Status: Active Date: 2026-06-14 Author: Cytognosis Foundation Audience: engineers, researchers, technical writers Tags:
quick-reference,cytognosis-doc
cytognosis-doc — Quick Reference¶
One line: Load this skill for any documentation task; it owns all 34 doc types, templates, research methodology, and the ADHDfy transformation pipeline. Full doc: cytognosis-doc.md
Key Concepts¶
| Term | Definition |
|---|---|
| Diataxis | Documentation framework dividing content into tutorials, how-to guides, reference, and explanation. This skill covers reference and explanation doc types. |
| ADHDfy | 11-step transformation that converts a technical doc into a neurodivergent-friendly variant with BLUF, alerts, 101 sidebars, and bullet structure. |
| EARS notation | Requirements syntax: WHEN/WHILE/IF/THE SYSTEM SHALL patterns that eliminate ambiguity. |
| Metadata header | Required blockquote at the top of every doc: Status, Date, Author, Audience, Tags. |
| Two-variant pattern | High-stakes docs ship in a technical version (_technical.md) and an ADHD-friendly version (_adhd.md). |
| Docs-as-code | All docs live in Git, treated as part of the PR process, written in Markdown with Mermaid. |
Document Type by Stage¶
| Stage | Doc Type | Template |
|---|---|---|
| Research | Market Research | references/market-research-template.md |
| Research | Evaluation | references/evaluation-template.md |
| Research | Model Research | references/model-research-template.md |
| Research | Requirements | references/requirements-template.md |
| Development | ADR | references/adr-template.md |
| Development | Module Spec | references/module-spec-template.md |
| Development | RFC | references/rfc-template.md |
| Development | System Doc | references/system-doc-template.md |
| Development | Standards Inventory | references/standards-inventory-template.md |
| Development | Architecture Overview | references/architecture-overview-template.md |
| Post-Dev | Changelog | references/changelog-template.md |
| Post-Dev | Troubleshooting | references/troubleshooting-template.md |
| Post-Dev | API Reference | references/api-reference-template.md |
| Post-Dev | Deployment Runbook | references/deployment-runbook-template.md |
| Post-Dev | Operational SOP | references/operational-sop-template.md |
| Post-Dev | Walkthrough | references/walkthrough-template.md |
| Post-Dev | Tutorial | references/tutorial-template.md |
| Cross-cutting | ADHD-Friendly Variant | references/adhd-friendly-template.md |
| Cross-cutting | Agent Prompt | references/agent-prompt-template.md |
| Cross-cutting | Action Tracker | references/action-tracker-template.md |
| Domain | Dataset Doc | references/dataset-doc-template.md |
| Domain | DMP | references/dmp-template.md |
| Domain | Measurement Spec | references/sensor-spec-template.md |
| Domain | Protocol Implementation | references/protocol-impl-template.md |
| Domain | Platform Design | references/platform-design-template.md |
| Domain | Grant / Proposal Section | references/grant-section-template.md |
| Publication | CITATION.cff | references/citation-cff-template.md |
| Publication | Croissant Data Card | references/croissant-data-card-template.md |
| Publication | HF Model Card | references/hf-model-card-template.md |
| Publication | README | references/readme-template.md |
| Operational | Meeting Notes | references/meeting-notes-template.md |
| Operational | Decision Log | references/decision-log-template.md |
| Operational | Quick Reference | references/quick-reference-template.md |
Commands¶
| Command | What It Does |
|---|---|
cyto doc adhdfy <path> |
Transform one document to ADHD-friendly format |
cyto doc validate --adhd <path> |
Validate an ADHD variant |
cyto doc identify <path> |
Auto-classify a document type |
cyto doc standardize <path> |
Standardize to matching template |
cyto doc adhdfy-repo <repo> |
Batch transform all docs in a repo |
cyto doc ingest <path> |
Register in knowledge graph |
cyto research market "<topic>" |
Market/feature landscape research |
cyto research tool "<category>" |
Tool/library evaluation |
cyto research model "<task>" |
ML model comparison |
cyto research arch "<decision>" |
Architecture research |
Options / Parameters¶
| Option | Type | Default | Description |
|---|---|---|---|
--dry-run |
bool |
false |
Preview what would be changed without writing files. |
--prompt-only |
bool |
false |
Return the transformation prompt without executing it. |
--adhd |
bool |
false |
Target ADHD variant for validate command. |
Common Patterns¶
# Transform a doc to ADHD-friendly variant (dry run first)
cyto doc adhdfy design/system_docs/SYSTEM-platform.md --dry-run
cyto doc adhdfy design/system_docs/SYSTEM-platform.md
# Classify an unknown document
cyto doc identify path/to/unknown-doc.md
# Standardize a doc to its template
cyto doc standardize path/to/existing-doc.md
# Register a new doc in the knowledge graph
cyto doc ingest docs/adrs/ADR-001-use-linkml-for-schemas.md
# Run technology evaluation research
cyto research tool "vector database"
Naming Conventions (Most Common)¶
| Type | Pattern | Example |
|---|---|---|
| ADR | ADR-NNN-kebab-title.md |
ADR-001-use-linkml.md |
| RFC | RFC-NNN-kebab-title.md |
RFC-001-identity-pipeline.md |
| Module Spec | MODULE-name.md |
MODULE-semantic-scholar.md |
| Evaluation | EVAL-topic.md |
EVAL-scholarly-access.md |
| Meeting Notes | MEETING-YYYY-MM-DD-topic.md |
MEETING-2026-06-14-review.md |
| Quick Reference | QUICKREF-topic.md |
QUICKREF-cyto-doc.md |
Error Quick-Fix¶
| Error / Symptom | Fix |
|---|---|
cyto doc adhdfy produces no output |
Check --dry-run flag was removed; verify path exists |
| Metadata header missing on validate | Add the required blockquote block (Status/Date/Author/Audience/Tags) |
| ADR edit rejected | Do not edit existing ADRs; create a new ADR that supersedes the old one and link it |
| Wrong template used | Run cyto doc identify <path> to auto-classify, then check the matrix for the correct template |
See Also¶
- Full documentation — comprehensive reference + explanation
doc-type-guide.md— detailed "when to create" for all 34 types (see cytoskills repo)command-reference.md— full command specs with all flags (see cytoskills repo)adhdfy-pipeline.md— 11-step transformation pipeline (see cytoskills repo)- cytognosis-dev — coding standards (not documentation)
- cytognosis-writer — grant narrative strategy