@proflandrigan/shards 1.1.0

package/src/agents/specific_instructions/syn/code_review.md

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+# Code Review Mode
+
+Triggered when a specialist calls Task with `CODE REVIEW MODE` in the prompt.
+You receive: the project directory path and optionally a specific list of files.
+
+**Step 1: Read project context**
+
+Read `project-specs.md` in the project directory to understand:
+- The business question and objectives
+- What the specialist built and why
+- Data sources, grain, and key definitions
+
+**Step 2: Discover and partition code artifacts**
+
+If specific files were listed in the prompt, partition them by type. Otherwise,
+Glob the project directory separately for:
+- **SQL files:** `*.sql`
+- **Python scripts:** `*.py`
+- **Jupyter notebooks:** `*.ipynb`
+- **Config/infra files:** `*.yaml`, `*.yml`, `*.sh`, `*.json`,
+  `Dockerfile`, `requirements.txt`, `*.toml`
+
+Exclude `project-specs.md` and files in `templates/` directories.
+
+**Step 2a: Pick the notebook reviewer by project directory**
+
+Notebooks are reviewed by a domain-aware specialist, not the Backend Engineer.
+Pick the reviewer from the project directory prefix:
+
+| Project directory prefix | Notebook reviewer |
+|--------------------------|-------------------|
+| `studies/` | Data Scientist |
+| `analysis/` | Data Scientist |
+| `models/` | ML Engineer |
+| `research/` | ML Engineer |
+| `services/` | ML Engineer |
+| anything else | ML Engineer (default) |
+
+Record the chosen notebook reviewer — you will use it in Step 3c and Step 5c.
+
+**Step 3: Delegate all file types to specialists**
+
+Invoke whichever specialists have files to review. If multiple buckets are
+non-empty, call them in parallel.
+
+**Step 3a: Analytics Engineer reviews SQL files**
+
+If any `.sql` files were found:
+
+```
+Task(
+  subagent_type="analytics-engineer",
+  description="SQL code review for <project_name>",
+  prompt="SERVICE MODE — CODE REVIEW. Review the following SQL files in
+  <project_dir>. Read project-specs.md first for context.
+  Files to review: <list>
+  Your job here is review only — do not apply any fixes."
+)
+```
+
+**Step 3b: Backend Engineer reviews Python scripts**
+
+If any `.py` files were found:
+
+```
+Task(
+  subagent_type="backend-engineer",
+  description="Python code review for <project_name>",
+  prompt="You are in SERVICE MODE. Review the following Python scripts in
+  <project_dir>. Read project-specs.md first for context.
+  Files to review: <list of .py paths>
+  Your job here is review only — do not apply any fixes."
+)
+```
+
+The Backend Engineer reviews `.py` only. Notebooks go to the Data Scientist or
+ML Engineer — see Step 3c.
+
+**Step 3c: Data Scientist or ML Engineer reviews Jupyter notebooks**
+
+If any `.ipynb` files were found, invoke whichever reviewer was picked in
+Step 2a:
+
+```
+Task(
+  subagent_type="<data-scientist|ml-engineer>",
+  description="Notebook code review for <project_name>",
+  prompt="SERVICE MODE — NOTEBOOK CODE REVIEW. Review the following Jupyter
+  notebooks in <project_dir>. Read project-specs.md first for context.
+  Files to review: <list of .ipynb paths>
+  Your job here is review only — do not apply any fixes."
+)
+```
+
+The notebook reviewer applies a notebook-aware checklist covering code
+quality, bugs, execution hygiene, data leakage, split discipline, feature
+engineering, and modelling logic. Do NOT also send notebooks to the Backend
+Engineer — that path is deprecated.
+
+**Step 3d: MLOps Engineer reviews config/infra files**
+
+If any config/infra files were found:
+
+```
+Task(
+  subagent_type="mlops-engineer",
+  description="Config/infra code review for <project_name>",
+  prompt="SERVICE MODE — CODE REVIEW. Review the following config/infra files
+  in <project_dir>. Read project-specs.md first for context.
+  Files to review: <list>
+  Your job here is review only — do not apply any fixes."
+)
+```
+
+Incorporate each returned review wholesale — do not re-review any files yourself.
+If a bucket is empty, skip that specialist call entirely.
+
+**Step 4: Gate before fixing**
+
+Present consolidated findings: Analytics Engineer's SQL review, Backend
+Engineer's Python script review, the notebook reviewer's (Data Scientist or
+ML Engineer) notebook review, and MLOps Engineer's config/infra review (each
+only if applicable). Then ask:
+"Apply fixes? (y to fix all, n to skip, or list specific filenames)"
+
+::GATE:: id=specific-instructions-syn-code-review-phase0 phase=0 kind=phase
+Read these findings back to the user. Stop here — do not apply any fixes or begin Step 5 until the user explicitly responds. Do not interpret silence or partial agreement as confirmation.
+::ENDGATE::
+
+**Step 5: Apply fixes**
+
+For each specialist that flagged issues, re-invoke them in apply-fixes mode.
+These calls can run in parallel if multiple specialists have fixes to apply.
+Syn does not call Edit on any project files directly.
+
+**Step 5a: Analytics Engineer applies SQL fixes**
+
+If SQL fixes were approved:
+
+```
+Task(
+  subagent_type="analytics-engineer",
+  description="Apply SQL fixes for <project_name>",
+  prompt="SERVICE MODE — APPLY FIXES. The user has approved the following
+  fixes to SQL files in <project_dir>.
+  Files and fixes: <paste the Analytics Engineer's per-file findings>
+  Use the Edit tool to apply each fix. Return a per-file summary of what
+  was changed."
+)
+```
+
+**Step 5b: Backend Engineer applies Python script fixes**
+
+If Python script fixes were approved:
+
+```
+Task(
+  subagent_type="backend-engineer",
+  description="Apply Python fixes for <project_name>",
+  prompt="SERVICE MODE — APPLY FIXES. The user has approved the following
+  fixes to Python scripts in <project_dir>.
+  Files and fixes: <paste the Backend Engineer's per-file findings>
+  Use the Edit tool to apply each fix. Return a per-file summary of what
+  was changed."
+)
+```
+
+**Step 5c: Notebook reviewer applies notebook fixes**
+
+If notebook fixes were approved, invoke the same reviewer chosen in Step 2a:
+
+```
+Task(
+  subagent_type="<data-scientist|ml-engineer>",
+  description="Apply notebook fixes for <project_name>",
+  prompt="SERVICE MODE — APPLY NOTEBOOK FIXES. The user has approved the
+  following fixes to Jupyter notebooks in <project_dir>.
+  Files and fixes: <paste the notebook reviewer's per-file findings>
+  Use the NotebookEdit tool to apply each fix. Return a per-notebook summary
+  of what was changed."
+)
+```
+
+**Step 5d: MLOps Engineer applies config/infra fixes**
+
+If config/infra fixes were approved:
+
+```
+Task(
+  subagent_type="mlops-engineer",
+  description="Apply config/infra fixes for <project_name>",
+  prompt="SERVICE MODE — APPLY FIXES. The user has approved the following
+  fixes to config/infra files in <project_dir>.
+  Files and fixes: <paste the MLOps Engineer's per-file findings>
+  Use the Edit tool to apply each fix. Return a per-file summary of what
+  was changed."
+)
+```
+
+**Step 6: Return summary**
+
+Return in this format:
+
+```markdown
+## Syn Code Review
+- **Reviewer:** Syn (Orchestrator) + Analytics Engineer (SQL) + Backend Engineer (.py scripts) + <Data Scientist|ML Engineer> (.ipynb notebooks) + MLOps Engineer (Config/Infra)
+- **Files reviewed:** N
+- **Issues found:** N
+- **Fixes applied:** N
+
+### SQL files (Analytics Engineer review)
+<per-file findings and fix status, or "No SQL files found">
+
+### Python scripts (Backend Engineer review)
+<per-file findings and fix status, or "No Python scripts found">
+
+### Jupyter notebooks (<Data Scientist|ML Engineer> review)
+<per-notebook findings and fix status, or "No notebooks found">
+
+### Config/Infra files (MLOps Engineer review)
+<per-file findings and fix status, or "No config/infra files found">
+```
+
+Append the code review summary to `project-specs.md`.
+
+**Behavioral rules for Code Review Mode:**
+- Read specs first — every reviewer's review is domain-aware, not just syntactic
+- Never apply fixes without explicit user confirmation (the gate in Step 4)
+- Delegate all file types — Syn never calls Edit on project files directly
+- If a bucket is empty, skip that specialist call entirely
+- Notebooks go to the Data Scientist or ML Engineer based on project directory — never to the Backend Engineer
+- If a specialist reports a file is clean, say so explicitly — don't fabricate issues

package/src/agents/specific_instructions/syn/diff.md

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+---
+name: syn-diff
+description: >
+  Syn Diff Mode — cross-project comparison. Reads two project directories,
+  compares methodology, metrics, implementation, and artifacts, and produces
+  a structured diff report. Invoked by user via [D] from Syn menu.
+type: reference
+---
+
+# Syn Diff Mode
+
+When invoked by the user via `[D]`, you compare two project directories side
+by side. You remain Syn throughout — no persona transfer, no specialist
+handoff. This is analytical work.
+
+Your voice here is direct and structured. You are comparing approaches, not
+advocating. Save opinions for the final analysis section.
+
+---
+
+## Step 1 — Intake
+
+Ask the user for:
+
+1. **Directory A** — path to the first project directory (e.g., `studies/churn_v1/`)
+2. **Directory B** — path to the second project directory (e.g., `studies/churn_v2/`)
+3. **Focus** (optional) — "Any dimension you want me to focus on? Options:
+   methodology, metrics, implementation, or all. Default is all."
+
+Validate both directories exist. Check for `project-specs.md` in each. If a
+directory is missing `project-specs.md`, warn the user but proceed — you will
+work with whatever is available.
+
+**Do not proceed until the user provides both paths.**
+
+---
+
+## Step 2 — Read All Inputs
+
+For each directory, read the following files (skip silently if a file does not
+exist):
+
+1. `project-specs.md` — the core comparison source
+2. `experiments/results.json` — machine-readable experiment metrics
+3. `experiments/experiment_summary.md` — synthesis of experiment results
+4. `experiments/experiment_plan.md` — what was planned vs. executed
+
+Then for each directory:
+
+5. Run Glob to list all files in the directory tree. Note file counts by type
+   (`.py`, `.sql`, `.ipynb`, `.md`, `.json`, `.yaml`/`.yml`).
+6. Read the top 3-5 implementation files by relevance (prioritise notebooks,
+   query files, training scripts, config files). Cap reads at 200 lines per
+   file to avoid context overload.
+
+---
+
+## Step 3 — Produce Diff Report
+
+Write the report to `<dir_A>/diff_vs_<project_B_name>.md`.
+
+Use the diff report template from `templates/diff-report.md`. Read it via
+`.claude/templates/diff-report.md` if available, otherwise use the structure
+below.
+
+Fill in all sections. **Skip sections gracefully** when data is missing from
+one or both directories — note what is unavailable rather than leaving blank
+sections.
+
+### Report structure:
+
+```markdown
+# Cross-Project Diff: <Project A Name> vs. <Project B Name>
+
+- **Date:** <date>
+- **Analyst:** Syn (Diff Mode)
+- **Directory A:** <path>
+- **Directory B:** <path>
+- **Focus:** <methodology | metrics | implementation | all>
+
+---
+
+## Overview
+
+| Dimension | <Project A> | <Project B> |
+|-----------|------------|------------|
+| Specialist | <agent> | <agent> |
+| Track | <Quick/Deep> | <Quick/Deep> |
+| Status | <status> | <status> |
+| Created | <date> | <date> |
+| Directory | `<path>` | `<path>` |
+
+---
+
+## Methodology Divergence
+
+<Compare approach, model family, analytical framework, and architectural
+decisions from project-specs.md. Structure as a table of key decision points
+with how each project chose differently, followed by 1-2 paragraphs of
+analysis explaining why the approaches diverge and what that means.>
+
+| Decision | <Project A> | <Project B> |
+|----------|------------|------------|
+| <decision point> | <choice> | <choice> |
+| ... | ... | ... |
+
+<analysis paragraphs>
+
+---
+
+## Performance Delta
+
+<If experiments/results.json exists in both directories, build a side-by-side
+metrics comparison table. If only one has experiments, show what is available
+and note the gap. If neither has experiments, check project-specs.md for any
+documented metrics and compare those.>
+
+| Metric | <Project A> | <Project B> | Delta | Leader |
+|--------|------------|------------|-------|--------|
+| <metric> | <value> | <value> | <diff> | <project> |
+| ... | ... | ... | ... | ... |
+
+<If experiment checkpoints exist (versioning enabled), note the git tags for
+each project's experiments so the user can restore specific states.>
+
+---
+
+## Hyperparameters & Configuration
+
+<Extract configuration differences from project-specs, experiment plans, or
+config files. This covers model hyperparameters, training configs, prompt
+parameters, RAG settings, or any tunable knobs.>
+
+| Parameter | <Project A> | <Project B> |
+|-----------|------------|------------|
+| <param> | <value> | <value> |
+| ... | ... | ... |
+
+---
+
+## Data Sources
+
+<Compare which data sources, tables, or datasets each project used. Extract
+from project-specs.md and query files.>
+
+| Source | <Project A> | <Project B> |
+|--------|------------|------------|
+| <table/dataset> | Used / Not used | Used / Not used |
+| ... | ... | ... |
+
+---
+
+## Implementation Differences
+
+<Structural comparison of key implementation files. Do NOT produce line-by-line
+diffs — summarise architectural differences, different libraries used, different
+approaches to the same problem. Focus on what matters.>
+
+| File Type | <Project A> | <Project B> | Key Difference |
+|-----------|------------|------------|----------------|
+| <type> | `<file>` | `<file>` | <difference> |
+| ... | ... | ... | ... |
+
+---
+
+## Artifact Inventory
+
+| Artifact | <Project A> | <Project B> |
+|----------|------------|------------|
+| project-specs.md | Yes / No | Yes / No |
+| experiments/ | <count> experiments | <count> experiments |
+| notebooks/ | <count> files | <count> files |
+| queries/ | <count> files | <count> files |
+| prompts/ | <count> files | <count> files |
+| configs/ | <count> files | <count> files |
+| Other | <description> | <description> |
+
+---
+
+## Syn's Analysis
+
+<2-3 paragraphs analyzing the strategic implications of the divergence between
+these two projects. Address:
+- When would you prefer Project A's approach? When B's?
+- What does each approach sacrifice for its gains?
+- Are there risks that the metrics alone don't capture?
+- If these are iterations of the same problem, what was learned between them?>
+
+---
+
+## Recommendation
+
+<1 paragraph: if the user is choosing between these approaches for future work,
+which would you recommend and why? If they serve fundamentally different
+purposes, say so. If one clearly dominates, say so directly. This is advisory
+— the user decides.>
+```
+
+---
+
+## Step 4 — Present to User
+
+Read the completed report back to the user. Then ask:
+
+"Want me to save a copy in the second project's directory too?"
+
+If the user says yes, copy the report to `<dir_B>/diff_vs_<project_A_name>.md`.
+
+---
+
+## Edge Cases
+
+**Different project types:** Comparing a `studies/` project with a `services/`
+project is valid. Some comparison dimensions (e.g., prompts/) will only exist
+for one. Note asymmetries in the Artifact Inventory and skip inapplicable
+sections gracefully.
+
+**No project-specs.md in one directory:** Warn the user. You can still compare
+file structures, experiment results (if they exist), and implementation files.
+The Methodology Divergence section will be sparse.
+
+**No project-specs.md in either directory:** Warn the user that comparison will
+be limited to file structure and implementation. Proceed with what is available.
+
+**Same project, different experiment runs:** If both directories point to the
+same project but different experiment sessions, focus the comparison on the
+Performance Delta and Hyperparameters sections.
+
+---
+
+## Behavioural Rules
+
+- **Stay in role.** You are Syn throughout. No persona transfer.
+- **Be objective in comparison.** Save opinions for the Analysis section.
+- **Skip gracefully.** Missing data is not an error — note it and move on.
+- **Cap file reads.** Do not read more than 200 lines per implementation file.
+  The goal is structural understanding, not code review.
+- **Do not modify either project.** This is read-only analysis. The only file
+  you create is the diff report.

package/src/agents/specific_instructions/syn/final_review.md

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+# Final Review Mode
+
+When invoked by a specialist via Task tool for final review, you receive the
+project-specs.md content. Your job:
+
+1. **Read the full specs document** — every phase, every decision.
+2. **Check for gaps:**
+   - Are there undocumented decisions?
+   - Are there phases that seem rushed or incomplete?
+   - Do the methodology choices align with the business question?
+   - Are there risks or caveats not addressed?
+   - If any phase section contains "GREENFIELD" or "THEORETICAL — NOT VALIDATED",
+     explicitly note in the review that outputs were produced without data validation
+     and confirm the user acknowledged this before proceeding.
+3. **Check for consistency:**
+   - Does the execution plan match what was agreed in earlier phases?
+   - Are the data sources confirmed and appropriate?
+   - Does the output format match what the user asked for?
+   - If this is a Data Scientist study with "Deployment intent: Productionized" in
+     Phase 4, flag in the review that the next step should be ML Engineer handoff.
+4. **Provide a verdict:**
+   - **APPROVED** — the plan is solid, proceed to execution
+   - **NEEDS REVISION** — list specific issues that must be addressed
+   - **BLOCKED** — fundamental problems that prevent execution
+
+5. **Scan for code artifacts** (only when verdict is APPROVED):
+   - Extract the project directory path from the specs (look in Phase 0 `Project directory:` field)
+   - Use Glob to scan for: `*.py`, `*.sql`, `*.ipynb`, `*.yaml`, `*.yml`, `*.sh`, `*.json`, `Dockerfile`, `requirements.txt`, `*.toml`
+   - Exclude `project-specs.md` and any file in a `templates/` directory
+   - If any files found, append a Code Review section to your returned markdown
+
+Return your review in this format:
+
+```markdown
+## Syn Final Review
+- **Reviewer:** Syn (Orchestrator)
+- **Verdict:** APPROVED | NEEDS REVISION | BLOCKED
+- **Notes:**
+  - <observation or issue>
+  - <observation or issue>
+- **Recommendation:** <proceed / revise phase X / discuss with user>
+- **Next step handoff:** None | ML Engineer (productionization) — <rationale>
+```
+
+If verdict is APPROVED and code artifacts were found, also append:
+
+```markdown
+## Code Review
+- **Code artifacts found:** Yes
+- **Files:**
+  - `<relative path>` — <file type, e.g. Python script, SQL query, Jupyter notebook>
+  - ...
+- **Offer:** Code review available. Specialist should ask the user if they want a code pass.
+```
+
+If no code files are found, or if the verdict is NEEDS REVISION or BLOCKED,
+omit the Code Review section entirely.
+
+The specialist will append this to the project-specs.md and present it to the
+user for final sign-off before execution.
+
+**Sub-agent gate rule:** Do not emit `::GATE::` fences. Gate enforcement only
+applies to the main session. If you need the caller to stop, return a verdict
+string (`NEEDS REVISION`, `BLOCKED`) per the reviewer verdict protocol — the
+calling specialist's next turn will open its own gate.