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docs/ vs mintlify-docs/

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Short answer

  • mintlify-docs/ — Curated, user-facing documentation for the public Mintlify site: getting started, architecture, strategies, web UI, CLI, API overview, and selected ops guides.
  • docs/ — Full internal knowledge base: not 1:1 mirrored in Mintlify. It includes benchmarks (BixBench), Chinese-only notes, design RFCs, SkillRL comparisons, optional packages, and work-in-progress plans.
So: Mintlify does not automatically include every file under docs/. When you add important user-facing content to docs/, either sync a copy into mintlify-docs/ and add it to mint.json → navigation, or link readers to the GitHub docs/ tree.

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Pages in Mintlify (mintlify-docs/*.md)

Aligned with or extended from the former docs/ set: intro, getting-started, architecture, strategy-routing, multi-agent-pipeline, hybrid-retrieval, memory-system, self-correction, template-evolution, knowledge-graph, context-window-and-budget, adding-tools-and-agents, autofigure-ai-researcher, resources-page, browser-and-automation, web-ui, reports-and-presentations, automation-user-guide, api-reference, configuration, cli, provenance-and-reproducibility, quick-test-guide, plus Mintlify-only or extended topics: mcp, hypothesis-strategy, using-biomni-tools. Explicitly synced from docs/ for ops (Mintlify copies are English; the repo may still have a Chinese docs/google-login-setup.md for internal use):
Mintlify pageSource in repo
web-scaling-and-workersdocs/web_scaling_and_workers.md
google-login-setupdocs/google-login-setup.md (Mintlify = English edition)

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Examples of docs/-only content (not in Mintlify nav by default)

  • Benchmarks & methodology: BixBench_*, BIOCORTEX_OPTIMIZATION_AND_BIXBENCH.md
  • Platform summaries (ZH): BIOCORTEX_PLATFORM_UPGRADE_SUMMARY_ZH.md
  • Auth evaluation: auth-and-admin-evaluation.md
  • LLM providers list: SUPPORTED_LLM_PROVIDERS.md
  • Slurm / celltype / Biomni comparisons: comparison_*, STRATEGY_BIOMNI_VS_NATIVE_TOOLS.md
  • Engineering plans: CODE_OPTIMIZER_PLAN.md, CLI_PANTHEON_STYLE_PLAN.md
  • WebSocket run design: project_scoped_websocket_runs.md
  • Skill templates: SKILL_ENRICHMENT_TEMPLATE.md
  • H5AD guidelines: anndata-h5ad-code-guidelines.md
  • Optional packages: optional-analysis-packages.md
Add any of these to Mintlify when they become stable user-facing references; keep volatile RFCs in docs/ only.