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.
New skill establishing markdown + Mermaid diagrams as the default and
canonical documentation format for all scientific skill outputs.
Core principle (from K-Dense Discord, 2026-02-19): Mermaid in markdown
is the source of truth — text-based, version-controlled, token-efficient,
universally renderable. Python/AI images are downstream conversions only.
SKILL.md includes:
- Full 'source format' philosophy with three-phase workflow diagram
- 24-entry diagram type selection table with links to each guide
- 9-entry document template index
- Per-skill integration guides (scientific-schematics, scientific-writing,
literature-review, and any other output-producing skill)
- Quality checklist for finalizing documents from any skill
- Full attribution for ported Apache-2.0 content
Originated from conversation between Clayton Young (Boreal Bytes) and the
K-Dense team regarding documentation standards for shared scientific skills.
All content ported from borealBytes/opencode under Apache-2.0 license with
attribution headers prepended to each file.
- references/markdown_style_guide.md (~733 lines): full markdown formatting,
citation, collapsible sections, emoji, Mermaid integration, and template
selection guide
- references/mermaid_style_guide.md (~458 lines): full Mermaid standards —
emoji set, classDef color palette, accessibility (accTitle/accDescr),
theme neutrality (no %%{init}), and diagram type selection table
- references/diagrams/ (24 files): per-type exemplars, tips, and templates
for all Mermaid diagram types
- templates/ (9 files): PR, issue, kanban, ADR, presentation, how-to,
status report, research paper, project docs
Source: https://github.com/borealBytes/opencode
