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

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.

docs/project/issues/issue-00000001-markdown-mermaid-skill.md

@@ -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.
 
 ---
 

docs/project/pr/pr-00000001-markdown-mermaid-skill.md

@@ -16,7 +16,7 @@
 
 ### 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
 
 ---

scientific-skills/markdown-mermaid-writing/SKILL.md

@@ -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
 

scientific-skills/markdown-mermaid-writing/assets/examples/example-research-report.md

@@ -0,0 +1,218 @@
+# 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

scientific-skills/markdown-mermaid-writing/references/diagrams/architecture.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/block.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/c4.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/class.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/complex_examples.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/er.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/flowchart.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/gantt.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/git_graph.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/kanban.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/mindmap.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/packet.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/pie.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/quadrant.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/radar.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/requirement.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/sankey.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/sequence.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/state.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/timeline.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/treemap.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/user_journey.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/xy_chart.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/diagrams/zenuml.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/markdown_style_guide.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/references/mermaid_style_guide.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/templates/decision_record.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/templates/how_to_guide.md

@@ -1,4 +1,4 @@
-<!-- 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]
 
 ---
 

scientific-skills/markdown-mermaid-writing/templates/issue.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/templates/kanban.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/templates/presentation.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/templates/project_documentation.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/templates/pull_request.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/templates/research_paper.md

@@ -1,4 +1,4 @@
-<!-- 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
 

scientific-skills/markdown-mermaid-writing/templates/status_report.md

@@ -1,4 +1,4 @@
-<!-- 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