Guides
======

These guides recover and curate workflow knowledge from the legacy notebooks
(``00_data-prep.ipynb``, ``01a_run-tsa.ipynb``, ``01b_run-tsa.ipynb``) archived in
``reference/legacy_notebooks/``, and align it with the current FEMIC CLI and
export modules.

.. toctree::
   :maxdepth: 2

   pipeline-overview
   developer-environment-bootstrap
   vscode-coding-agent-onboarding
   deployment-instances
   rebuild-repro-contract
   author-instance-rebuild-spec
   interpret-rebuild-reports
   data-access-inventory
   bc-data-catalogue-discovery
   tsr-intelligence-workflow
   document-figure-recovery
   freshforge-provider-integration
   tsr-thlb-reconstruction-ladder
   github-datalad-arbutus-pattern
   windows-arbutus-auth-workflow
   public-data-mirror-runbook
   case-onboarding
   stage-00-data-prep
   stage-01a-vdyp-tipsy-input
   stage-01b-post-tipsy
   btc-fansier-runtime-and-extraction
   model-input-bundle-and-export
   patchworks-variant-and-scenario-management
   diagnostics-playbook
   troubleshooting
   limitations-and-boundaries
   patchworks-wine-runtime
   ubc-vpn-license-connectivity
   geospatial-runtime-bootstrap
   cross-platform-runtime-smoke
   pypi-release-runbook
   legacy-traceability
   sphinx-template-baseline