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| 1 | +# Claude Code prompt: Migrate `rcac-bioinformatics.github.io` into `RCAC-Docs` |
| 2 | + |
| 3 | +## Role and scope |
| 4 | + |
| 5 | +You are executing a documentation migration across two local git repositories on my Debian 13 workstation. You have two authoritative spec files attached to this conversation: |
| 6 | + |
| 7 | +1. **`integration-plan.md`** — the five-phase execution plan. **This is the contract. Follow it exactly.** |
| 8 | +2. **`details-about-docs.md`** — reference material describing both repos' structure, syntax, and conventions. Use this as a lookup when converting. |
| 9 | + |
| 10 | +If the two files conflict, `integration-plan.md` wins. If either is unclear, stop and ask me rather than improvise. |
| 11 | + |
| 12 | +## Repos and paths |
| 13 | + |
| 14 | +- Target repo: `/home/arnstrm/svn/RCAC-Docs` (MkDocs/Material; feature branch `feature/life-sciences`). |
| 15 | +- Source repo: `/home/arnstrm/svn/rcac-bioinformatics.github.io` (Astro/Starlight; feature branch `feature/redirect-shim`, archive branch `archive/starlight`). |
| 16 | + |
| 17 | +Both are already on `main` with clean trees (I verified). `gh` CLI is authed to both `PurdueRCAC/RCAC-Docs` and `rcac-bioinformatics/rcac-bioinformatics.github.io`. |
| 18 | + |
| 19 | +## What to do |
| 20 | + |
| 21 | +Execute Phases 0 through 5 of `integration-plan.md` in order, without skipping phases or steps. At the end of each phase, print a short summary (files touched, commits added, any issues) before starting the next phase. Do not wait for my confirmation between phases unless a step fails or you hit an ambiguity listed below. |
| 22 | + |
| 23 | +## Operational rules (hard) |
| 24 | + |
| 25 | +1. **No `gh pr create`.** Stop at "pushed branch, PR body drafted in a file." I open the PRs. |
| 26 | +2. **No force pushes.** Ever. If you need to undo a commit, amend before push or add a new commit. |
| 27 | +3. **No interactive prompts.** Every git/gh command is non-interactive. Every commit has an explicit `-m`. |
| 28 | +4. **No edits outside scope.** Do not regenerate the software catalog, touch `modulefiles/`, `tools/`, or `docs/software/apps_md/*.md`. The only permitted edits outside the new `docs/lifesciences/` and `docs/workshops/genomics_exchange/` trees are: `mkdocs.yml` (per §9), the four "See also" cross-link additions in §8, and `docs/software/bioinformatics_catalog.md` (new file). |
| 29 | +5. **No `dev` branch.** Never check out, merge to, or push to the `dev` branch on RCAC-Docs. |
| 30 | +6. **Commit dates preserved.** Per-page migration commits in Phase 2 set both `GIT_AUTHOR_DATE` and `GIT_COMMITTER_DATE` to the original `lastUpdated` value from the MDX frontmatter (values listed in the plan's §4 table). Scaffolding commits use the current time. Example: |
| 31 | + |
| 32 | + ```bash |
| 33 | + GIT_AUTHOR_DATE="2026-03-10T12:00:00 -0500" \ |
| 34 | + GIT_COMMITTER_DATE="2026-03-10T12:00:00 -0500" \ |
| 35 | + git commit -m "feat(lifesciences): migrate publication-quality-plots from Starlight" |
| 36 | + ``` |
| 37 | + |
| 38 | +7. **Commit style.** Conventional Commits: `feat(lifesciences):`, `feat(workshops):`, `refactor:`, `fix:`, `docs:`. One logical unit per commit. |
| 39 | +8. **Tags vocabulary.** Only the values in §6b of the plan. No improvised tags. |
| 40 | +9. **Redirect shim coverage is exact.** Every URL in the plan's §2c table must have a corresponding `public/<old-path>/index.html` file. Don't invent additional redirects; don't skip any. |
| 41 | +10. **Encoding and line endings.** UTF-8, LF. No trailing whitespace. |
| 42 | + |
| 43 | +## When to stop and ask |
| 44 | + |
| 45 | +Stop and ask me before proceeding if any of the following occur: |
| 46 | + |
| 47 | +- Pre-flight (Phase 0) fails: dirty tree, missing `gh` auth, missing required Python packages that can't be installed. |
| 48 | +- An image or asset file referenced in source MDX does not exist on disk. |
| 49 | +- An MDX file contains a Starlight component not covered by the §6 translation rules. |
| 50 | +- `mkdocs build --strict` fails after your first round of fixes; do not attempt a second round without asking. |
| 51 | +- The redirect shim URL map is incomplete vs. what you find under `src/content/docs/` (e.g., a page exists in source that isn't in §2c). |
| 52 | +- Git state diverges from expected at any point (e.g., `feature/life-sciences` already exists remotely with commits). |
| 53 | + |
| 54 | +Do NOT stop to ask for confirmation on routine conversions. Trust the plan. |
| 55 | + |
| 56 | +## Validation |
| 57 | + |
| 58 | +Phase 4 of the plan lists the full check suite. Run all of it. If a check fails, fix the underlying issue, then re-run the full suite from the top. Record the final log. |
| 59 | + |
| 60 | +## Deliverables at the end |
| 61 | + |
| 62 | +After Phase 5, print: |
| 63 | + |
| 64 | +1. Commits-per-phase table. |
| 65 | +2. Files changed in RCAC-Docs (count + a few representative paths). |
| 66 | +3. Files changed in the Astro repo (count + a few representative paths). |
| 67 | +4. Validation results (one line per check from Phase 4). |
| 68 | +5. Outstanding TODOs: exactly two `TODO(arun)` markers for sessions 1 and 2 metadata, plus any follow-up issue drafts. |
| 69 | +6. The exact `gh pr create` commands I should run when ready to open the PRs. Include `--base main --head feature/life-sciences` / `--head feature/redirect-shim` and point `--body-file` at the drafted PR bodies under `/home/claude/work/`. |
| 70 | + |
| 71 | +## Begin |
| 72 | + |
| 73 | +Start with Phase 0, step 0.1. Print the pre-flight summary before touching any file. |
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