@saibolla/ada 0.1.2
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.
- package/.ada/SYSTEM.md +81 -0
- package/.ada/agents/researcher.md +69 -0
- package/.ada/agents/reviewer.md +92 -0
- package/.ada/agents/verifier.md +45 -0
- package/.ada/agents/writer.md +54 -0
- package/.ada/settings.json +32 -0
- package/.ada/themes/ada.json +85 -0
- package/.env.example +31 -0
- package/AGENTS.md +79 -0
- package/LICENSE +191 -0
- package/README.md +188 -0
- package/bin/ada.js +26 -0
- package/dist/bootstrap/sync.js +143 -0
- package/dist/cli.js +404 -0
- package/dist/config/paths.js +32 -0
- package/dist/index.js +10 -0
- package/dist/model/catalog.js +255 -0
- package/dist/model/commands.js +180 -0
- package/dist/pi/launch.js +33 -0
- package/dist/pi/package-presets.js +55 -0
- package/dist/pi/runtime.js +81 -0
- package/dist/pi/settings.js +108 -0
- package/dist/pi/web-access.js +74 -0
- package/dist/search/commands.js +12 -0
- package/dist/setup/doctor.js +126 -0
- package/dist/setup/preview.js +117 -0
- package/dist/setup/prompts.js +34 -0
- package/dist/setup/setup.js +98 -0
- package/dist/setup/update.js +133 -0
- package/dist/system/executables.js +38 -0
- package/dist/system/node-version.js +31 -0
- package/dist/system/open-url.js +35 -0
- package/dist/system/promise-polyfill.js +12 -0
- package/dist/ui/terminal.js +64 -0
- package/dist/web/launch.js +48 -0
- package/dist/web-search.js +1 -0
- package/extensions/docparser/constants.ts +62 -0
- package/extensions/docparser/deps.ts +584 -0
- package/extensions/docparser/doctor.ts +353 -0
- package/extensions/docparser/index.ts +9 -0
- package/extensions/docparser/input.ts +230 -0
- package/extensions/docparser/request.ts +67 -0
- package/extensions/docparser/schema.ts +82 -0
- package/extensions/docparser/tool.ts +305 -0
- package/extensions/docparser/types.ts +99 -0
- package/extensions/research-tools/alpha.ts +107 -0
- package/extensions/research-tools/header.ts +284 -0
- package/extensions/research-tools/help.ts +93 -0
- package/extensions/research-tools/project-scaffold.ts +64 -0
- package/extensions/research-tools/project.ts +123 -0
- package/extensions/research-tools/shared.ts +16 -0
- package/extensions/research-tools.ts +42 -0
- package/logo.d.mts +3 -0
- package/logo.mjs +14 -0
- package/metadata/commands.d.mts +46 -0
- package/metadata/commands.mjs +133 -0
- package/package.json +80 -0
- package/prompts/audit.md +17 -0
- package/prompts/autoresearch.md +66 -0
- package/prompts/compare.md +18 -0
- package/prompts/deepresearch.md +189 -0
- package/prompts/draft.md +19 -0
- package/prompts/jobs.md +16 -0
- package/prompts/litreview.md +18 -0
- package/prompts/log.md +14 -0
- package/prompts/replicate.md +24 -0
- package/prompts/review.md +18 -0
- package/prompts/watch.md +16 -0
- package/scripts/build-native-bundle.mjs +349 -0
- package/scripts/check-node-version.mjs +35 -0
- package/scripts/patch-embedded-pi.mjs +588 -0
- package/scripts/prepare-runtime-workspace.mjs +162 -0
- package/scripts/prune-runtime-deps.mjs +131 -0
- package/scripts/release.sh +152 -0
- package/skills/adaptyv/SKILL.md +112 -0
- package/skills/adaptyv/reference/api_reference.md +308 -0
- package/skills/adaptyv/reference/examples.md +913 -0
- package/skills/adaptyv/reference/experiments.md +360 -0
- package/skills/adaptyv/reference/protein_optimization.md +637 -0
- package/skills/aeon/SKILL.md +372 -0
- package/skills/aeon/references/anomaly_detection.md +154 -0
- package/skills/aeon/references/classification.md +144 -0
- package/skills/aeon/references/clustering.md +123 -0
- package/skills/aeon/references/datasets_benchmarking.md +387 -0
- package/skills/aeon/references/distances.md +256 -0
- package/skills/aeon/references/forecasting.md +140 -0
- package/skills/aeon/references/networks.md +289 -0
- package/skills/aeon/references/regression.md +118 -0
- package/skills/aeon/references/segmentation.md +163 -0
- package/skills/aeon/references/similarity_search.md +187 -0
- package/skills/aeon/references/transformations.md +246 -0
- package/skills/alpha-research/SKILL.md +42 -0
- package/skills/alpha-vantage/SKILL.md +142 -0
- package/skills/alpha-vantage/references/commodities.md +153 -0
- package/skills/alpha-vantage/references/economic-indicators.md +158 -0
- package/skills/alpha-vantage/references/forex-crypto.md +154 -0
- package/skills/alpha-vantage/references/fundamentals.md +223 -0
- package/skills/alpha-vantage/references/intelligence.md +138 -0
- package/skills/alpha-vantage/references/options.md +93 -0
- package/skills/alpha-vantage/references/technical-indicators.md +374 -0
- package/skills/alpha-vantage/references/time-series.md +157 -0
- package/skills/alphafold-database/SKILL.md +511 -0
- package/skills/alphafold-database/references/api_reference.md +423 -0
- package/skills/anndata/SKILL.md +398 -0
- package/skills/anndata/references/best_practices.md +525 -0
- package/skills/anndata/references/concatenation.md +396 -0
- package/skills/anndata/references/data_structure.md +314 -0
- package/skills/anndata/references/io_operations.md +404 -0
- package/skills/anndata/references/manipulation.md +516 -0
- package/skills/arboreto/SKILL.md +241 -0
- package/skills/arboreto/references/algorithms.md +138 -0
- package/skills/arboreto/references/basic_inference.md +151 -0
- package/skills/arboreto/references/distributed_computing.md +242 -0
- package/skills/arboreto/scripts/basic_grn_inference.py +97 -0
- package/skills/arxiv-database/SKILL.md +362 -0
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- package/skills/arxiv-database/scripts/arxiv_search.py +414 -0
- package/skills/astropy/SKILL.md +329 -0
- package/skills/astropy/references/coordinates.md +273 -0
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- package/skills/autoresearch/SKILL.md +12 -0
- package/skills/benchling-integration/SKILL.md +478 -0
- package/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/skills/benchling-integration/references/authentication.md +379 -0
- package/skills/benchling-integration/references/sdk_reference.md +774 -0
- package/skills/bgpt-paper-search/SKILL.md +81 -0
- package/skills/bindingdb-database/SKILL.md +332 -0
- package/skills/bindingdb-database/references/affinity_queries.md +178 -0
- package/skills/biopython/SKILL.md +441 -0
- package/skills/biopython/references/advanced.md +577 -0
- package/skills/biopython/references/alignment.md +362 -0
- package/skills/biopython/references/blast.md +455 -0
- package/skills/biopython/references/databases.md +484 -0
- package/skills/biopython/references/phylogenetics.md +566 -0
- package/skills/biopython/references/sequence_io.md +285 -0
- package/skills/biopython/references/structure.md +564 -0
- package/skills/biorxiv-database/SKILL.md +481 -0
- package/skills/biorxiv-database/references/api_reference.md +280 -0
- package/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
- package/skills/bioservices/SKILL.md +359 -0
- package/skills/bioservices/references/identifier_mapping.md +685 -0
- package/skills/bioservices/references/services_reference.md +636 -0
- package/skills/bioservices/references/workflow_patterns.md +811 -0
- package/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/skills/bioservices/scripts/compound_cross_reference.py +378 -0
- package/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
- package/skills/brenda-database/SKILL.md +717 -0
- package/skills/brenda-database/references/api_reference.md +537 -0
- package/skills/brenda-database/scripts/brenda_queries.py +844 -0
- package/skills/brenda-database/scripts/brenda_visualization.py +772 -0
- package/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
- package/skills/cbioportal-database/SKILL.md +367 -0
- package/skills/cbioportal-database/references/study_exploration.md +128 -0
- package/skills/cellxgene-census/SKILL.md +509 -0
- package/skills/cellxgene-census/references/census_schema.md +182 -0
- package/skills/cellxgene-census/references/common_patterns.md +351 -0
- package/skills/chembl-database/SKILL.md +387 -0
- package/skills/chembl-database/references/api_reference.md +272 -0
- package/skills/chembl-database/scripts/example_queries.py +278 -0
- package/skills/cirq/SKILL.md +344 -0
- package/skills/cirq/references/building.md +307 -0
- package/skills/cirq/references/experiments.md +572 -0
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- package/skills/cirq/references/transformation.md +416 -0
- package/skills/citation-management/SKILL.md +1113 -0
- package/skills/citation-management/assets/bibtex_template.bib +264 -0
- package/skills/citation-management/assets/citation_checklist.md +386 -0
- package/skills/citation-management/references/bibtex_formatting.md +908 -0
- package/skills/citation-management/references/citation_validation.md +794 -0
- package/skills/citation-management/references/google_scholar_search.md +725 -0
- package/skills/citation-management/references/metadata_extraction.md +870 -0
- package/skills/citation-management/references/pubmed_search.md +839 -0
- package/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- package/skills/citation-management/scripts/extract_metadata.py +569 -0
- package/skills/citation-management/scripts/format_bibtex.py +349 -0
- package/skills/citation-management/scripts/search_google_scholar.py +282 -0
- package/skills/citation-management/scripts/search_pubmed.py +398 -0
- package/skills/citation-management/scripts/validate_citations.py +497 -0
- package/skills/clinical-decision-support/SKILL.md +510 -0
- package/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
- package/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
- package/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
- package/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
- package/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
- package/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
- package/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
- package/skills/clinical-decision-support/references/README.md +129 -0
- package/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
- package/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
- package/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
- package/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
- package/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
- package/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
- package/skills/clinical-decision-support/scripts/biomarker_classifier.py +384 -0
- package/skills/clinical-decision-support/scripts/build_decision_tree.py +447 -0
- package/skills/clinical-decision-support/scripts/create_cohort_tables.py +524 -0
- package/skills/clinical-decision-support/scripts/generate_survival_analysis.py +422 -0
- package/skills/clinical-decision-support/scripts/validate_cds_document.py +335 -0
- package/skills/clinical-reports/SKILL.md +1131 -0
- package/skills/clinical-reports/assets/case_report_template.md +352 -0
- package/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
- package/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
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- package/skills/clinical-reports/assets/pathology_report_template.md +249 -0
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- package/skills/clinical-reports/scripts/check_deidentification.py +346 -0
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- package/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
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- package/skills/clinical-reports/scripts/generate_report_template.py +163 -0
- package/skills/clinical-reports/scripts/terminology_validator.py +133 -0
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- package/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
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- package/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
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- package/skills/venue-templates/references/grants_requirements.md +787 -0
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- package/skills/venue-templates/references/nature_science_style.md +405 -0
- package/skills/venue-templates/references/posters_guidelines.md +628 -0
- package/skills/venue-templates/references/reviewer_expectations.md +417 -0
- package/skills/venue-templates/references/venue_writing_styles.md +321 -0
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- package/skills/writing/SKILL.md +414 -0
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- package/skills/xlsx/SKILL.md +292 -0
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- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
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+
| 💡 | Idea / insight / inspiration | `[💡 Feature idea]` |
|
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149
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+
|
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150
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+
### Emoji Rules
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151
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+
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152
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1. **Place at start:** `[🔐 Authenticate]` not `[Authenticate 🔐]`
|
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153
|
+
2. **Max one per node** — never stack
|
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154
|
+
3. **Consistency is mandatory** — same emoji = same concept across all diagrams
|
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155
|
+
4. **Not every node needs one** — use on key nodes that benefit from visual distinction
|
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156
|
+
5. **No decorative emoji:** 🎉 💯 🔥 🎊 💥 ✨ — they add noise, not meaning
|
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157
|
+
|
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158
|
+
---
|
|
159
|
+
|
|
160
|
+
## GitHub-Compatible Color Classes
|
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161
|
+
|
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162
|
+
Use **only** when you genuinely need color-coding (multi-actor diagrams, severity levels). Prefer shapes + emoji first.
|
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163
|
+
|
|
164
|
+
**Approved palette (tested in both GitHub light and dark modes):**
|
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|
+
|
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166
|
+
| Semantic Use | `classDef` Definition | Visual |
|
|
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|
+
| ---------------------- | ------------------------------------------------------------ | -------------------------------------------------- |
|
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|
+
| **Primary / action** | `fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f` | Light blue fill, blue border, dark navy text |
|
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169
|
+
| **Success / positive** | `fill:#dcfce7,stroke:#16a34a,stroke-width:2px,color:#14532d` | Light green fill, green border, dark forest text |
|
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|
+
| **Warning / caution** | `fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12` | Light yellow fill, amber border, dark brown text |
|
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171
|
+
| **Danger / critical** | `fill:#fee2e2,stroke:#dc2626,stroke-width:2px,color:#7f1d1d` | Light red fill, red border, dark crimson text |
|
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|
+
| **Neutral / info** | `fill:#f3f4f6,stroke:#6b7280,stroke-width:2px,color:#1f2937` | Light gray fill, gray border, near-black text |
|
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173
|
+
| **Accent / highlight** | `fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#3b0764` | Light violet fill, purple border, dark purple text |
|
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174
|
+
| **Warm / commercial** | `fill:#ffedd5,stroke:#ea580c,stroke-width:2px,color:#7c2d12` | Light peach fill, orange border, dark rust text |
|
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175
|
+
|
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176
|
+
**Live preview — all 7 classes rendered:**
|
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+
|
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|
+
```mermaid
|
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|
+
flowchart LR
|
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180
|
+
accTitle: Color Palette Preview
|
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181
|
+
accDescr: Visual reference showing all seven approved classDef color classes side by side
|
|
182
|
+
|
|
183
|
+
primary[🔵 Primary] ~~~ success[✅ Success] ~~~ warning[⚠️ Warning] ~~~ danger[❌ Danger]
|
|
184
|
+
neutral[ℹ️ Neutral] ~~~ accent[🟣 Accent] ~~~ warm[🟠 Warm]
|
|
185
|
+
|
|
186
|
+
classDef primary fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f
|
|
187
|
+
classDef success fill:#dcfce7,stroke:#16a34a,stroke-width:2px,color:#14532d
|
|
188
|
+
classDef warning fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12
|
|
189
|
+
classDef danger fill:#fee2e2,stroke:#dc2626,stroke-width:2px,color:#7f1d1d
|
|
190
|
+
classDef neutral fill:#f3f4f6,stroke:#6b7280,stroke-width:2px,color:#1f2937
|
|
191
|
+
classDef accent fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#3b0764
|
|
192
|
+
classDef warm fill:#ffedd5,stroke:#ea580c,stroke-width:2px,color:#7c2d12
|
|
193
|
+
|
|
194
|
+
class primary primary
|
|
195
|
+
class success success
|
|
196
|
+
class warning warning
|
|
197
|
+
class danger danger
|
|
198
|
+
class neutral neutral
|
|
199
|
+
class accent accent
|
|
200
|
+
class warm warm
|
|
201
|
+
```
|
|
202
|
+
|
|
203
|
+
**Rules:**
|
|
204
|
+
|
|
205
|
+
1. Always include `color:` (text color) — dark-mode backgrounds can hide default text
|
|
206
|
+
2. Use `classDef` + `class` — **never** inline `style` directives
|
|
207
|
+
3. Max **3–4 color classes** per diagram
|
|
208
|
+
4. **Never rely on color alone** — always pair with emoji, shape, or label text
|
|
209
|
+
|
|
210
|
+
---
|
|
211
|
+
|
|
212
|
+
## Node Naming & Labels
|
|
213
|
+
|
|
214
|
+
| Rule | ✅ Good | ❌ Bad |
|
|
215
|
+
| --------------------- | -------------------------- | ----------------------------------- | --- | ----- | ----------------------------- | --- |
|
|
216
|
+
| `snake_case` IDs | `run_tests`, `deploy_prod` | `A`, `B`, `node1` |
|
|
217
|
+
| IDs match labels | `open_pr` → "Open PR" | `x` → "Open PR" |
|
|
218
|
+
| Specific names | `check_unit_tests` | `check` |
|
|
219
|
+
| Verbs for actions | `run_lint`, `deploy_app` | `linter`, `deployment` |
|
|
220
|
+
| Nouns for states | `review_state`, `error` | `reviewing`, `erroring` |
|
|
221
|
+
| 3–6 word labels | `[📥 Fetch raw data]` | `[Raw data is fetched from source]` |
|
|
222
|
+
| Active voice | `[🧪 Run tests]` | `[Tests are run]` |
|
|
223
|
+
| Sentence case | `[Start pipeline]` | `[Start Pipeline]` |
|
|
224
|
+
| Edge labels 1–4 words | `--> | All green | |`---> | All tests passed successfully | |
|
|
225
|
+
|
|
226
|
+
---
|
|
227
|
+
|
|
228
|
+
## Node Shapes
|
|
229
|
+
|
|
230
|
+
Use shapes consistently to convey node type without color:
|
|
231
|
+
|
|
232
|
+
| Shape | Syntax | Meaning |
|
|
233
|
+
| ----------------- | ---------- | ---------------------------- |
|
|
234
|
+
| Rounded rectangle | `([text])` | Start / end / terminal |
|
|
235
|
+
| Rectangle | `[text]` | Process / action / step |
|
|
236
|
+
| Diamond | `{text}` | Decision / condition |
|
|
237
|
+
| Subroutine | `[[text]]` | Subprocess / grouped action |
|
|
238
|
+
| Cylinder | `[(text)]` | Database / data store |
|
|
239
|
+
| Asymmetric | `>text]` | Event / trigger / external |
|
|
240
|
+
| Hexagon | `{{text}}` | Preparation / initialization |
|
|
241
|
+
|
|
242
|
+
---
|
|
243
|
+
|
|
244
|
+
## Bold Text
|
|
245
|
+
|
|
246
|
+
Use `**bold**` on **one** key term per node — the word the reader's eye should land on first.
|
|
247
|
+
|
|
248
|
+
- ✅ `[🚀 **Gradual** rollout]` — highlights the distinguishing word
|
|
249
|
+
- ❌ `[**Gradual** **Rollout** **Process**]` — everything bold = nothing bold
|
|
250
|
+
- Max 1–2 bold terms per node. Never bold entire labels.
|
|
251
|
+
|
|
252
|
+
---
|
|
253
|
+
|
|
254
|
+
## Subgraphs
|
|
255
|
+
|
|
256
|
+
Subgraphs are the primary tool for organizing complex diagrams. They create visual groupings that help readers parse structure at a glance.
|
|
257
|
+
|
|
258
|
+
```
|
|
259
|
+
subgraph name ["📋 Descriptive Title"]
|
|
260
|
+
node1 --> node2
|
|
261
|
+
end
|
|
262
|
+
```
|
|
263
|
+
|
|
264
|
+
**Subgraph rules:**
|
|
265
|
+
|
|
266
|
+
- Quoted titles with emoji: `["🔍 Code Quality"]`
|
|
267
|
+
- Group by stage, domain, team, or layer — whatever creates the clearest mental model
|
|
268
|
+
- 2–6 nodes per subgraph is ideal; up to 8 if tightly related
|
|
269
|
+
- Subgraphs can connect to each other via edges between their internal nodes
|
|
270
|
+
- One level of nesting is acceptable when it genuinely clarifies hierarchy (e.g., a "Backend" subgraph containing "API" and "Workers" subgraphs). Avoid deeper nesting.
|
|
271
|
+
- Give every subgraph a meaningful ID and title — `subgraph deploy ["🚀 Deployment"]` not `subgraph sg3`
|
|
272
|
+
|
|
273
|
+
**Connecting subgraphs — choose the right level of detail:**
|
|
274
|
+
|
|
275
|
+
Use **subgraph-to-subgraph** edges when the audience needs the high-level flow and internal details would be noise:
|
|
276
|
+
|
|
277
|
+
```
|
|
278
|
+
subgraph build ["📦 Build"]
|
|
279
|
+
compile --> package
|
|
280
|
+
end
|
|
281
|
+
subgraph deploy ["🚀 Deploy"]
|
|
282
|
+
stage --> prod
|
|
283
|
+
end
|
|
284
|
+
build --> deploy
|
|
285
|
+
```
|
|
286
|
+
|
|
287
|
+
Use **internal-node-to-internal-node** edges when the audience needs to see exactly which step hands off to which:
|
|
288
|
+
|
|
289
|
+
```
|
|
290
|
+
subgraph build ["📦 Build"]
|
|
291
|
+
compile --> package
|
|
292
|
+
end
|
|
293
|
+
subgraph deploy ["🚀 Deploy"]
|
|
294
|
+
stage --> prod
|
|
295
|
+
end
|
|
296
|
+
package --> stage
|
|
297
|
+
```
|
|
298
|
+
|
|
299
|
+
**Pick based on your audience:**
|
|
300
|
+
|
|
301
|
+
| Audience | Connect via | Why |
|
|
302
|
+
| --------------------- | ----------------------------- | ---------------------------------- |
|
|
303
|
+
| Leadership / overview | Subgraph → subgraph | They need phases, not steps |
|
|
304
|
+
| Engineers / operators | Internal node → internal node | They need the exact handoff points |
|
|
305
|
+
| Mixed / documentation | Both in separate diagrams | Overview diagram + detail diagram |
|
|
306
|
+
|
|
307
|
+
---
|
|
308
|
+
|
|
309
|
+
## Managing Complexity
|
|
310
|
+
|
|
311
|
+
Not every diagram is simple, and that's fine. The goal is **clarity at every scale** — a 5-node flowchart and a 30-node system diagram should both be immediately understandable. Use the right strategy for the complexity level.
|
|
312
|
+
|
|
313
|
+
### Complexity tiers
|
|
314
|
+
|
|
315
|
+
| Tier | Node count | Strategy |
|
|
316
|
+
| ---------------- | ----------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
|
|
317
|
+
| **Simple** | 1–10 nodes | Flat diagram, no subgraphs needed |
|
|
318
|
+
| **Moderate** | 10–20 nodes | **Use subgraphs** to group related nodes into 2–4 logical clusters |
|
|
319
|
+
| **Complex** | 20–30 nodes | **Subgraphs are mandatory.** 3–6 subgraphs, each with a clear title and purpose. Consider whether an overview + detail approach would be clearer. |
|
|
320
|
+
| **Very complex** | 30+ nodes | **Split into multiple diagrams.** Create an overview diagram showing subgraph-level relationships, then a detail diagram per subgraph. Link them in prose. |
|
|
321
|
+
|
|
322
|
+
### When to use subgraphs vs. split into multiple diagrams
|
|
323
|
+
|
|
324
|
+
**Use subgraphs when:**
|
|
325
|
+
|
|
326
|
+
- The connections _between_ groups are essential to understanding (splitting would lose that)
|
|
327
|
+
- A reader needs to see the full picture in one place (e.g., deployment pipeline, request lifecycle)
|
|
328
|
+
- Each group has 2–6 nodes and there are 3–5 groups total
|
|
329
|
+
|
|
330
|
+
**Split into multiple diagrams when:**
|
|
331
|
+
|
|
332
|
+
- Groups are mostly independent (few cross-group connections)
|
|
333
|
+
- The single diagram would exceed ~30 nodes even with subgraphs
|
|
334
|
+
- Different audiences need different views (overview for leadership, detail for engineers)
|
|
335
|
+
- The diagram is too wide/tall to read without scrolling
|
|
336
|
+
|
|
337
|
+
**Use overview + detail pattern when:**
|
|
338
|
+
|
|
339
|
+
- You need both the big picture AND the details
|
|
340
|
+
- The overview shows subgraph-level blocks with key connections
|
|
341
|
+
- Each detail diagram zooms into one subgraph with full internal structure
|
|
342
|
+
- Link them: _"See [Managing complexity](#managing-complexity) for the full scaling guidance."_
|
|
343
|
+
|
|
344
|
+
### Best practices at any scale
|
|
345
|
+
|
|
346
|
+
- **One primary flow direction** per diagram — `TB` for hierarchies/processes, `LR` for pipelines/timelines. Mixed directions confuse readers.
|
|
347
|
+
- **Decision points** — keep to ≤3 per subgraph. If a single subgraph has 4+ decisions, it deserves its own focused diagram.
|
|
348
|
+
- **Edge crossings** — minimize by grouping tightly-connected nodes together. If edges are crossing multiple subgraphs chaotically, reorganize the groupings.
|
|
349
|
+
- **Labels stay concise** regardless of diagram size — 3–6 words per node, 1–4 words per edge. Complexity comes from structure, not verbose labels.
|
|
350
|
+
- **Color-code subgraph purpose** — in complex diagrams, use `classDef` classes to visually distinguish layers (e.g., all "data" nodes in one color, all "API" nodes in another). Max 3–4 classes even in large diagrams.
|
|
351
|
+
|
|
352
|
+
### Composing multiple diagrams
|
|
353
|
+
|
|
354
|
+
When a single diagram isn't enough — multiple audiences, overview + detail needs, or before/after migration docs — see **[Composing Complex Diagram Sets](mermaid_diagrams/complex_examples.md)** for patterns and production-quality examples showing how to combine flowcharts, sequences, ER diagrams, and more into cohesive documentation.
|
|
355
|
+
|
|
356
|
+
---
|
|
357
|
+
|
|
358
|
+
## Choosing the Right Diagram
|
|
359
|
+
|
|
360
|
+
Read the "best for" column, then follow the link to the type file for the exemplar diagram, tips, and template.
|
|
361
|
+
|
|
362
|
+
| You want to show... | Type | File |
|
|
363
|
+
| ---------------------------------------- | ---------------- | --------------------------------------------------- |
|
|
364
|
+
| Steps in a process / decisions | **Flowchart** | [flowchart.md](mermaid_diagrams/flowchart.md) |
|
|
365
|
+
| Who talks to whom, when | **Sequence** | [sequence.md](mermaid_diagrams/sequence.md) |
|
|
366
|
+
| Class hierarchy / type relationships | **Class** | [class.md](mermaid_diagrams/class.md) |
|
|
367
|
+
| Status transitions / lifecycle | **State** | [state.md](mermaid_diagrams/state.md) |
|
|
368
|
+
| Database schema / data model | **ER** | [er.md](mermaid_diagrams/er.md) |
|
|
369
|
+
| Project timeline / roadmap | **Gantt** | [gantt.md](mermaid_diagrams/gantt.md) |
|
|
370
|
+
| Parts of a whole (proportions) | **Pie** | [pie.md](mermaid_diagrams/pie.md) |
|
|
371
|
+
| Git branching / merge strategy | **Git Graph** | [git_graph.md](mermaid_diagrams/git_graph.md) |
|
|
372
|
+
| Concept hierarchy / brainstorm | **Mindmap** | [mindmap.md](mermaid_diagrams/mindmap.md) |
|
|
373
|
+
| Events over time (chronological) | **Timeline** | [timeline.md](mermaid_diagrams/timeline.md) |
|
|
374
|
+
| User experience / satisfaction map | **User Journey** | [user_journey.md](mermaid_diagrams/user_journey.md) |
|
|
375
|
+
| Two-axis prioritization / comparison | **Quadrant** | [quadrant.md](mermaid_diagrams/quadrant.md) |
|
|
376
|
+
| Requirements traceability | **Requirement** | [requirement.md](mermaid_diagrams/requirement.md) |
|
|
377
|
+
| System architecture (zoom levels) | **C4** | [c4.md](mermaid_diagrams/c4.md) |
|
|
378
|
+
| Flow magnitude / resource distribution | **Sankey** | [sankey.md](mermaid_diagrams/sankey.md) |
|
|
379
|
+
| Numeric trends (bar + line charts) | **XY Chart** | [xy_chart.md](mermaid_diagrams/xy_chart.md) |
|
|
380
|
+
| Component layout / spatial arrangement | **Block** | [block.md](mermaid_diagrams/block.md) |
|
|
381
|
+
| Work item status board | **Kanban** | [kanban.md](mermaid_diagrams/kanban.md) |
|
|
382
|
+
| Binary protocol / data format | **Packet** | [packet.md](mermaid_diagrams/packet.md) |
|
|
383
|
+
| Infrastructure topology | **Architecture** | [architecture.md](mermaid_diagrams/architecture.md) |
|
|
384
|
+
| Multi-dimensional comparison / skills | **Radar** | [radar.md](mermaid_diagrams/radar.md) |
|
|
385
|
+
| Hierarchical proportions / budget | **Treemap** | [treemap.md](mermaid_diagrams/treemap.md) |
|
|
386
|
+
| Code-style sequence (programming syntax) | **ZenUML** | [zenuml.md](mermaid_diagrams/zenuml.md) |
|
|
387
|
+
|
|
388
|
+
**Pick the most specific type.** Don't default to flowcharts — match your content to the diagram type that was designed for it. A sequence diagram communicates service interactions better than a flowchart ever will.
|
|
389
|
+
|
|
390
|
+
---
|
|
391
|
+
|
|
392
|
+
## Known Parser Gotchas
|
|
393
|
+
|
|
394
|
+
These will save you debugging time:
|
|
395
|
+
|
|
396
|
+
| Diagram Type | Gotcha | Fix |
|
|
397
|
+
| ---------------- | ----------------------------------------------- | ------------------------------------------------------------------- |
|
|
398
|
+
| **Architecture** | Emoji in `[]` labels causes parse errors | Use plain text labels only |
|
|
399
|
+
| **Architecture** | Hyphens in `[]` labels parsed as edge operators | `[US East Region]` not `[US-East Region]` |
|
|
400
|
+
| **Architecture** | `-->` arrow syntax is strict about spacing | Use `lb:R --> L:api` format exactly |
|
|
401
|
+
| **Requirement** | `id` field with dashes (`REQ-001`) can fail | Use numeric IDs: `id: 1` |
|
|
402
|
+
| **Requirement** | Capitalized risk/verify values can fail | Use lowercase: `risk: high`, `verifymethod: test` |
|
|
403
|
+
| **C4** | Long descriptions cause label overlaps | Keep descriptions under 4 words; use `UpdateRelStyle()` for offsets |
|
|
404
|
+
| **C4** | Emoji in labels render but look odd | Skip emoji in C4 — renderer has its own icons |
|
|
405
|
+
| **Flowchart** | The word `end` breaks parsing | Wrap in quotes: `["End"]` or use `end_node` as ID |
|
|
406
|
+
| **Sankey** | No emoji in node names | Parser doesn't support them — use plain text |
|
|
407
|
+
| **ZenUML** | Requires external plugin | May not render on GitHub — prefer `sequenceDiagram` |
|
|
408
|
+
| **Treemap** | Very new (v11.12.0+) | Verify GitHub supports it before using |
|
|
409
|
+
| **Radar** | Requires v11.6.0+ | Verify GitHub supports it before using |
|
|
410
|
+
|
|
411
|
+
---
|
|
412
|
+
|
|
413
|
+
## Quality Checklist
|
|
414
|
+
|
|
415
|
+
### Every Diagram
|
|
416
|
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- [ ] `accTitle` + `accDescr` present (or italic Markdown paragraph for unsupported types)
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- [ ] Complexity managed: ≤10 nodes flat, 10–30 with subgraphs, 30+ split into multiple diagrams
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- [ ] Subgraphs used if >10 nodes (grouped by stage, domain, team, or layer)
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- [ ] ≤3 decision points per subgraph
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- [ ] Semantic `snake_case` IDs
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- [ ] Labels: 3–6 words, active voice, sentence case
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- [ ] Edge labels: 1–4 words
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- [ ] Consistent shapes for consistent meanings
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- [ ] Single primary flow direction (`TB` or `LR`)
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- [ ] No inline `style` directives
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- [ ] Minimal edge crossings (reorganize groupings if chaotic)
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- [ ] Colors from approved palette using `classDef` + `class`
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- [ ] Text `color:` included in every `classDef`
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- [ ] ≤4 color classes
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- [ ] Emoji from approved set, max 1 per node
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- [ ] Bold on max 1–2 words per node
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- [ ] Meaning never conveyed by color alone
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### Before Merge
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- [ ] Renders in GitHub **light** mode
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- [ ] Renders in GitHub **dark** mode
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- [ ] Emoji meanings consistent across all diagrams in the document
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---
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## Testing
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1. **GitHub:** Push to branch → toggle Profile → Settings → Appearance → Theme
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2. **VS Code:** "Markdown Preview Mermaid Support" extension → `Cmd/Ctrl + Shift + V`
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3. **Live editor:** [mermaid.live](https://mermaid.live/) — paste and toggle themes
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4. **Screen reader:** Verify `accTitle`/`accDescr` announced (VoiceOver, NVDA, JAWS)
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---
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## Resources
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- [Markdown Style Guide](markdown_style_guide.md) — Formatting, citations, and document structure for the markdown that wraps your diagrams
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- [Mermaid Docs](https://mermaid.js.org/) · [Live Editor](https://mermaid.live/) · [Accessibility](https://mermaid.js.org/config/accessibility.html) · [GitHub Support](https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/) · [VS Code Extension](https://marketplace.visualstudio.com/items?itemName=vstirbu.vscode-mermaid-preview)
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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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# Decision Record (ADR/RFC) Template
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> **Back to [Markdown Style Guide](../markdown_style_guide.md)** — Read the style guide first for formatting, citation, and emoji rules.
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**Use this template for:** Architecture Decision Records (ADRs), Requests for Comment (RFCs), technical design documents, or any decision that needs to be documented with its context, options considered, and rationale. Designed so that future teams understand not just _what_ was decided, but _why_ — and can evaluate whether the decision still holds.
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**Key features:** Structured options comparison with explicit tradeoffs, decision matrix, consequences section that captures both benefits and risks, and status tracking for the decision lifecycle.
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**Philosophy:** Decisions rot faster than code. Six months from now, someone will ask "why did we do it this way?" If the answer is "nobody remembers," the decision is as good as random. This template makes the reasoning permanent, searchable, and evaluable. It also forces the author to genuinely consider alternatives — if you can't articulate why you rejected Option B, you haven't done enough analysis.
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---
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## How to Use
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1. Copy this file to your project's `docs/decisions/` or `adr/` directory
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2. Name it sequentially: `001-use-postgresql-over-mongodb.md`
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3. Replace all `[bracketed placeholders]` with your content
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4. **Present options honestly** — don't set up straw men just to knock them down
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5. Add [Mermaid diagrams](../mermaid_style_guide.md) for architecture comparisons, data flow changes, or migration paths
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---
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## The Template
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Everything below the line is the template. Copy from here:
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---
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# [ADR-NNN]: [Decision Title — Clear and Specific]
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| Field | Value |
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| ------------------- | ---------------------------------------------------------- |
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| **Status** | [Proposed / Accepted / Deprecated / Superseded by ADR-NNN] |
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| **Date** | [YYYY-MM-DD] |
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| **Decision makers** | [Names or roles] |
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| **Consulted** | [Who was asked for input] |
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| **Informed** | [Who needs to know the outcome] |
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---
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## 📋 Context
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### What prompted this decision?
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[Describe the situation that requires a decision. What changed? What problem emerged? What opportunity appeared? Be specific — include metrics, incidents, or user feedback that triggered this.]
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### Current state
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[How things work today. What architecture, tool, or process is currently in place. Include a diagram if it helps.]
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```mermaid
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flowchart LR
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accTitle: Current State Architecture
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accDescr: How the system works today before this decision is implemented
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a[⚙️ Current component] --> b[💾 Current dependency]
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b --> c[📤 Current output]
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```
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### Constraints
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- **[Constraint 1]:** [Budget, timeline, team size, compliance requirement, etc.]
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- **[Constraint 2]:** [Technical constraint, backward compatibility, SLA, etc.]
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- **[Constraint 3]:** [Organizational constraint, vendor lock-in, skills gap, etc.]
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### Requirements
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This decision must:
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- [ ] [Requirement 1 — specific and measurable]
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- [ ] [Requirement 2]
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- [ ] [Requirement 3]
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---
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## 🔍 Options Considered
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### Option A: [Name]
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**Description:** [What this option entails — 2–3 sentences]
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**Pros:**
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- [Specific benefit with evidence if available]
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- [Another benefit]
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**Cons:**
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- [Specific drawback with impact assessment]
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- [Another drawback]
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**Estimated effort:** [T-shirt size or days/weeks]
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**Estimated cost:** [If relevant — licensing, infrastructure, personnel]
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### Option B: [Name]
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**Description:** [What this option entails]
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**Pros:**
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- [Benefit]
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- [Benefit]
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**Cons:**
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- [Drawback]
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- [Drawback]
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**Estimated effort:** [Estimate]
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**Estimated cost:** [If relevant]
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### Option C: [Name] _(if applicable)_
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**Description:** [What this option entails]
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**Pros:**
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- [Benefit]
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**Cons:**
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- [Drawback]
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**Estimated effort:** [Estimate]
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### Decision matrix
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| Criterion | Weight | Option A | Option B | Option C |
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| --------------------------------------- | -------------- | ------------------- | -------- | -------- |
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| [Criterion 1 — e.g., Performance] | [High/Med/Low] | [Score or ✅/⚠️/❌] | [Score] | [Score] |
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| [Criterion 2 — e.g., Team expertise] | [Weight] | [Score] | [Score] | [Score] |
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| [Criterion 3 — e.g., Migration effort] | [Weight] | [Score] | [Score] | [Score] |
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| [Criterion 4 — e.g., Long-term cost] | [Weight] | [Score] | [Score] | [Score] |
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| [Criterion 5 — e.g., Community/support] | [Weight] | [Score] | [Score] | [Score] |
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---
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## 🎯 Decision
|
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**We chose Option [X]: [Name].**
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[2–3 sentences explaining the core rationale. What tipped the decision? Which criteria mattered most and why?]
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### Why not the others?
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- **Option [Y] was rejected because:** [Specific reason — not "it wasn't good enough" but "the migration effort would take 3 sprints and delay the Q2 launch"]
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- **Option [Z] was rejected because:** [Specific reason]
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---
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## ⚡ Consequences
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### Positive
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- [Benefit 1 — what improves, with expected impact]
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- [Benefit 2]
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### Negative
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- [Tradeoff 1 — what we lose or what becomes harder]
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- [Tradeoff 2]
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### Risks
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|
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| Risk | Likelihood | Impact | Mitigation |
|
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| -------- | -------------- | -------------- | --------------------- |
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| [Risk 1] | [Low/Med/High] | [Low/Med/High] | [How we'll handle it] |
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| [Risk 2] | [Likelihood] | [Impact] | [Mitigation] |
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### Implementation impact
|
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```mermaid
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flowchart LR
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accTitle: Post-Decision Architecture
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accDescr: How the system will work after this decision is implemented
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a[⚙️ New component] --> b[💾 New dependency]
|
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b --> c[📤 New output]
|
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```
|
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---
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|
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## 📋 Implementation plan
|
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|
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| Step | Owner | Target date | Status |
|
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+
| -------- | ------------- | ----------- | ---------------------------------- |
|
|
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+
| [Step 1] | [Person/Team] | [Date] | [Not started / In progress / Done] |
|
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+
| [Step 2] | [Person/Team] | [Date] | [Status] |
|
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|
+
| [Step 3] | [Person/Team] | [Date] | [Status] |
|
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+
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---
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|
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## 🔗 References
|
|
196
|
+
|
|
197
|
+
- [Related ADR or RFC](../adr/ADR-001-agent-optimized-documentation-system.md)
|
|
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|
+
- [External documentation or benchmark](https://example.com)
|
|
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|
+
- [Relevant issue or discussion thread](../../docs/project/issues/issue-00000001-agentic-documentation-system.md)
|
|
200
|
+
|
|
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|
+
---
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|
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|
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|
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|
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## Review log
|
|
204
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+
|
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205
|
+
| Date | Reviewer | Outcome |
|
|
206
|
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| ------ | -------- | ----------------------------------------- |
|
|
207
|
+
| [Date] | [Name] | [Proposed / Approved / Requested changes] |
|
|
208
|
+
|
|
209
|
+
---
|
|
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|
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|
|
211
|
+
_Last updated: [Date]_
|