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docs: centralize setup guides and breaking-change migration notes - #4

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docs/audit-cleanup-migration
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Winter-Soren wants to merge 1 commit into
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docs/audit-cleanup-migration

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@Winter-Soren

@Winter-Soren Winter-Soren commented Oct 31, 2026 •

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Problem and result

Setup and integration guidance was scattered across the application tree, while credential requirements and upgrade behavior were unclear. This PR preserves 41 moved documents, adds a path index, and provides current environment, validation, and migration guides. Historical claims and formatting stay marked as historical.

The companion application PR #7 uses fix/audit-cleanup-breaking. Merge this documentation PR first using a merge commit so the parent repository's pinned commit remains reachable. If squash/rebase merging, update the application submodule pointer to the resulting commit before merging that PR.

Breaking-change guidance

Migration guide distinguishes confirmed configuration/API/install/path changes from probable regressions, and includes rollout/rollback steps. It covers server-only storage keys, Mongo database preservation, run/chat/pharma authentication, optional chemistry, deployment behavior, and relocated automatic tool guidance.

Missing credentials for merged integrations are setup gaps; this work preserves their code and explains where to obtain access. No real credentials are included.

Validation and limits

  • 98 local links checked across both repositories; no missing targets.
  • New guide whitespace and credential-pattern checks passed. Existing Markdown hard breaks and archive formatting are preserved.
  • Application results are recorded in the validation guide: backend 1,198 passed/114 skipped; frontend 196 passed; TypeScript/build/lint passed (17 existing lint warnings).
  • Docker, live providers/wallets, native chemistry, and hosted backend deployment remain unverified. AWS access is unavailable.

This is a draft for contributor review. It does not merge main, create a release tag, or deploy production source.

Preserve 41 application documents in the documentation repository, with a
path migration index, a minimal setup guide, and credential acquisition
instructions for optional integrations. Keep existing feature documentation.

Document confirmed breaking changes separately from possible regressions,
including configuration names, authentication, packaging, storage removal,
and deployment behavior. Include rollout/rollback steps and validation limits.

Validation: 98 local documentation links checked across both repositories;
Authored-guide whitespace checks pass. Historical document claims and
formatting are preserved.
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