@pikaa-ai/pikaa 0.3.0 → 0.3.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1870) hide show
  1. package/dist/cli.js +1170 -602
  2. package/dist/index.js +525 -204
  3. package/package.json +5 -3
  4. package/skills/adaptyv/references/api-endpoints.md +0 -690
  5. package/skills/aeon/references/anomaly_detection.md +0 -154
  6. package/skills/aeon/references/classification.md +0 -144
  7. package/skills/aeon/references/clustering.md +0 -123
  8. package/skills/aeon/references/datasets_benchmarking.md +0 -392
  9. package/skills/aeon/references/distances.md +0 -256
  10. package/skills/aeon/references/forecasting.md +0 -109
  11. package/skills/aeon/references/networks.md +0 -289
  12. package/skills/aeon/references/regression.md +0 -118
  13. package/skills/aeon/references/segmentation.md +0 -163
  14. package/skills/aeon/references/similarity_search.md +0 -187
  15. package/skills/aeon/references/transformations.md +0 -246
  16. package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
  17. package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
  18. package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
  19. package/skills/analytical-method-validation/references/framework-selection.md +0 -87
  20. package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
  21. package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
  22. package/skills/analytical-method-validation/references/source-ledger.md +0 -125
  23. package/skills/analytical-method-validation/references/statistics.md +0 -209
  24. package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
  25. package/skills/analytical-method-validation/scripts/_common.py +0 -955
  26. package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
  27. package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
  28. package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
  29. package/skills/analytical-method-validation/scripts/check_response.py +0 -243
  30. package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
  31. package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
  32. package/skills/anndata/references/best_practices.md +0 -532
  33. package/skills/anndata/references/concatenation.md +0 -399
  34. package/skills/anndata/references/data_structure.md +0 -314
  35. package/skills/anndata/references/io_operations.md +0 -466
  36. package/skills/anndata/references/manipulation.md +0 -516
  37. package/skills/arbor/references/arbor-upstream.md +0 -91
  38. package/skills/arbor/references/executor-brief.md +0 -68
  39. package/skills/arbor/references/htr-methodology.md +0 -177
  40. package/skills/arbor/references/report-template.md +0 -39
  41. package/skills/arbor/scripts/tree.py +0 -564
  42. package/skills/arboreto/references/algorithms.md +0 -152
  43. package/skills/arboreto/references/basic_inference.md +0 -181
  44. package/skills/arboreto/references/distributed_computing.md +0 -242
  45. package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
  46. package/skills/astropy/references/coordinates.md +0 -280
  47. package/skills/astropy/references/cosmology.md +0 -309
  48. package/skills/astropy/references/fits.md +0 -398
  49. package/skills/astropy/references/tables.md +0 -495
  50. package/skills/astropy/references/time.md +0 -412
  51. package/skills/astropy/references/units.md +0 -178
  52. package/skills/astropy/references/wcs_and_other_modules.md +0 -377
  53. package/skills/autoskill/config.yaml +0 -53
  54. package/skills/autoskill/references/https-proxy.md +0 -62
  55. package/skills/autoskill/references/screenpipe-config.yaml +0 -61
  56. package/skills/autoskill/scripts/autoskill.py +0 -35
  57. package/skills/autoskill/scripts/backends.py +0 -116
  58. package/skills/autoskill/scripts/cluster.py +0 -54
  59. package/skills/autoskill/scripts/doctor.py +0 -108
  60. package/skills/autoskill/scripts/fetch_window.py +0 -33
  61. package/skills/autoskill/scripts/match_skills.py +0 -46
  62. package/skills/autoskill/scripts/promote.py +0 -58
  63. package/skills/autoskill/scripts/redact.py +0 -40
  64. package/skills/autoskill/scripts/run.py +0 -194
  65. package/skills/autoskill/scripts/synthesize.py +0 -72
  66. package/skills/benchling-integration/references/api_endpoints.md +0 -883
  67. package/skills/benchling-integration/references/authentication.md +0 -390
  68. package/skills/benchling-integration/references/core_capabilities.md +0 -355
  69. package/skills/benchling-integration/references/eventbridge.md +0 -255
  70. package/skills/benchling-integration/references/sdk_reference.md +0 -772
  71. package/skills/bids/references/beps.yml +0 -637
  72. package/skills/bids/references/bids_schema.json +0 -21015
  73. package/skills/bids/references/bids_specification.md +0 -165
  74. package/skills/bids/references/conversion_tools.md +0 -475
  75. package/skills/bids/references/core_workflows.md +0 -552
  76. package/skills/bids/references/metadata_fields.md +0 -365
  77. package/skills/bids/scripts/update_schema.py +0 -89
  78. package/skills/biopython/references/advanced.md +0 -580
  79. package/skills/biopython/references/alignment.md +0 -377
  80. package/skills/biopython/references/blast.md +0 -463
  81. package/skills/biopython/references/databases.md +0 -492
  82. package/skills/biopython/references/phylogenetics.md +0 -566
  83. package/skills/biopython/references/sequence_io.md +0 -289
  84. package/skills/biopython/references/structure.md +0 -564
  85. package/skills/bioservices/references/identifier_mapping.md +0 -685
  86. package/skills/bioservices/references/services_reference.md +0 -638
  87. package/skills/bioservices/references/workflow_patterns.md +0 -813
  88. package/skills/bioservices/scripts/batch_id_converter.py +0 -347
  89. package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
  90. package/skills/bioservices/scripts/pathway_analysis.py +0 -309
  91. package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
  92. package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
  93. package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
  94. package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
  95. package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
  96. package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
  97. package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
  98. package/skills/cellxgene-census/references/census_schema.md +0 -218
  99. package/skills/cellxgene-census/references/common_patterns.md +0 -368
  100. package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
  101. package/skills/cirq/references/building.md +0 -307
  102. package/skills/cirq/references/experiments.md +0 -572
  103. package/skills/cirq/references/hardware.md +0 -527
  104. package/skills/cirq/references/noise.md +0 -514
  105. package/skills/cirq/references/simulation.md +0 -353
  106. package/skills/cirq/references/transformation.md +0 -416
  107. package/skills/citation-management/assets/bibtex_template.bib +0 -264
  108. package/skills/citation-management/assets/citation_checklist.md +0 -386
  109. package/skills/citation-management/references/best_practices.md +0 -91
  110. package/skills/citation-management/references/bibtex_formatting.md +0 -908
  111. package/skills/citation-management/references/citation_validation.md +0 -835
  112. package/skills/citation-management/references/core_workflow.md +0 -569
  113. package/skills/citation-management/references/example_workflows.md +0 -126
  114. package/skills/citation-management/references/google_scholar_search.md +0 -732
  115. package/skills/citation-management/references/metadata_extraction.md +0 -870
  116. package/skills/citation-management/references/pubmed_search.md +0 -839
  117. package/skills/citation-management/references/script_reference.md +0 -250
  118. package/skills/citation-management/references/search_strategies.md +0 -110
  119. package/skills/citation-management/scripts/_common.py +0 -331
  120. package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  121. package/skills/citation-management/scripts/extract_metadata.py +0 -690
  122. package/skills/citation-management/scripts/format_bibtex.py +0 -356
  123. package/skills/citation-management/scripts/search_google_scholar.py +0 -268
  124. package/skills/citation-management/scripts/search_openalex.py +0 -297
  125. package/skills/citation-management/scripts/search_pubmed.py +0 -419
  126. package/skills/citation-management/scripts/validate_citations.py +0 -688
  127. package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
  128. package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
  129. package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
  130. package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
  131. package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
  132. package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
  133. package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
  134. package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
  135. package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
  136. package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
  137. package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
  138. package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
  139. package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
  140. package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
  141. package/skills/clinical-decision-support/references/security_validation.md +0 -60
  142. package/skills/clinical-decision-support/references/sources.md +0 -119
  143. package/skills/clinical-decision-support/references/study_reporting.md +0 -134
  144. package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
  145. package/skills/clinical-decision-support/scripts/_common.py +0 -223
  146. package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
  147. package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
  148. package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
  149. package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
  150. package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
  151. package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
  152. package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
  153. package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
  154. package/skills/clinical-reports/assets/case_report_template.json +0 -43
  155. package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
  156. package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
  157. package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
  158. package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
  159. package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
  160. package/skills/clinical-reports/assets/lab_report_template.json +0 -36
  161. package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
  162. package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
  163. package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
  164. package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
  165. package/skills/clinical-reports/assets/research_summary_template.json +0 -36
  166. package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
  167. package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
  168. package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
  169. package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
  170. package/skills/clinical-reports/references/data_presentation.md +0 -92
  171. package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
  172. package/skills/clinical-reports/references/medical_terminology.md +0 -84
  173. package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
  174. package/skills/clinical-reports/references/professional_review.md +0 -78
  175. package/skills/clinical-reports/references/report_type_routing.md +0 -57
  176. package/skills/clinical-reports/references/safety_reporting.md +0 -109
  177. package/skills/clinical-reports/references/sources.md +0 -75
  178. package/skills/clinical-reports/scripts/_common.py +0 -263
  179. package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
  180. package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
  181. package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
  182. package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
  183. package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
  184. package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
  185. package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
  186. package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
  187. package/skills/cobrapy/references/api_quick_reference.md +0 -665
  188. package/skills/cobrapy/references/workflows.md +0 -600
  189. package/skills/consciousness-council/references/advanced-configurations.md +0 -96
  190. package/skills/dask/references/arrays.md +0 -495
  191. package/skills/dask/references/bags.md +0 -468
  192. package/skills/dask/references/best-practices.md +0 -277
  193. package/skills/dask/references/dataframes.md +0 -370
  194. package/skills/dask/references/futures.md +0 -541
  195. package/skills/dask/references/schedulers.md +0 -517
  196. package/skills/database-lookup/references/addgene.md +0 -38
  197. package/skills/database-lookup/references/alphafold.md +0 -52
  198. package/skills/database-lookup/references/alphavantage.md +0 -261
  199. package/skills/database-lookup/references/bea.md +0 -409
  200. package/skills/database-lookup/references/bindingdb.md +0 -85
  201. package/skills/database-lookup/references/biogrid.md +0 -110
  202. package/skills/database-lookup/references/bls.md +0 -235
  203. package/skills/database-lookup/references/brenda.md +0 -71
  204. package/skills/database-lookup/references/cbioportal.md +0 -206
  205. package/skills/database-lookup/references/census.md +0 -251
  206. package/skills/database-lookup/references/chebi.md +0 -103
  207. package/skills/database-lookup/references/chembl.md +0 -80
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  210. package/skills/database-lookup/references/clinvar.md +0 -91
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  212. package/skills/database-lookup/references/cosmic.md +0 -59
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  218. package/skills/database-lookup/references/drugbank.md +0 -54
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  229. package/skills/database-lookup/references/gene-ontology.md +0 -147
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  236. package/skills/database-lookup/references/human-protein-atlas.md +0 -57
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- <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
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-
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- # Markdown Style Guide
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-
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- > **For AI agents:** Read this file for all core formatting rules. When creating any markdown document, follow these conventions for consistent, professional output. When a template exists for your document type, start from it — see [Templates](#templates).
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- >
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- > **For humans:** This guide ensures every markdown document in your project is clean, scannable, well-cited, and renders beautifully on GitHub. Reference it from your `AGENTS.md` or contributing guide.
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-
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- **Target platform:** GitHub Markdown (Issues, PRs, Discussions, Wikis, `.md` files)
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- **Design goal:** Clear, professional documents that communicate effectively through consistent structure, meaningful formatting, proper citations, and strategic use of diagrams.
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-
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- ---
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-
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- ## Quick Start for Agents
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- 1. **Identify the document type** → Check if a [template](#templates) exists
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- 2. **Structure first** → Heading hierarchy, then content
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- 3. **Apply formatting from this guide** → Headings, text, lists, tables, images, links
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- 4. **Add citations** → Footnote references for all claims and sources
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- 5. **Consider diagrams** → Would a [Mermaid diagram](mermaid_style_guide.md) communicate this better than text?
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- 6. **Add collapsible sections** → For supplementary detail, speaker notes, or lengthy context
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- 7. **Verify** → Run through the [quality checklist](#quality-checklist)
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- ---
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-
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- ## Core Principles
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-
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- | # | Principle | Rule |
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- | --- | --------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
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- | 1 | **Answer before they ask** | Anticipate reader questions and address them inline. A great document resolves doubts as they form — the reader finishes with no lingering "but what about...?" |
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- | 2 | **Scannable first** | Readers skim before they read. Use headings, bold, and lists to make the structure visible at a glance. |
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- | 3 | **Cite everything** | Every claim, statistic, or external reference gets a footnote citation with a full URL. No orphan claims. |
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- | 4 | **Diagrams over walls of text** | If a concept involves flow, relationships, or structure, use a [Mermaid diagram](mermaid_style_guide.md) alongside the text. |
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- | 5 | **Generous with information** | Don't hide the details — surface them. Use collapsible sections for depth without clutter, but never omit information because "they probably don't need it." If it's relevant, include it. |
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- | 6 | **Consistent structure** | Same heading hierarchy, same formatting patterns, same emoji placement across every document. |
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- | 7 | **One idea per section** | Each heading should cover one topic. If you're covering two ideas, split into two headings. |
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- | 8 | **Professional but approachable** | Clean formatting, no clutter, no decorative noise — but not stiff or academic. Write like a senior engineer explains to a colleague. |
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- ---
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-
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- ## 🗂️ Everything is Code
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- Everything is code. PRs, issues, kanban boards — they're all markdown files in your repo, not data trapped in a platform's database.
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- ### Why this matters
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-
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- - **Portable** — GitHub → GitLab → Gitea → anywhere. Your project management data isn't locked into any vendor. Switch platforms and your issues, PR records, and boards come with you — they're just files.
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- - **AI-native** — Agents can read every issue, PR record, and kanban board with local file access. No API tokens, no rate limits, no platform-specific queries. `grep` beats `gh api` every time.
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- - **Auditable** — Project management changes go through the same PR review process as code changes. Every board update, every issue status change — it's all in git history with attribution and timestamps.
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- ### How it works
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-
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- | What | Where it lives | What GitHub does |
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- | -------------------- | --------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
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- | **Pull requests** | `docs/project/pr/pr-NNNNNNNN-short-description.md` | GitHub PR is a thin pointer — humans go there to comment on diffs, approve, and watch CI. The record of what changed, why, and what was learned lives in the file. |
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- | **Issues** | `docs/project/issues/issue-NNNNNNNN-short-description.md` | GitHub Issues is a notification and comment layer. Bug reports, feature requests, investigation logs, and resolutions live in the file. |
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- | **Kanban boards** | `docs/project/kanban/{scope}-{id}-short-description.md` | No external board tool needed. Modify the board in your branch, merge it with your PR. The board evolves with the codebase. |
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- | **Decision records** | `docs/decisions/NNN-{slug}.md` | Not tracked in GitHub at all — purely repo-native. |
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-
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- ### The rule
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-
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- > 📌 **Don't capture information in GitHub's UI that should be captured in a file.** Approve PRs in GitHub. Watch CI in GitHub. Comment in GitHub. But the actual content — the description, the investigation, the decision — lives in a committed file. If it's worth writing down, it's worth committing.
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-
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- ### Templates for tracked documents
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-
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- - [Pull request record](../templates/pull_request.md) — the PR description IS this file
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- - [Issue record](../templates/issue.md) — bug reports and feature requests as repo files
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- - [Kanban board](../templates/kanban.md) — sprint/project boards that merge with your code
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- See [File conventions](#file-conventions-for-tracked-documents) for directory structure and naming.
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-
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- ---
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-
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- ## Document Structure
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-
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- ### Title and metadata
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- # Document Title Here
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- _Brief context — project name, date, or purpose in one line_
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- ```
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- - **One H1 per document** — never more
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- - Context line in italics — what this document is, when, and for whom
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- ### Heading hierarchy
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- | Level | Syntax | Use | Max per document |
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- | ----- | --------------- | ----------------------- | ------------------- |
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- | H1 | `# Title` | Document title | **1** (exactly one) |
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- | H2 | `## Section` | Major sections | 4–10 |
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- | H3 | `### Topic` | Topics within a section | 2–5 per H2 |
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- | H4 | `#### Subtopic` | Subtopics when needed | 2–4 per H3 |
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- | H5+ | Never use | — | 0 |
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- - **Never skip levels** — don't jump from H2 to H4
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- - **Emoji in H2 headings** — one emoji per H2, at the start: `## 📋 Project Overview`
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- - **No emoji in H3/H4** — keep sub-headings clean
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- - **Sentence case** — `## 📋 Project overview` not `## 📋 Project Overview` (exception: proper nouns)
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- - **Descriptive headings** — `### Authentication flow` not `### Details`
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- ---
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- ## Text Formatting
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- ### Bold, italic, code
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- | Format | Syntax | When to use | Example |
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- | **Bold** | `**text**` | Key terms, important concepts, emphasis | **Primary database** handles writes |
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- | _Italic_ | `*text*` | Definitions, titles, subtle emphasis | The process is called _sharding_ |
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- | `Code` | `` `text` `` | Technical terms, commands, file names, values | Run `npm install` to install |
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- | ~~Strike~~ | `~~text~~` | Deprecated content, corrections | ~~Old approach~~ replaced by v2 |
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- **Rules:**
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- - **Bold sparingly** — if everything is bold, nothing is. Max 2–3 bold terms per paragraph.
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- - **Don't combine** bold and italic (`***text***`) — pick one
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- - **Code for anything technical** — file names (`README.md`), commands (`git push`), config values (`true`), environment variables (`NODE_ENV`)
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- - **Never bold entire sentences** — bold the key word(s) within the sentence
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- ### Blockquotes
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- > **Definition:** A _load balancer_ distributes incoming network traffic
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- ```
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- ```markdown
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- > ⚠️ **Warning:** This operation is destructive and cannot be undone.
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- > 💡 **Tip:** Use `--dry-run` to preview changes before applying.
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- > 📌 **Note:** This requires admin permissions on the repository.
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- ```
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-
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- - Prefix with emoji + bold label for typed callouts
150
- - Keep blockquotes to 1–3 lines
151
- - Don't nest blockquotes (`>>`)
152
-
153
- ---
154
-
155
- ## Lists
156
-
157
- ### When to use each type
158
-
159
- | List type | Syntax | Use when |
160
- | --------- | ------------ | ----------------------------------------- |
161
- | Bullet | `- item` | Items have no inherent order |
162
- | Numbered | `1. step` | Steps must happen in sequence |
163
- | Checkbox | `- [ ] item` | Tracking completion (agendas, checklists) |
164
-
165
- ### Formatting rules
166
-
167
- - **Consistent indentation** — 2 spaces for sub-items (some renderers use 4; pick one, stick with it)
168
- - **Parallel structure** — every item in a list should have the same grammatical form
169
- - **No period at end** unless items are full sentences
170
- - **Keep items concise** — if a bullet needs a paragraph, it should be a sub-section instead
171
- - **Max nesting depth: 2 levels** — if you need a third level, restructure
172
-
173
- ```markdown
174
- ✅ Good — parallel structure, concise:
175
-
176
- - Configure the database connection
177
- - Run the migration scripts
178
- - Verify the schema changes
179
-
180
- ❌ Bad — mixed structure, verbose:
181
-
182
- - You need to configure the database
183
- - Migration scripts
184
- - After that, you should verify that the schema looks correct
185
- ```
186
-
187
- ---
188
-
189
- ## Links and Citations
190
-
191
- ### Inline links
192
-
193
- ```markdown
194
- See the [Mermaid Style Guide](mermaid_style_guide.md) for diagram conventions.
195
- ```
196
-
197
- - **Meaningful link text** — `[Mermaid Style Guide]` not `[click here]` or `[link]`
198
- - **Relative paths** for internal links — `[Guide](./README.md)` not absolute URLs
199
- - **Full URLs** for external links — always `https://`
200
-
201
- ### Footnote citations
202
-
203
- **Every claim, statistic, or reference to external work MUST have a footnote citation.** This is non-negotiable for credibility.
204
-
205
- ```markdown
206
- Markdown was created by John Gruber in 2004 as a lightweight
207
- markup language designed for readability[^1]. GitHub adopted
208
- Mermaid diagram support in February 2022[^2].
209
-
210
- [^1]: Gruber, J. (2004). "Markdown." _Daring Fireball_. https://daringfireball.net/projects/markdown/
211
-
212
- [^2]: GitHub Blog. (2022). "Include diagrams in your Markdown files with Mermaid." https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/
213
- ```
214
-
215
- **Citation format:**
216
-
217
- ```
218
- [^N]: Author/Org. (Year). "Title." *Publication*. https://full-url
219
- ```
220
-
221
- **Rules:**
222
-
223
- - **Number sequentially** — `[^1]`, `[^2]`, `[^3]` in order of appearance
224
- - **Full URL always included** — the reader must be able to reach the source
225
- - **Group all footnotes at the document bottom** — under a `## References` section or at the very end
226
- - **Every external claim needs one** — statistics, quotes, methodologies, tools mentioned
227
- - **Internal project links don't need footnotes** — use inline links instead
228
-
229
- ### Reference-style links (for repeated URLs)
230
-
231
- When the same URL appears multiple times, use reference-style links to keep the text clean:
232
-
233
- ```markdown
234
- The [official docs][mermaid-docs] cover all diagram types.
235
- See [Mermaid documentation][mermaid-docs] for the full syntax.
236
-
237
- [mermaid-docs]: https://mermaid.js.org/ 'Mermaid Documentation'
238
- ```
239
-
240
- ---
241
-
242
- ## Images and Figures
243
-
244
- ### Placement and syntax
245
-
246
- ```markdown
247
- ![Descriptive alt text for screen readers](images/architecture_overview.png)
248
- _Figure 1: System architecture showing the three-tier deployment model_
249
- ```
250
-
251
- **Rules:**
252
-
253
- - **Inline with content** — place images where they're relevant, not in a separate "Images" section
254
- - **Descriptive alt text** — `![Three-tier architecture diagram]` not `![image]` or `![screenshot]`
255
- - **Italic caption below** — `*Figure N: What this image shows*`
256
- - **Number figures sequentially** — Figure 1, Figure 2, etc. if multiple images
257
- - **Relative paths** — `images/file.png` not absolute paths
258
- - **Reasonable file sizes** — compress PNGs, use SVG where possible
259
-
260
- ### Image naming convention
261
-
262
- ```
263
- {document-slug}_{description}.{ext}
264
-
265
- Examples:
266
- auth_flow_overview.png
267
- deployment_architecture.svg
268
- api_response_example.png
269
- ```
270
-
271
- ### When NOT to use an image
272
-
273
- If the content could be expressed as a **Mermaid diagram**, prefer that over a static image:
274
-
275
- | Scenario | Use |
276
- | -------------------------- | ------------------------------------------ |
277
- | Architecture diagram | Mermaid `flowchart` or `architecture-beta` |
278
- | Sequence/interaction | Mermaid `sequenceDiagram` |
279
- | Data model | Mermaid `erDiagram` |
280
- | Timeline | Mermaid `timeline` or `gantt` |
281
- | Screenshot of UI | Image (Mermaid can't do this) |
282
- | Photo / real-world image | Image |
283
- | Complex data visualization | Image or Mermaid `xychart-beta` |
284
-
285
- See the [Mermaid Style Guide](mermaid_style_guide.md) for diagram type selection and styling.
286
-
287
- ---
288
-
289
- ## Tables
290
-
291
- ### When to use tables
292
-
293
- - **Structured comparisons** — features, options, tradeoffs
294
- - **Reference data** — configuration values, API parameters, status codes
295
- - **Schedules and matrices** — timelines, responsibility assignments
296
-
297
- ### When NOT to use tables
298
-
299
- - **Narrative content** — use paragraphs instead
300
- - **Simple lists** — use bullet points
301
- - **More than 5 columns** — becomes unreadable on mobile; restructure
302
-
303
- ### Formatting
304
-
305
- ```markdown
306
- | Feature | Free Tier | Pro Tier | Enterprise |
307
- | ------- | --------- | -------- | ---------- |
308
- | Users | 5 | 50 | Unlimited |
309
- | Storage | 1 GB | 100 GB | Custom |
310
- | Support | Community | Email | Dedicated |
311
- ```
312
-
313
- **Rules:**
314
-
315
- - **Header row always** — no headerless tables
316
- - **Left-align text columns** — `|---|` (default)
317
- - **Right-align number columns** — `|---:|` when appropriate
318
- - **Concise cell content** — 1–5 words per cell. If you need more, it's not a table problem
319
- - **Bold key column** — the first column or the column the reader scans first
320
- - **Consistent formatting within columns** — don't mix sentences and fragments
321
-
322
- ---
323
-
324
- ## Code Blocks
325
-
326
- ### Inline code
327
-
328
- Use backticks for technical terms within prose:
329
-
330
- ```markdown
331
- Run `git status` to check for uncommitted changes.
332
- The `NODE_ENV` variable controls the runtime environment.
333
- ```
334
-
335
- ### Fenced code blocks
336
-
337
- Always specify the language for syntax highlighting:
338
-
339
- ````markdown
340
- ```python
341
- def calculate_average(values: list[float]) -> float:
342
- """Return the arithmetic mean of a list of values."""
343
- return sum(values) / len(values)
344
- ```
345
- ````
346
-
347
- **Rules:**
348
-
349
- - **Always include language identifier** — ` ```python `, ` ```bash `, ` ```json `, etc.
350
- - **Use ` ```text ` for plain output** — not ` ``` ` with no language
351
- - **Keep blocks focused** — show the relevant snippet, not the entire file
352
- - **Add a comment if context needed** — `# Configure the database connection` at the top of the block
353
-
354
- ---
355
-
356
- ## Collapsible Sections
357
-
358
- Use HTML `<details>` for supplementary content that shouldn't clutter the main flow — speaker notes, implementation details, verbose logs, or optional deep-dives.
359
-
360
- ```markdown
361
- <details>
362
- <summary><strong>💬 Speaker Notes</strong></summary>
363
-
364
- - Key talking point one
365
- - Transition to next topic
366
- - **Bold** emphasis works inside details
367
- - [Links](https://example.com) work too
368
-
369
- </details>
370
-
371
- ---
372
- ```
373
-
374
- **Rules:**
375
-
376
- - **Collapsed by default** — the `<details>` tag collapses automatically
377
- - **Descriptive summary** — `<strong>💬 Speaker Notes</strong>` or `<strong>📋 Implementation Details</strong>`
378
- - **Blank line after `<summary>` tag** — required for markdown to render inside the block
379
- - **ALWAYS follow with `---`** — horizontal rule after every `</details>` for visual separation
380
- - **Any markdown works inside** — bullets, bold, links, code blocks, tables
381
-
382
- ### Common collapsible patterns
383
-
384
- | Summary label | Use for |
385
- | --------------------- | ------------------------------------------------ |
386
- | 💬 **Speaker Notes** | Presentation talking points, timing, transitions |
387
- | 📋 **Details** | Extended explanation, verbose context |
388
- | 🔧 **Implementation** | Technical details, code samples, config |
389
- | 📊 **Raw Data** | Full output, logs, data tables |
390
- | 💡 **Background** | Context that helps but isn't essential |
391
-
392
- ---
393
-
394
- ## Horizontal Rules
395
-
396
- Use `---` (three hyphens) for visual separation:
397
-
398
- ```markdown
399
- ---
400
- ```
401
-
402
- **When to use:**
403
-
404
- - **After every `</details>` block** — mandatory, creates clear separation
405
- - **After title/metadata** — separates document header from content
406
- - **Between major sections** — when an H2 heading alone doesn't create enough visual break
407
- - **Before footnotes/references** — separates content from citation list
408
-
409
- **When NOT to use:**
410
-
411
- - Between every paragraph (too busy)
412
- - Between H3 sub-sections within the same H2 (use whitespace instead)
413
-
414
- ---
415
-
416
- ## Approved Emoji Set
417
-
418
- One emoji per H2 heading, at the start. Use sparingly in body text for callouts and emphasis only.
419
-
420
- ### Section headings
421
-
422
- | Emoji | Use for |
423
- | ----- | -------------------------------------- |
424
- | 📋 | Overview, summary, agenda, checklist |
425
- | 🎯 | Goals, objectives, outcomes, targets |
426
- | 📚 | Content, documentation, main body |
427
- | 🔗 | Resources, references, links |
428
- | 📍 | Agenda, navigation, current position |
429
- | 🏠 | Housekeeping, logistics, announcements |
430
- | ✍️ | Tasks, assignments, action items |
431
-
432
- ### Status and outcomes
433
-
434
- | Emoji | Meaning |
435
- | ----- | ------------------------------------ |
436
- | ✅ | Success, complete, correct, approved |
437
- | ❌ | Failure, incorrect, avoid, rejected |
438
- | ⚠️ | Warning, caution, important notice |
439
- | 💡 | Tip, insight, idea, best practice |
440
- | 📌 | Important, key point, remember |
441
- | 🚫 | Prohibited, do not, blocked |
442
-
443
- ### Technical and process
444
-
445
- | Emoji | Meaning |
446
- | ----- | --------------------------------- |
447
- | ⚙️ | Configuration, settings, process |
448
- | 🔧 | Tools, utilities, setup |
449
- | 🔍 | Analysis, investigation, review |
450
- | 📊 | Data, metrics, analytics |
451
- | 📈 | Growth, trends, improvement |
452
- | 🔄 | Cycle, refresh, iteration |
453
- | ⚡ | Performance, speed, quick action |
454
- | 🔐 | Security, authentication, privacy |
455
- | 🌐 | Web, API, network, global |
456
- | 💾 | Storage, database, persistence |
457
- | 📦 | Package, artifact, deployment |
458
-
459
- ### People and collaboration
460
-
461
- | Emoji | Meaning |
462
- | ----- | ----------------------------------- |
463
- | 👤 | User, person, individual |
464
- | 👥 | Team, group, collaboration |
465
- | 💬 | Discussion, comments, speaker notes |
466
- | 🎓 | Learning, education, knowledge |
467
- | 🤔 | Question, consideration, reflection |
468
-
469
- ### Emoji rules
470
-
471
- 1. **One per H2 heading** at the start — `## 📋 Overview`
472
- 2. **None in H3/H4** — keep sub-headings clean
473
- 3. **Sparingly in body text** — for callouts (`> ⚠️ **Warning:**`) and key markers only
474
- 4. **Never in**: titles (H1), code blocks, link text, table data cells
475
- 5. **No decorative emoji** — 🎉 💯 🔥 🎊 💥 ✨ add noise, not meaning
476
- 6. **Consistency** — same emoji = same meaning across all documents in the project
477
-
478
- ---
479
-
480
- ## Mermaid Diagram Integration
481
-
482
- **Whenever content describes flow, structure, relationships, or processes, consider whether a Mermaid diagram would communicate it better than prose alone.** Diagrams and text together are more effective than either alone.
483
-
484
- ### When to add a diagram
485
-
486
- **Any time your text describes flow, structure, relationships, timing, or comparisons, there's a Mermaid diagram that communicates it better.** Scan the table below to identify the right type, then follow this workflow:
487
-
488
- 1. **Read the [Mermaid Style Guide](mermaid_style_guide.md) first** — emoji, color palette, accessibility, complexity management
489
- 2. **Then open the specific type file** — exemplar, tips, template, complex example
490
-
491
- | Your content describes... | Add a... | Type file |
492
- | ---------------------------------------------------- | ------------------------ | --------------------------------------------------- |
493
- | Steps in a process, workflow, decision logic | **Flowchart** | [flowchart.md](diagrams/flowchart.md) |
494
- | Who talks to whom and when (API calls, messages) | **Sequence diagram** | [sequence.md](diagrams/sequence.md) |
495
- | Class hierarchy, type relationships, interfaces | **Class diagram** | [class.md](diagrams/class.md) |
496
- | Status transitions, entity lifecycle, state machine | **State diagram** | [state.md](diagrams/state.md) |
497
- | Database schema, data model, entity relationships | **ER diagram** | [er.md](diagrams/er.md) |
498
- | Project timeline, roadmap, task dependencies | **Gantt chart** | [gantt.md](diagrams/gantt.md) |
499
- | Parts of a whole, proportions, distribution | **Pie chart** | [pie.md](diagrams/pie.md) |
500
- | Git branching strategy, merge/release flow | **Git Graph** | [git_graph.md](diagrams/git_graph.md) |
501
- | Concept hierarchy, brainstorm, topic map | **Mindmap** | [mindmap.md](diagrams/mindmap.md) |
502
- | Chronological events, milestones, history | **Timeline** | [timeline.md](diagrams/timeline.md) |
503
- | User experience, satisfaction scores, journey | **User Journey** | [user_journey.md](diagrams/user_journey.md) |
504
- | Two-axis comparison, prioritization matrix | **Quadrant chart** | [quadrant.md](diagrams/quadrant.md) |
505
- | Requirements traceability, compliance mapping | **Requirement diagram** | [requirement.md](diagrams/requirement.md) |
506
- | System architecture at varying zoom levels | **C4 diagram** | [c4.md](diagrams/c4.md) |
507
- | Flow magnitude, resource distribution, budgets | **Sankey diagram** | [sankey.md](diagrams/sankey.md) |
508
- | Numeric trends, bar charts, line charts | **XY Chart** | [xy_chart.md](diagrams/xy_chart.md) |
509
- | Component layout, spatial arrangement, layers | **Block diagram** | [block.md](diagrams/block.md) |
510
- | Work item tracking, status board, task columns | **Kanban board** | [kanban.md](diagrams/kanban.md) |
511
- | Binary protocol layout, data packet format | **Packet diagram** | [packet.md](diagrams/packet.md) |
512
- | Cloud infrastructure, service topology, networking | **Architecture diagram** | [architecture.md](diagrams/architecture.md) |
513
- | Multi-dimensional comparison, skills, radar analysis | **Radar chart** | [radar.md](diagrams/radar.md) |
514
- | Hierarchical proportions, budget breakdown | **Treemap** | [treemap.md](diagrams/treemap.md) |
515
-
516
- > 💡 **Pick the right type, not the easy type.** Don't default to flowcharts for everything — a timeline is better than a flowchart for chronological events, a sequence diagram is better for service interactions, an ER diagram is better for data models. Scan the table above and match your content to the most specific type. **If you catch yourself writing a paragraph that describes a visual concept, stop and diagram it.**
517
-
518
- ### How to integrate
519
-
520
- Place the diagram **inline with the related text**, not in a separate section:
521
-
522
- ````markdown
523
- ### Authentication Flow
524
-
525
- The login process validates credentials, checks MFA status,
526
- and issues session tokens. Failed attempts are logged for
527
- security monitoring.
528
-
529
- ‎```mermaid
530
- sequenceDiagram
531
- accTitle: Login Authentication Flow
532
- accDescr: User login sequence through API and auth service
533
-
534
- participant U as 👤 User
535
- participant A as 🌐 API
536
- participant S as 🔐 Auth Service
537
-
538
- U->>A: POST /login
539
- A->>S: Validate credentials
540
- S-->>A: ✅ Token issued
541
- A-->>U: 200 OK + session
542
-
543
- ‎```
544
-
545
- The token expires after 24 hours. See [Authentication flow](#authentication-flow)
546
- for refresh token details.
547
- ````
548
-
549
- **Always follow the [Mermaid Style Guide](mermaid_style_guide.md)** for diagram styling — emoji, color classes, accessibility (`accTitle`/`accDescr`), and type-specific conventions.
550
-
551
- ---
552
-
553
- ## Whitespace and Spacing
554
-
555
- - **Blank line between paragraphs** — always
556
- - **Blank line before and after headings** — always
557
- - **Blank line before and after code blocks** — always
558
- - **Blank line before and after blockquotes** — always
559
- - **No blank line between list items** — keep lists tight
560
- - **No trailing whitespace** — clean line endings
561
- - **One blank line at end of file** — standard convention
562
- - **No more than one consecutive blank line** — two blank lines = too much space
563
-
564
- ---
565
-
566
- ## Quality Checklist
567
-
568
- ### Structure
569
-
570
- - [ ] Exactly one H1 title
571
- - [ ] Heading hierarchy is correct (H1 → H2 → H3 → H4, no skips)
572
- - [ ] Each H2 has exactly one emoji at the start
573
- - [ ] H3 and H4 have no emoji
574
- - [ ] Horizontal rules after title metadata and after every `</details>` block
575
-
576
- ### Content
577
-
578
- - [ ] Every external claim has a footnote citation
579
- - [ ] All footnotes have full URLs
580
- - [ ] All links tested and working
581
- - [ ] Meaningful link text (no "click here")
582
- - [ ] Bold used for key terms, not entire sentences
583
- - [ ] Code formatting for all technical terms
584
-
585
- ### Visual elements
586
-
587
- - [ ] Images have descriptive alt text
588
- - [ ] Images have italic figure captions
589
- - [ ] Images placed inline with related content (not in separate section)
590
- - [ ] Tables have header rows and consistent formatting
591
- - [ ] Mermaid diagrams considered where applicable (with `accTitle`/`accDescr`)
592
-
593
- ### Collapsible sections
594
-
595
- - [ ] `<details>` blocks have descriptive `<summary>` labels
596
- - [ ] Blank line after `<summary>` tag (for markdown rendering)
597
- - [ ] Horizontal rule `---` after every `</details>` block
598
- - [ ] Content inside collapses renders correctly
599
-
600
- ### Polish
601
-
602
- - [ ] No spelling or grammar errors
603
- - [ ] Consistent whitespace (no trailing spaces, no double blanks)
604
- - [ ] Parallel grammatical structure in lists
605
- - [ ] Renders correctly in GitHub light and dark mode
606
-
607
- ---
608
-
609
- ## Templates
610
-
611
- Templates provide pre-built structures for common document types. Copy the template, fill in your content, and follow this style guide for formatting. Every template enforces the principles above — citations, diagrams, collapsible depth, and self-answering structure.
612
-
613
- | Document type | Template | Best for |
614
- | ------------------------------- | ----------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- |
615
- | Presentation / briefing | [presentation.md](../templates/presentation.md) | Slide-deck-style documents with speaker notes, structured sections, and visual flow |
616
- | Research paper / analysis | [research_paper.md](../templates/research_paper.md) | Data-driven analysis, literature reviews, methodology + findings with heavy citations |
617
- | Project documentation | [project_documentation.md](../templates/project_documentation.md) | Software/product docs — architecture, getting started, API reference, contribution guide |
618
- | Decision record (ADR/RFC) | [decision_record.md](../templates/decision_record.md) | Recording why a decision was made — context, options evaluated, outcome, consequences |
619
- | How-to / tutorial guide | [how_to_guide.md](../templates/how_to_guide.md) | Step-by-step instructions with prerequisites, verification steps, and troubleshooting |
620
- | Status report / executive brief | [status_report.md](../templates/status_report.md) | Progress updates, risk summaries, decisions needed — for leadership and stakeholders |
621
- | Pull request record | [pull_request.md](../templates/pull_request.md) | PR documentation with change inventory, testing evidence, rollback plan, and review notes |
622
- | Issue record | [issue.md](../templates/issue.md) | Bug reports (reproduction steps, root cause) and feature requests (acceptance criteria, user stories) |
623
- | Kanban board | [kanban.md](../templates/kanban.md) | Sprint/release/project work tracking with visual board, WIP limits, metrics, and blocked items |
624
-
625
- ### File conventions for tracked documents
626
-
627
- Some templates produce documents that accumulate over time. Use these directory conventions:
628
-
629
- | Document type | Directory | Naming pattern | Example |
630
- | ---------------- | ---------------------- | ------------------------------------------- | ----------------------------------------------------------------------- |
631
- | Pull requests | `docs/project/pr/` | `pr-NNNNNNNN-short-description.md` | `docs/project/pr/pr-00000123-fix-auth-timeout.md` |
632
- | Issues | `docs/project/issues/` | `issue-NNNNNNNN-short-description.md` | `docs/project/issues/issue-00000456-add-export-filter.md` |
633
- | Kanban boards | `docs/project/kanban/` | `{scope}-{identifier}-short-description.md` | `docs/project/kanban/sprint-2026-w07-agentic-template-modernization.md` |
634
- | Decision records | `docs/decisions/` | `NNN-{slug}.md` | `docs/decisions/001-use-postgresql.md` |
635
- | Status reports | `docs/status/` | `status-{date}.md` | `docs/status/status-2026-02-14.md` |
636
-
637
- ### Choosing a template
638
-
639
- - **Presenting to people?** → Presentation
640
- - **Publishing analysis or research?** → Research paper
641
- - **Documenting a codebase or product?** → Project documentation
642
- - **Recording why you chose X over Y?** → Decision record
643
- - **Teaching someone how to do something?** → How-to guide
644
- - **Updating leadership on progress?** → Status report
645
- - **Documenting a PR for posterity?** → Pull request record
646
- - **Tracking a bug or requesting a feature?** → Issue record
647
- - **Managing work items for a sprint or project?** → Kanban board
648
- - **None of these fit?** → Start from this style guide's rules directly — no template required
649
-
650
- ---
651
-
652
- ## Common Mistakes
653
-
654
- ### ❌ Multiple emoji per heading
655
-
656
- ```markdown
657
- ## 📚📊📈 Content Topics ← Too many
658
- ```
659
-
660
- ✅ Fix: One emoji per H2
661
-
662
- ```markdown
663
- ## 📚 Content topics
664
- ```
665
-
666
- ### ❌ Missing citations
667
-
668
- ```markdown
669
- Studies show 73% of developers prefer Markdown. ← Where's the source?
670
- ```
671
-
672
- ✅ Fix: Add footnote
673
-
674
- ```markdown
675
- Studies show 73% of developers prefer Markdown[^1].
676
-
677
- [^1]: Stack Overflow. (2024). "Developer Survey Results." https://survey.stackoverflow.co/2024
678
- ```
679
-
680
- ### ❌ Wall of text without structure
681
-
682
- ```markdown
683
- The system handles authentication by first checking the JWT token
684
- validity, then verifying the user exists in the database, then
685
- checking their permissions against the requested resource...
686
- ```
687
-
688
- ✅ Fix: Use a list, heading, or diagram
689
-
690
- ```markdown
691
- ### Authentication flow
692
-
693
- 1. Validate JWT token signature and expiration
694
- 2. Verify user exists in the database
695
- 3. Check user permissions against the requested resource
696
- ```
697
-
698
- ### ❌ Images in a separate section
699
-
700
- ```markdown
701
- ## Content
702
-
703
- [paragraphs of text]
704
-
705
- ## Screenshots
706
-
707
- [all images grouped here] ← Disconnected from context
708
- ```
709
-
710
- ✅ Fix: Place images inline where relevant
711
-
712
- ### ❌ No horizontal rule after collapsible sections
713
-
714
- ```markdown
715
- </details>
716
- ### Next Topic ← Runs together visually
717
- ```
718
-
719
- ✅ Fix: Always add `---` after `</details>`
720
-
721
- ```markdown
722
- </details>
723
-
724
- ---
725
-
726
- ### Next topic ← Clear separation
727
- ```
728
-
729
- ---
730
-
731
- ## Resources
732
-
733
- - [GitHub Flavored Markdown Spec](https://github.github.com/gfm/) · [Mermaid Style Guide](mermaid_style_guide.md) · [GitHub Basic Formatting](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax)