Build rc-0.5.0 docs from a single monorepo checkout

[andrewherren]

What

Points every rc-0.5.0 ref in versions.json at the monorepo rc-0.5.0 branch and bootstraps the CRAN package the same way latest does.

cpp_ref      main            → rc-0.5.0
r_ref        r-rc-0.5.0      → rc-0.5.0
py_ref       py-rc-0.5.0     → rc-0.5.0
r_bootstrap  false           → true
r_pkg_path   stochtree_repo  → stochtree_repo/stochtree_cran

Why

The RC version pinned its R and Python builds to the generated r-rc-0.5.0 / py-rc-0.5.0 deploy branches, which exist solely to ship installable packages. That caused three problems:

1. r-rc-0.5.0 carries no _pkgdown.yml, so the RC R docs fell back to pkgdown's auto-generated reference index.
2. cpp_ref pointed at main, so the RC sub-site published main's Doxygen output.
3. The changelog was sourced from the packaged branch's NEWS.md rather than the monorepo copy, so RC release notes could lag.

Consolidating onto the monorepo branch fixes all three, and drops two moving parts from the matrix.

No change to installed code

py-rc-0.5.0 is deployed from rc-0.5.0 HEAD exactly, and r-rc-0.5.0 trailed it only by Python-only commits — so the R and Python packages built here are the same code that was being built before.

Verification

Run locally against a fresh rc-0.5.0 checkout:

• Rscript cran-bootstrap.R 0 1 0 — clean, emits stochtree_cran/ with _pkgdown.yml and NEWS.md
• pkgdown::check_pkgdown() — No problems found
• pkgdown::build_site_github_pages(install = TRUE) — exit 0, no errors in the log
• All 9 previously unindexed topics (continueSampling, extractForest, extractRandomEffectSamples, each plus .bartmodel / .bcfmodel) have reference pages and index entries
• Python package installs from the monorepo root, matching the consolidated pip install . step
• Doxyfile on rc-0.5.0 carries the exact OUTPUT_DIRECTORY / GENERATE_XML / GENERATE_HTML lines the workflow's sed rewrites

Depends on StochasticTree/stochtree@b420d079, which fixes the _pkgdown.yml reference index and points the pkgdown url at the sub-site. Already pushed to rc-0.5.0.

Note on testing

This workflow has no push trigger, so this PR builds latest only and does not exercise the RC path. After merge, run it via workflow_dispatch to test the consolidated RC build — the first real RC run will be a deploy.

Also updates two workflow comments that this change makes inaccurate.

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