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All 40 references to borealBytes/opencode updated to the correct source: https://github.com/SuperiorByteWorks-LLC/agent-project Affected files: SKILL.md, all 24 diagram guides, 9 templates, issue and PR docs, plus assets/examples/example-research-report.md (new file). The example report demonstrates full skill usage: flowchart, sequence, timeline, xychart, radar diagrams — all with accTitle/accDescr and classDef colors, no %%{init}. Covers HEK293T CRISPR editing efficiency as a realistic scientific context.
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Pull Request Documentation Template
Back to Markdown Style Guide — Read the style guide first for formatting, citation, and emoji rules.
Use this template for: Documenting pull requests as persistent, searchable markdown records. This file IS the PR — not a companion document. It captures everything: what changed, why, how to verify, security impact, deployment strategy, and what was learned.
Key features: Summary with impact classification, change inventory with before/after, testing evidence, security review, breaking change documentation, deployment strategy, observability plan, rollback plan, and reviewer checklist.
Philosophy: This file IS the PR description — not a companion, not a supplement, not a copy. The GitHub PR is a thin pointer: humans go there to comment on diffs, approve, and watch CI. But the actual record — what changed, why it changed, testing evidence, rollback plan, and lessons learned — lives HERE, committed to the repo.
When someone asks "what was PR #123 about?" six months from now, they grep docs/project/pr/, not the GitHub API. When you migrate from GitHub to GitLab, every PR record comes with you. When an AI agent needs to understand the history of a module, it reads these files locally — no tokens, no rate limits, no platform dependency.
This is the Everything is Code philosophy: project management data lives in the repo, versioned and portable. Don't capture information in GitHub's UI that should be captured in this file. Invest the 10 minutes. A great PR file eliminates the "what was this PR about?" Slack message and the "can someone check the GitHub PR?" context switch — the answer is already in the repo.
File Convention
docs/project/pr/pr-00000123-fix-auth-timeout.md
docs/project/pr/pr-00000124-add-job-retry-metrics.md
docs/project/pr/pr-00000125-refactor-ci-stage-order.md
- Directory:
docs/project/pr/ - Naming:
pr-+ PR number zero-padded to 8 digits +-+ short lowercase hyphenated description - Cross-reference: Link to the live PR in the metadata table
- GitHub PR body: Use only the full branch URL to this file (for example,
https://github.com/<org>/<repo>/blob/<branch>/docs/project/pr/pr-00000123-fix-auth-timeout.md)
The Template
Everything below the line is the template. Copy from here:
PR-[NUMBER]: [Concise Title — What This Changes]
| Field | Value |
|---|---|
| PR | #NUMBER (add tracker URL if your project uses one) |
| Author | [Name] |
| Date | [YYYY-MM-DD] |
| Status | [Open / Merged / Closed] |
| Branch | [feature/branch-name] → main |
| Related issues | #ISSUE, #ISSUE2 |
| Deploy strategy | [Standard / Canary / Blue-green / Feature flag] |
📋 Summary
What changed and why
[2–4 sentences. What this PR does at a business/product level, not code level. Why was this change necessary? What problem does it solve or what feature does it enable?]
Impact classification
| Dimension | Level | Notes |
|---|---|---|
| Risk | 🟢 Low / 🟡 Medium / 🔴 High | [Why this risk level] |
| Scope | [Narrow / Moderate / Broad] | [What areas are affected] |
| Reversibility | [Easily reversible / Requires migration / Irreversible] | [Rollback complexity] |
| Security | [None / Low / Medium / High] | [Auth, data, or permissions changes?] |
🔍 Changes
Change inventory
| File / Area | Change type | Description |
|---|---|---|
[path/to/file] |
[Added / Modified / Deleted / Renamed] | [What changed and why] |
[path/to/file] |
[Type] | [Description] |
[path/to/file] |
[Type] | [Description] |
Before and after
[For behavioral changes, show the difference. Use code blocks, screenshots, or diagrams as appropriate.]
Before:
[Previous behavior, output, or code pattern]
After:
[New behavior, output, or code pattern]
Architecture impact
[If this PR changes how components interact, include a diagram. Skip this section for small changes.]
flowchart LR
accTitle: Architecture Change
accDescr: How this PR modifies the component interaction pattern
a[⚙️ Component A] -->|New path| b[📦 Component B]
b --> c[💾 Data Store]
📋 Detailed Change Notes
[Extended context for complex PRs — design tradeoffs, alternative approaches considered, migration details, performance benchmarks, or anything that helps reviewers understand the depth of the change.]
🧪 Testing
How to verify
# Steps a reviewer can follow to test this change locally
[command 1]
[command 2]
[command 3 — with expected output]
Test coverage
| Test type | Status | Notes |
|---|---|---|
| Unit tests | ✅ Passing | [N new / N modified] |
| Integration tests | ✅ Passing | [Details] |
| Manual testing | ✅ Verified | [What was tested manually] |
| Performance | ⬜ N/A | [Or benchmark results if relevant] |
Edge cases considered
- [Edge case 1 — how it's handled]
- [Edge case 2 — how it's handled]
- [Edge case 3 — or "not applicable" for this change]
🔒 Security
Security checklist
- No secrets, credentials, API keys, or PII in the diff
- Authentication/authorization changes reviewed (if applicable)
- Input validation added for new user-facing inputs
- Injection protections maintained (SQL, XSS, CSRF)
- Dependencies scanned for known vulnerabilities
- Data encryption at rest/in transit maintained
Security impact: [None / Low / Medium / High] — [Brief justification]
[If security-sensitive: Reviewed by: [security reviewer name, date]]
🔐 Security Details
[For security-sensitive changes: threat model, attack vectors considered, mitigations applied. This section helps future security audits understand what was evaluated.]
⚡ Breaking Changes
This PR introduces breaking changes: [Yes / No]
[If no, delete the rest of this section.]
What breaks
| What breaks | Who's affected | Migration path |
|---|---|---|
| [API endpoint / behavior / config] | [Service / team / users] | [How to migrate] |
Migration guide
Before:
[Old usage, API call, config, or behavior]
After:
[New usage — what consumers need to change]
Deprecation timeline: [When the old behavior will be removed, if applicable]
🔄 Rollback Plan
[How to revert this change if something goes wrong in production.]
Revert command:
git revert [commit-sha]
Additional steps needed:
- [Database migration rollback if applicable]
- [Feature flag disable if applicable]
- [Cache invalidation if applicable]
- [Notify affected teams]
⚠️ Rollback risk: [Any caveats — data migration that's one-way, API consumers that may have adopted the new contract, etc.]
🚀 Deployment
Strategy
Approach: [Standard deploy / Canary (N% → 100%) / Blue-green / Feature flag]
Feature flags: [Flag name: [flag_name] — default: [off/on], rollout: [%/audience]]
Pre-deployment
- [Database migrations applied]
- [Environment variables set]
- [Dependent services deployed first: [service names]]
- [Feature flag configured in [flag management tool]]
Post-deployment verification
- [Health check endpoint returns 200]
- [Key user flow verified: [which flow]]
- [Metrics baseline captured: [which metrics]]
- [No error rate spike in first [N] minutes]
📡 Observability
Monitoring
- Dashboard: [Link to relevant dashboard or "existing dashboards sufficient"]
- Key metrics to watch: [Latency p95, error rate, throughput — be specific]
- Watch window: [How long to monitor post-deploy: 15m / 1h / 24h]
Alerts
- [New alerts added: [alert name, threshold, channel]]
- [Existing alerts affected: [which ones and how]]
- [Or: "No alert changes needed"]
Logging
- [New log entries: [what's logged, at what level]]
- [Changed log levels: [what changed and why]]
- [Or: "No logging changes"]
Success criteria
[How do you know this deploy is healthy? Be specific: "p95 latency stays under 200ms, error rate stays below 0.1%, no new error types in logs for 1 hour."]
✅ Reviewer Checklist
- Code follows project style guide and linting rules
- No
TODOorFIXMEcomments introduced without linked issues - Error handling covers failure modes (no empty catch blocks)
- No secrets, credentials, or PII in the diff
- Tests cover the happy path and at least one error path
- Documentation updated if public API or behavior changed
- Database migrations are reversible (if applicable)
- Performance impact considered (no N+1 queries, no unbounded lists)
- Breaking changes documented with migration guide (if applicable)
- Feature flag configured correctly (if applicable)
- Monitoring/alerting updated for new failure modes (if applicable)
- Security review completed (if security-sensitive)
💬 Discussion
[Capture key review feedback and decisions made during the review process. This is the institutional memory — future developers will read this.]
Release note
Category: [Feature / Fix / Enhancement / Breaking / Security / Performance]
[One-line release note for changelog — written for end users, not developers]
Key review decisions
- [Topic]: [What was discussed and what was decided]
- [Topic]: [Discussion and resolution]
Follow-up items
🔗 References
Last updated: [Date]