.md` before building.
+
+### Incremental testing — checkpoint gates between components
+
+Follow `.claude/agents/specific_instructions/shared/incremental_testing.md` during this build. Each component below is a checkpoint seam — after you write and execute a component, emit a `kind=checkpoint` gate fence (template below) and wait for user confirmation before starting the next component. Do not leave run-all until the end: test each component in isolation as you build it.
+
+Checkpoint gate fence — emit exactly this shape. Both `::GATE::` and `::ENDGATE::` fences are required, as are all three attributes (`id`, `phase`, `kind`). No prose outside the fence.
+
+```
+::GATE:: id=<agent-name>-phase-<N>-checkpoint-<component> phase=<N> kind=checkpoint
+Component: <human-readable name>
+Test command: <exact command you ran>
+Evidence:
+  - <measured fact 1, e.g. "df.shape = (48211, 47)">
+  - <measured fact 2, e.g. "null rate on join key = 0.00%">
+  - <measured fact 3, e.g. "sample head matches expected schema">
+Status: PASS | FAIL — <one-line summary>
+Next: <what you'll build after this is confirmed>
+Stop here — await explicit confirmation before writing the next component.
+::ENDGATE::
+```
+
+Expected checkpoint gate IDs for this phase (emit in order as you build):
+
+- `deep-learning-engineer-phase-4-checkpoint-data` — dataset load + sample batch visualization; shape assertions hold; class distribution (if classification) matches prior.
+- `deep-learning-engineer-phase-4-checkpoint-forward` — model forward pass on a dummy batch; shapes at each component match expectation; no NaNs.
+- `deep-learning-engineer-phase-4-checkpoint-smoke-train` — smoke-fit on ≤1% of data for a handful of epochs; loss decreases, gradient norms finite; tiny-batch overfitting sanity check passes.
+- `deep-learning-engineer-phase-4-checkpoint-full-train` — full training completes on target hardware; peak memory within budget; best validation metric logged.
+- `deep-learning-engineer-phase-4-checkpoint-eval` — evaluation + diagnostics (gradient history, activation stats, dead-neuron check) produced and reviewed.
+
+The hook blocks all non-read tools while a checkpoint is open. If a checkpoint fails, diagnose and re-emit with updated evidence before advancing. Use the fence body format shown above (Component / Test command / Evidence / Status / Next).
+
+Then create:
+
+**`models/<project_name>/notebooks/model_development.ipynb`**
+
+Structure:
+1. **Setup** — imports, config load, device setup, seed setting
+2. **Dataset Sanity Check** — data loading, shape assertions, sample batch
+   visualization, class distribution (if classification)
+3. **Model Trace** — instantiate model, run forward pass with dummy input,
+   print shape at each major component via hooks or explicit prints
+4. **Training Loop** — full training with logging: loss, eval metric, gradient
+   norm, LR per epoch; inline loss curves after training
+5. **Evaluation** — metric table vs baseline, confusion matrix or equivalent,
+   per-class breakdown if applicable
+6. **Diagnostics** — gradient norm history plot, activation statistics,
+   loss curve analysis, dead neuron check (if ReLU backbone)
+
+**`models/<project_name>/src/model.py`**
+- Every `forward()` method has a shape comment on the return tensor
+- No magic numbers — all sizes come from config
+- Normalization and dropout layers instantiated in `__init__`, applied in `forward()`
+
+**`models/<project_name>/src/dataset.py`**
+- `Dataset` class with `__len__` and `__getitem__`
+- Transform pipeline built from Phase 2 augmentation table
+- `get_dataloaders(config)` convenience function
+
+**`models/<project_name>/src/train.py`**
+- `train_epoch(model, loader, optimizer, scheduler, device)` function
+- Optimizer and scheduler construction
+- Checkpoint logic: save best validation metric, load from checkpoint
+
+**`models/<project_name>/src/evaluate.py`**
+- `evaluate(model, loader, device)` evaluation loop
+- Primary and secondary metric computation
+- `predict(model, sample, device)` single-sample inference function
+
+**`models/<project_name>/configs/config.yaml`**
+- All hyperparameters from Phases 1, 2, and 3
+- No hardcoded values in src/ — everything references config
+
+**`models/<project_name>/requirements.txt`**
+- Pinned major dependencies (torch==X.Y, torchvision==X.Y, etc.)
+
+### Document Phase 4
+
+Append to `project-specs.md`:
+
+```markdown
+## Phase 4: Build Log
+
+- **Notebook:** `notebooks/model_development.ipynb`
+- **Source modules:** model.py, dataset.py, train.py, evaluate.py
+- **Training run summary:**
+  - Hardware: <GPU model, VRAM>
+  - Precision: <bf16 | fp16 | fp32>
+  - Effective batch size: <N>
+  - Steps / epochs: <N>
+  - Peak GPU memory: ~<X>GB
+  - Loss trajectory: <converged at epoch N | diverged | oscillating — describe>
+  - Best validation metric: <metric name>=<value> at epoch <N>
+- **Baseline comparison:**
+  | Model | <Metric> | Notes |
+  |-------|---------|-------|
+  | Baseline (<type>) | <value> | — |
+  | **Ours** | <value> | — |
+- **Gradient diagnostics:** <healthy convergence | anomalies observed — describe>
+- **Known implementation limitations:** <what prototype doesn't handle>
+```
+
+::GATE:: id=deep-learning-engineer-phase-4 phase=4 kind=phase validates=deep_learning_engineer
+Read this section back to the user. Stop here — do not begin the next phase or output any further content. Wait for the user to explicitly confirm before proceeding. Do not interpret silence or partial agreement as confirmation.
+::ENDGATE::
+
+---
+
+## When this gate is confirmed
+
+Read `.claude/agents/specific_instructions/deep_learning_engineer/phases/phase-5.md` in full and follow its instructions starting from Phase 5. Do not pre-read further phase files.

package/src/agents/specific_instructions/deep_learning_engineer/phases/phase-5.md

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+> **Previous:** phase-4.md confirmed
+> **Next:** This is the final phase — follow the Syn sign-off instructions in this phase to close the project.
+
+---
+
+## Create Mode — Phase 5: Review and Handoff (Gated)
+
+Goal: Dual specialist review before writing the final report.
+
+Both reviews happen before writing `report.md`. If either raises a blocking
+concern, discuss with the user and revise before proceeding.
+
+**ML Engineer review (production infrastructure and deployment feasibility):**
+
+Tell the user: "Requesting ML Engineer review for production infrastructure
+and deployment feasibility..."
+
+```
+Task(
+  subagent_type="ml-engineer",
+  description="Production readiness review for deep learning model: <project name>",
+  prompt="I am the Deep Learning Engineer shard. I have built a custom deep
+  learning model and need a production infrastructure review.
+
+  Project: <project name>
+  Directory: models/<project_name>/
+  Specs: models/<project_name>/project-specs.md
+
+  Summary:
+  - Task: <input/output tensor shapes from Phase 0>
+  - Architecture: <selected backbone + head from Phase 1>
+  - Parameters: ~<N>M
+  - Training: <optimizer, LR schedule, augmentation summary from Phase 2>
+  - Hardware: <GPU, precision, gradient checkpointing from Phase 3>
+  - Results: <best validation metric vs baseline from Phase 4>
+  - Serving format: <from Phase 3>
+
+  Please review for production readiness:
+  1. Is the serving format (or absence of one) appropriate for the stated
+     latency budget?
+  2. Are there infrastructure or pipeline concerns for integrating this model
+     into production?
+  3. Is the model size and inference cost acceptable for the stated hardware
+     constraints?
+  4. What monitoring and retraining triggers would you recommend?
+  5. Are there production failure modes (data drift, distribution shift,
+     cold start) not addressed in the current design?
+
+  Please read project-specs.md for full context."
+)
+```
+
+**Applied ML Scientist review (methodology soundness and cutting-edge alternatives):**
+
+Tell the user: "Requesting Applied ML Scientist review for methodology soundness
+and cutting-edge alternatives assessment..."
+
+```
+Task(
+  subagent_type="applied-ml-scientist",
+  description="Methodology review for deep learning model: <project name>",
+  prompt="I am the Deep Learning Engineer shard. I have built a custom deep
+  learning model and need a methodology and theory review.
+
+  Project: <project name>
+  Directory: models/<project_name>/
+
+  Summary:
+  - Task: <problem description and input/output from Phase 0>
+  - Core hypothesis: <why this architecture for this data>
+  - Architecture: <selected approach from Phase 1>
+  - Loss function: <formula and justification from Phase 2>
+  - Results: <metric table from Phase 4>
+
+  Please review for methodology soundness:
+  1. Is the inductive bias argument for the selected architecture sound given
+     the data structure?
+  2. Are there recent methods (post-2022) that would clearly outperform this
+     approach for this problem type?
+  3. Is the loss function well-aligned with the task objective?
+  4. Are there theoretical gaps in the training protocol (optimizer choice,
+     regularization, augmentation strategy)?
+  5. What experiments would most efficiently validate or invalidate the core
+     design hypothesis?
+
+  Please read models/<project_name>/project-specs.md for full context."
+)
+```
+
+**MLOps Engineer review (production platform and operationalization):**
+
+Tell the user: "And finally, asking the MLOps Engineer to review the production
+platform requirements and operationalization plan..."
+
+```
+Task(
+  subagent_type="mlops-engineer",
+  description="Production platform review for deep learning model: <project name>",
+  prompt="I am the Deep Learning Engineer shard. I have built a custom deep
+  learning model and need a production platform and operationalization review.
+
+  Project: <project name>
+  Directory: models/<project_name>/
+  Specs: models/<project_name>/project-specs.md
+
+  Summary:
+  - Architecture: <selected backbone + head from Phase 1>
+  - Parameters: ~<N>M
+  - Serving format: <from Phase 3>
+  - Hardware: <GPU, precision from Phase 3>
+  - Results: <best validation metric vs baseline from Phase 4>
+
+  Please review:
+  1. Is the serving format appropriate for the stated latency budget and
+     operational constraints?
+  2. What CI/CD pipeline would you recommend for retraining and model
+     registry management?
+  3. Is the experiment tracking and model versioning plan sufficient for
+     production operation?
+  4. What monitoring and retraining triggers would you build for this model?
+  5. What infrastructure is needed that isn't yet in the plan?
+
+  Please read project-specs.md for full context."
+)
+```
+
+Append MLOps Engineer's review to specs.
+
+**Backend Engineer code review (Python artifacts):**
+
+Glob the project directory (`models/<project_name>/`) for `.py` and `.ipynb` files.
+If any are found:
+
+Tell the user: "Before we write the report, the Backend Engineer is reviewing
+the Python artifacts. Code quality is not optional."
+
+```
+Task(
+  subagent_type="backend-engineer",
+  description="Python code review for [project_name]",
+  prompt="You are in SERVICE MODE. Review the following Python files in the
+  project at models/[project_name]/. Read project-specs.md first for context.
+  Files to review: [list of .py and .ipynb files found]"
+)
+```
+
+Append the Backend Engineer's review to project-specs.md. If no Python files are
+found, skip this step.
+
+**Consult Syn for final sign-off:**
+
+Tell the user: "I'm asking Syn to review the deep learning model design,
+training protocol, and results before we close..."
+
+```
+Task(
+  subagent_type="syn",
+  description="Final review of deep learning model: <project name>",
+  prompt="I am the Deep Learning Engineer shard. I have completed a custom
+  deep learning model project. Please review and provide APPROVED / NEEDS
+  REVISION / BLOCKED.
+
+  Project: <project name>
+  Directory: models/<project_name>/
+  Specs: models/<project_name>/project-specs.md
+
+  Summary:
+  - Task: <input → output from Phase 0>
+  - Architecture: <selected backbone + head from Phase 1>, ~<N>M parameters
+  - Training: <optimizer, LR schedule, loss function from Phase 2>
+  - Hardware: <GPU, precision, gradient checkpointing from Phase 3>
+  - Results: <best validation metric vs baseline from Phase 4>
+  - Known limitations: <from Phase 4>
+
+  Reviewer verdicts already collected:
+  - ML Engineer (production readiness): <DEPLOY | OPTIMIZE | REDESIGN> — <one-line reason>
+  - Applied ML Scientist (methodology): <Sound | Consider Alternatives | Revise> — <one-line reason>
+  - MLOps Engineer (operationalization): <Approved | Concerns | Redesign needed> — <one-line reason>
+  - Backend Engineer (code quality): <Clean | Minor Issues | Refactor Required | Blocked | N/A> — <one-line reason>
+
+  Please read project-specs.md for full context and confirm whether the
+  project is ready to close given the reviewer verdicts above."
+)
+```
+
+Append Syn's verdict to project-specs.md. If Syn returns NEEDS REVISION or
+BLOCKED, discuss with the user and address before proceeding.
+
+**Multi-reviewer conflict protocol:**
+
+If no reviewer returns a blocking verdict (REDESIGN, Revise, or Redesign needed):
+→ Proceed to report.md. Document all three verdicts.
+
+If all reviewers with blocking concerns agree on the same root cause:
+→ Discuss with the user and revise the binding issue before proceeding.
+
+If reviewers disagree — one or two block while the other(s) do not:
+→ Present the conflict explicitly to the user:
+
+  "The reviewers disagree:
+   - ML Engineer verdict: [DEPLOY | OPTIMIZE | REDESIGN] — [key reason]
+   - Applied ML Scientist verdict: [Sound | Consider Alternatives | Revise] — [key reason]
+   - MLOps Engineer verdict: [Approved | Concerns | Redesign needed] — [key reason]
+
+   This is a genuine constraint conflict. Which is the binding constraint for
+   this project: production feasibility, methodological rigor, or operational
+   readiness? Your answer determines what we fix first."
+
+Document the user's decision in project-specs.md:
+
+**Reviewer conflict resolution:** Production-first | Methodology-first | Operations-first | User override — <rationale>
+
+Then address the binding constraint before proceeding. If the non-binding concern
+remains unresolved after iteration, note it explicitly in report.md Limitations.
+
+**Create `models/<project_name>/report.md`:**
+
+```markdown
+# <Project Name> — Deep Learning Engineering Report
+
+## System Specification
+- **Task:** <input → output>
+- **Architecture:** <name, parameter count>
+- **Training:** <optimizer, schedule, key regularization>
+- **Hardware:** <GPU, precision>
+
+## Architecture Rationale
+<Inductive bias argument for the selected architecture. Cite the paper that
+established why this architecture class works for this data modality.>
+
+### Candidate Comparison
+<Table from Phase 1>
+
+## Training Protocol Rationale
+<Justification for optimizer, LR schedule, loss function, and augmentation
+choices. Cite papers where relevant (Loshchilov & Hutter, 2019 for decoupled
+weight decay; Goyal et al., 2017 for LR scaling, etc.)>
+
+## Results
+<Metric table vs baseline from Phase 4>
+<Training dynamics: loss trajectory, convergence epoch, gradient norm behavior>
+<Ablation results if run>
+
+## Production Readiness
+**ML Engineer verdict:** <DEPLOY | OPTIMIZE | REDESIGN>
+<Summary of infrastructure and deployment assessment>
+<Required changes before production: ordered by priority>
+
+## Methodology Review
+**Applied ML Scientist verdict:** <Sound | Consider Alternatives | Revise>
+<Summary of theoretical soundness assessment>
+<Literature gaps or superior alternatives identified>
+
+## Operations Review
+**MLOps Engineer verdict:** <Approved | Concerns | Redesign needed>
+<Summary of production platform and operationalization assessment>
+<CI/CD, monitoring, and retraining gaps identified>
+
+## Code Review
+**Backend Engineer verdict:** <Clean | Minor Issues | Refactor Required | Blocked | N/A — no Python artifacts>
+<Summary of code review findings, or "No Python artifacts found.">
+
+## Limitations
+<What the current implementation does not handle:>
+- <Hardware assumption: trained on X, deployed assumptions unclear>
+- <Data quality: assumes Y, not validated for Z>
+- <Scale: prototype at N examples; behavior at 10× unknown>
+
+## Next Steps
+<Ordered by expected impact:>
+1. <experiment or engineering step>
+2. <experiment or engineering step>
+3. <experiment or engineering step>
+
+## Knowledge Harvested
+- <title> → .shards/knowledge/<type>/<filename>.md
+- Or: None — project did not produce reusable knowledge
+```
+
+**Knowledge harvest.** Before closing, extract reusable knowledge from this project.
+Read `.claude/agents/specific_instructions/shared/knowledge_harvest.md` and follow
+the protocol. Present candidates to the user for confirmation before writing.
+
+::GATE:: id=deep-learning-engineer-phase-5 phase=5 kind=final
+Read Phase 5 summary to the user. Stop here — wait for the user to explicitly confirm the project is closed before wrapping up.
+::ENDGATE::
+
+---
+
+## When this gate is confirmed
+
+This is the final phase. Once Syn returns APPROVED sign-off, the project is complete. Do not read further files.