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fix(attribution): correct source repo URL to SuperiorByteWorks-LLC/agent-project

Browse Source 
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.
This commit is contained in:
Clayton Young
2026-02-19 18:29:14 -05:00
parent 97d7901870
commit ea5a287cf9
39 changed files with 261 additions and 43 deletions
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docs/project/issues/issue-00000001-markdown-mermaid-skill.md
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@@ -116,7 +116,7 @@ flowchart LR
### Content sources
All style guides and templates ported from the `borealBytes/opencode` repository under Apache-2.0 license with attribution retained[^3].
All style guides and templates ported from the `SuperiorByteWorks-LLC/agent-project` repository under Apache-2.0 license with attribution retained[^3].
| Source path | Destination |
| ------------------------------------------- | ---------------------------------------------------- |
@@ -154,7 +154,7 @@ scientific-skills/markdown-mermaid-writing/
[^2]: Orion Li (K-Dense), responding: "Thanks for letting us know! We'll make sure to include this into our sauce when we implement our upcoming reorganization of the skills." — K-Dense Discord, 2026-02-19.
[^3]: Boreal Bytes / Superior Byte Works, LLC. `opencode` repository. https://github.com/borealBytes/opencode. Apache-2.0 License.
[^3]: Boreal Bytes / Superior Byte Works, LLC. `opencode` repository. https://github.com/SuperiorByteWorks-LLC/agent-project. Apache-2.0 License.
---

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### What changed and why
This PR adds a new skill — `markdown-mermaid-writing` — that establishes markdown with embedded Mermaid diagrams as the **default and canonical documentation format** for all scientific skills. The skill ports comprehensive style guides, 24 diagram type references, and 9 document templates from the `borealBytes/opencode` project, and codifies the "source format" philosophy proposed in the K-Dense Discord on 2026-02-19.
This PR adds a new skill — `markdown-mermaid-writing` — that establishes markdown with embedded Mermaid diagrams as the **default and canonical documentation format** for all scientific skills. The skill ports comprehensive style guides, 24 diagram type references, and 9 document templates from the `SuperiorByteWorks-LLC/agent-project` project, and codifies the "source format" philosophy proposed in the K-Dense Discord on 2026-02-19.
The motivation: scientific outputs currently default to Python-generated or AI-generated images for diagrams. This PR inverts that priority — text-based Mermaid diagrams are the source of truth, downstream image generation is secondary. This gives users version-controlled, token-efficient, universally renderable documentation by default.
@@ -179,7 +179,7 @@ No ADR created — this is a documentation addition with no architectural tradeo
## 🔗 References
- [Issue #00000001](../issues/issue-00000001-markdown-mermaid-skill.md) — Feature request
- [opencode repository](https://github.com/borealBytes/opencode) — Source of ported style guides (Apache-2.0)
- [opencode repository](https://github.com/SuperiorByteWorks-LLC/agent-project) — Source of ported style guides (Apache-2.0)
- [K-Dense Discord thread](https://discord.com/channels/k-dense) — Originating conversation, 2026-02-19
---

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scientific-skills/markdown-mermaid-writing/SKILL.md
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@@ -12,7 +12,7 @@ allowed-tools: [Read, Write, Edit, Bash]
license: Apache-2.0
metadata:
skill-author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes)
skill-source: https://github.com/borealBytes/opencode
skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project
skill-version: "1.0.0"
skill-contributors:
- name: Clayton Young
@@ -273,9 +273,9 @@ Each file contains: production-quality exemplar, tips specific to that type, and
## 📝 Attribution
All style guides, diagram type guides, and document templates in this skill are ported from the `borealBytes/opencode` repository under the Apache-2.0 License.
All style guides, diagram type guides, and document templates in this skill are ported from the `SuperiorByteWorks-LLC/agent-project` repository under the Apache-2.0 License.
- **Source**: https://github.com/borealBytes/opencode
- **Source**: https://github.com/SuperiorByteWorks-LLC/agent-project
- **Author**: Clayton Young / Superior Byte Works, LLC (Boreal Bytes)
- **License**: Apache-2.0

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# CRISPR-Based Gene Editing Efficiency Analysis
_Example research report — demonstrates markdown-mermaid-writing skill standards. All diagrams use Mermaid embedded in markdown as the source format._
---
## 📋 Overview
This report analyzes the efficiency of CRISPR-Cas9 gene editing across three cell line models under variable guide RNA (gRNA) conditions. Editing efficiency was quantified by T7E1 assay and next-generation sequencing (NGS) of on-target loci[^1].
**Key findings:**
- HEK293T cells show highest editing efficiency (mean 78%) across all gRNA designs
- GC content between 40–65% correlates with editing efficiency (r = 0.82)
- Off-target events occur at <0.1% frequency across all conditions tested
---
## 🔄 Experimental workflow
CRISPR editing experiments followed a standardized five-stage protocol. Each stage has defined go/no-go criteria before proceeding.
```mermaid
flowchart TD
accTitle: CRISPR Editing Experimental Workflow
accDescr: Five-stage experimental pipeline from gRNA design through data analysis, with quality checkpoints between each stage.
design["🧬 Stage 1\ngRNA Design\n(CRISPRscan + Cas-OFFinder)"]
synth["⚙️ Stage 2\nOligo Synthesis\n& Annealing"]
transfect["🔬 Stage 3\nCell Transfection\n(Lipofectamine 3000)"]
screen["🧪 Stage 4\nPrimary Screen\n(T7E1 assay)"]
ngs["📊 Stage 5\nNGS Validation\n(150 bp PE reads)"]
qc1{GC 40-65%?}
qc2{Yield ≥ 2 µg?}
qc3{Viability ≥ 85%?}
qc4{Band visible?}
design --> qc1
qc1 -->|"✅ Pass"| synth
qc1 -->|"❌ Redesign"| design
synth --> qc2
qc2 -->|"✅ Pass"| transfect
qc2 -->|"❌ Re-synthesize"| synth
transfect --> qc3
qc3 -->|"✅ Pass"| screen
qc3 -->|"❌ Optimize"| transfect
screen --> qc4
qc4 -->|"✅ Pass"| ngs
qc4 -->|"❌ Repeat"| screen
classDef stage fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f
classDef gate fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12
classDef fail fill:#fee2e2,stroke:#dc2626,stroke-width:2px,color:#7f1d1d
class design,synth,transfect,screen,ngs stage
class qc1,qc2,qc3,qc4 gate
```
---
## 🔬 Methods
### Cell lines and culture
Three cell lines were used: HEK293T (human embryonic kidney), K562 (chronic myelogenous leukemia), and Jurkat (T-lymphocyte). All lines were maintained in RPMI-1640 with 10% FBS at 37°C / 5% CO₂[^2].
### gRNA design and efficiency prediction
gRNAs targeting the _EMX1_ locus were designed using CRISPRscan[^3] with the following criteria:
| Criterion | Threshold | Rationale |
| -------------------- | --------- | ------------------------------------- |
| GC content | 40–65% | Optimal Tm and Cas9 binding |
| CRISPRscan score | ≥ 0.6 | Predicted on-target activity |
| Off-target sites | ≤ 5 (≤3 mismatches) | Reduce off-target editing risk |
| Homopolymer runs | None (>4 nt) | Prevents premature transcription stop |
### Transfection protocol
RNP complexes were assembled at 1:1.2 molar ratio (Cas9:gRNA) and delivered by lipofection. Cells were harvested 72 hours post-transfection for genomic DNA extraction.
### Analysis pipeline
```mermaid
sequenceDiagram
accTitle: NGS Data Analysis Pipeline
accDescr: Sequence of computational steps from raw FASTQ files through variant calling to final efficiency report.
participant raw as 📥 Raw FASTQ
participant qc as 🔍 FastQC
participant trim as ✂️ Trimmomatic
participant align as 🗺️ BWA-MEM2
participant call as ⚙️ CRISPResso2
participant report as 📊 Report
raw->>qc: Per-base quality scores
qc-->>trim: Flag low-Q reads (Q<20)
trim->>align: Cleaned reads
align->>align: Index reference genome (hg38)
align->>call: BAM + target region BED
call->>call: Quantify indel frequency
call-->>report: Editing efficiency (%)
call-->>report: Off-target events
report-->>report: Statistical summary
```
---
## 📊 Results
### Editing efficiency by cell line
| Cell line | n (replicates) | Mean efficiency (%) | SD (%) | Range (%) |
| ---------- | -------------- | ------------------- | ------ | --------- |
| **HEK293T** | 6 | **78.4** | 4.2 | 71.2–84.6 |
| K562 | 6 | 52.1 | 8.7 | 38.4–63.2 |
| Jurkat | 6 | 31.8 | 11.3 | 14.2–47.5 |
HEK293T cells showed significantly higher editing efficiency than both K562 (p < 0.001) and Jurkat (p < 0.001) lines by one-way ANOVA with Tukey post-hoc correction.
### Effect of GC content on efficiency
GC content between 40–65% was strongly correlated with editing efficiency (Pearson r = 0.82, p < 0.0001, n = 48 gRNAs).
```mermaid
xychart-beta
accTitle: Editing Efficiency vs gRNA GC Content
accDescr: Bar chart showing mean editing efficiency grouped by GC content bins, demonstrating optimal performance in the 40 to 65 percent GC range
title "Mean Editing Efficiency by GC Content Bin (HEK293T)"
x-axis ["< 30%", "30–40%", "40–50%", "50–65%", "> 65%"]
y-axis "Editing Efficiency (%)" 0 --> 100
bar [18, 42, 76, 81, 38]
```
### Timeline of key experimental milestones
```mermaid
timeline
accTitle: Experiment Timeline — CRISPR Efficiency Study
accDescr: Chronological milestones from study design through manuscript submission across six months
section Month 1
Study design and gRNA library design : 48 gRNAs across 3 target loci
Cell line authentication : STR profiling confirmed all three lines
section Month 2
gRNA synthesis and QC : 46/48 gRNAs passed yield threshold
Pilot transfections (HEK293T) : Optimized lipofection conditions
section Month 3
Full transfection series : All 3 cell lines, all 46 gRNAs, 6 replicates
T7E1 primary screening : Passed go/no-go for all conditions
section Month 4
NGS library preparation : 276 samples processed
Sequencing run (NovaSeq) : 150 bp PE, mean 50k reads/sample
section Month 5
Bioinformatic analysis : CRISPResso2 pipeline
Statistical analysis : ANOVA, correlation, regression
section Month 6
Manuscript preparation : This report
```
---
## 🔍 Discussion
### Why HEK293T outperforms suspension lines
HEK293T's superior editing efficiency relative to K562 and Jurkat likely reflects three factors[^4]:
1. **Adherent morphology** — enables more uniform lipofection contact
2. **High transfection permissiveness** — HEK293T expresses the SV40 large T antigen, which may facilitate nuclear import
3. **Cell cycle distribution** — higher proportion in S/G2 phase where HDR is favored
<details>
<summary><strong>🔧 Technical details — off-target analysis</strong></summary>
Off-target editing was assessed by GUIDE-seq at the 5 highest-activity gRNAs. No off-target sites exceeding 0.1% editing frequency were detected. The three potential sites flagged by Cas-OFFinder (≤2 mismatches) showed 0.00%, 0.02%, and 0.04% indel frequencies — all below the assay noise floor of 0.05%.
Full GUIDE-seq data available in supplementary data package (GEO accession pending).
</details>
---
### Comparison with published benchmarks
```mermaid
radar
accTitle: CRISPR Method Comparison Radar
accDescr: Multi-dimensional radar chart comparing our protocol against published Cas9 and base editing benchmarks across five performance axes
title Performance vs. Published Methods
x-axis ["Efficiency", "Specificity", "Delivery ease", "Cost", "Cell viability"]
"This study (RNP + Lipo)" : [78, 95, 80, 85, 90]
"Plasmid Cas9 (lit.)" : [55, 70, 90, 95, 75]
"Electroporation RNP (lit.)" : [88, 96, 50, 60, 65]
```
---
## 🎯 Conclusions
1. RNP-lipofection in HEK293T achieves >75% CRISPR editing efficiency — competitive with electroporation without the associated viability cost
2. gRNA GC content is the single strongest predictor of editing efficiency in our dataset (r = 0.82)
3. This protocol is not directly transferable to suspension lines without further optimization; K562 and Jurkat require electroporation or viral delivery for comparable efficiency
---
## 🔗 References
[^1]: Ran, F.A. et al. (2013). "Genome engineering using the CRISPR-Cas9 system." _Nature Protocols_, 8(11), 2281–2308. https://doi.org/10.1038/nprot.2013.143
[^2]: ATCC. (2024). "Cell Line Authentication and Quality Control." https://www.atcc.org/resources/technical-documents/cell-line-authentication
[^3]: Moreno-Mateos, M.A. et al. (2015). "CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo." _Nature Methods_, 12(10), 982–988. https://doi.org/10.1038/nmeth.3543
[^4]: Molla, K.A. & Yang, Y. (2019). "CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications." _Trends in Biotechnology_, 37(10), 1121–1142. https://doi.org/10.1016/j.tibtech.2019.03.008

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Architecture Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Block Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# C4 Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Class Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Composing Complex Diagram Sets

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Entity Relationship (ER) Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Flowchart

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Gantt Chart

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Git Graph

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Kanban Board

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Mindmap

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Packet Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Pie Chart

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Quadrant Chart

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Radar Chart

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Requirement Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Sankey Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Sequence Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# State Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Timeline

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Treemap Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# User Journey

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# XY Chart

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# ZenUML Sequence Diagram

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Markdown Style Guide

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Mermaid Diagram Style Guide

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Decision Record (ADR/RFC) Template

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# How-To / Tutorial Guide Template
@@ -268,7 +268,7 @@ Key commands and values from this guide for future reference:
## 🔗 References
- [Official documentation](https://example.com) — [Which section is most relevant]
- [Source repository](https://github.com/borealBytes) — [For bug reports and contributions]
- [Source repository](https://github.com/SuperiorByteWorks-LLC) — [For bug reports and contributions]
---

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scientific-skills/markdown-mermaid-writing/templates/issue.md
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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Issue Documentation Template

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scientific-skills/markdown-mermaid-writing/templates/kanban.md
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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Kanban Board Documentation Template

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Presentation / Briefing Template

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Project Documentation Template

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Pull Request Documentation Template

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Research Paper / Technical Analysis Template

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<!-- Source: https://github.com/borealBytes/opencode | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
# Status Report / Executive Briefing Template