refactor: migrate package installation from pak to uvr (#147)

`bincraft` dropped pak in favour of uvr (5.0.x, "Dependencies and their system requirements are now installed with `uvr` instead of pak during `build_binary_package()`"), so the pipelines, helper scripts and images in this repo move with it.

## Approach

uvr is project-scoped in a way pak is not: `uvr add` refuses to run outside a project and always installs into `.uvr/library/`, and only `uvr sync` honours `--library`. So there is no one-line `pak::pak(...)` equivalent. `local/uvr-install.sh` encapsulates the dance — bootstrap a pinned uvr, mint a throwaway project under `TMPDIR`, `uvr add --no-install`, then `uvr sync --library <target>`. Keeping the project outside the checkout also keeps `uvr init`'s `.Rprofile` from hijacking `.libPaths()` for every other R call in the pipeline.

This matches what bincraft itself does (`uvr sync --install-system-deps --library <lib>`), and bincraft requires `uvr` on `PATH`, which the bootstrap provides: every pipeline that calls `bincraft::` runs `install-bincraft.R` (and therefore the bootstrap) first.

## Changes

| File | Change |
| --- | --- |
| `local/uvr-install.sh` | **New.** The single replacement for `pak::pak(...)`. Bootstraps uvr `v0.4.4`, resolves the R interpreter from `UVR_R_BIN`/`R_VERSION`/`PATH`, pins the manifest to that R's exact version, and syncs into `UVR_TARGET_LIB`/`R_LIBS_USER`. |
| `local/install-bincraft.R` | Installs `forgejo::codefloe.com/rpkgs/bincraft@<tag>` instead of a `git::` URL; keeps the `git ls-remote` tag resolution. Exports `UVR_R_BIN`/`UVR_TARGET_LIB` from `R.home()`/`.libPaths()[1]` so the per-R-minor passes target their own R and library. |
| `.crow/auto-apply-patches.yaml`, `.crow/weekly-patch-proposals.yaml`, `.crow/weekly-audit-missing.yaml`, `.crow/weekly-rebuild-missing.yaml`, `.crow/build-all-versions-install-deps.yaml` | `pak::pak(...)` → `UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh ...`. The explicit `UVR_R_BIN` matters in `build-all-versions-install-deps.yaml`, which has no `R_VERSION` in its step environment. |
| `.crow/build-all-versions.yaml`, `.crow/process-updates.yaml`, `.crow/weekly-rebuild-missing.yaml` | `R_PKG_CACHE_DIR` → `UVR_CACHE_DIR` + `UVR_PACKAGES_DIR` on the same `/mnt/cache` volume, preserving the amd64-off/arm64-on split. Drops the `rm -rf .../pkgcache/_metadata/...` cleanup. |
| `local/r-minor-helpers.R`, `local/build-all.R`, `local/tests/test-trim-pkgcache.R` | Removes `trim_pkgcache_metadata()`, its every-25-packages call and its tests. uvr's cache does not mint a fresh ~70 MB snapshot per `PACKAGES` change. |
| `.crow/build-all-versions-install-deps.yaml` | Drops `pak::sysreqs_db_update()`; uvr resolves sysreqs from its vendored `r-system-requirements` rules via `--install-system-deps`. |
| `docker/Containerfile-shiny-app` | Bootstraps uvr and drives both dependency installs through one uvr project with `UVR_LIBRARY` pointed at the image's R library. |
| `docker/build-one.Dockerfile` | Ships `uvr-install.sh` at `/work/local/` so `install-bincraft.R` finds it. |
| `docker/reprex/alpine.sh` | Replaces `pak::local_install_deps()` with DESCRIPTION parsing + `uvr add`. |
| `local/test-package-loading.R` | Installs via the helper instead of `pak::pkg_install()`. |
| `README.md` | Documents uvr for sysreq inference, archived-version installs and cache clearing. |
| `renovate.json` | Tracks the `UVR_PIN` in `uvr-install.sh` via `github-releases`. |

## Behaviour notes

- **`weekly-audit-missing` still takes bincraft from the default branch**, not the latest release tag, matching what the `git::` pak call did. Called out in a comment rather than silently changed.
- **The uvr pin is repo-wide.** bincraft resolves `uvr` from `PATH` and pins no version of its own, so `UVR_PIN` in `uvr-install.sh` governs the whole pipeline.
- **Persistent caches now also benefit bincraft**, which reads `UVR_CACHE_DIR`/`UVR_PACKAGES_DIR` from the inherited pipeline environment.
- **`uvr sync` will not prune the shared library.** Pruning is disabled whenever `--library` is passed (`do_prune = prune && library_override.is_none()`), so `/mnt/cache/R-pkgs` keeps bincraft and its dependencies. The wipe-on-ABI-mismatch path is *not* similarly guarded, which is why the helper pins the manifest to the active R's exact version.
- **`plans/` and `specs/` are untouched** — they are dated records of decisions made in June 2026 and describe bincraft's then-pak-based internals; rewriting them would misstate history.

## Verification

`shellcheck`, all pre-commit hooks (on this commit's file range) and the `local/tests/` suite (100 assertions) pass.

Not yet exercised in CI: the build-env images do not ship `uvr`, so the per-step `curl install.sh` bootstrap is untested against a real image. Worth a manual `build-all-versions-install-deps` run before merging.

Reviewed-on: #147

README.md

@@ -112,9 +112,9 @@ Processing updates with an existing database file takes around 5 minutes.
 
 ### Inferring System Dependencies
 
-R package dependencies and their system dependencies are installed through {pak}.
-{pak} allows for parallel downloads and installation, significantly speeding up package installation compared to `install.packages()`.
-Additionally, it automatically infers package dependencies using JSON rules from [rstudio/r-system-requirements](https://github.com/rstudio/r-system-requirements).
+R package dependencies and their system dependencies are installed through [uvr](https://github.com/nbafrank/uvr).
+`uvr` allows for parallel downloads and installation, significantly speeding up package installation compared to `install.packages()`.
+Additionally, it automatically infers package dependencies using JSON rules vendored from [rstudio/r-system-requirements](https://github.com/rstudio/r-system-requirements).
 Not all R packages specify required system dependencies in their DESCRIPTION file, and not all listed dependencies have existing rules in `rstudio/r-system-requirements`.
 For Alpine, no rules existed until recently, establishing a foundation for semi-automated package installation on Alpine Linux.
 
@@ -152,12 +152,13 @@ A Shiny dashboard providing a search functionality of the database and grouped s
 
 Is supported by writing `Meta/archive.rds` during each package index update, listing all available archived packages.
 
-### `pak::pak(package@version)`
+### `uvr add package@version`
 
-`pak` searches for `Archive/<package>` and can install all versions it finds.
+Clients that resolve archived versions search for `Archive/<package>` and can install all versions they find.
+This holds for `uvr` as well as for older `pak`-based clients.
 
 Ensure to use a clean cache if other repositories have been used previously.
-If in doubt or when testing, call `pak::meta_clean(force = TRUE)`.
+If in doubt or when testing, call `uvr cache clean`.
 
 ## Lessons Learned
 
@@ -180,7 +181,7 @@ If in doubt or when testing, call `pak::meta_clean(force = TRUE)`.
 
 ## URL Composition and Platform Identifiers
 
-Platform identifiers have been aligned with those used in <https://github.com/rstudio/r-system-requirements> to ensure proper recognition by the automatic syslib dependency installer of `pak`, specifically via the environment variable `PKG_SYSREQS_PLATFORM`:
+Platform identifiers have been aligned with those used in <https://github.com/rstudio/r-system-requirements>, which `uvr` vendors and uses for its automatic syslib dependency installer (`uvr sync --install-system-deps`):
 
 - redhat-9
 - redhat-8
@@ -237,8 +238,8 @@ internal error 1 in memDecompress
 Solution:
 
 ```sh
-rm -rf  /mnt/cache/R-pkgs/pak /mnt/cache/pkgcache/ /root/.cache/R/
-R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
+uvr cache clean
+rm -rf /mnt/cache/uvr /root/.cache/R/
 ```
 
 </details>