refactor: migrate package installation from pak to uvr

bincraft dropped pak in favour of uvr, so the pipelines, helper scripts
and images in this repo move with it.

- add local/uvr-install.sh as the single replacement for pak::pak(); it
  bootstraps a pinned uvr, mints a throwaway project under TMPDIR and
  runs `uvr add --no-install` + `uvr sync --library`, because `uvr add`
  refuses to run outside a project and only `sync` honours --library
- install bincraft via its Forgejo spec (forgejo::codefloe.com/rpkgs/
  bincraft@<tag>) instead of a git:: URL, keeping the git ls-remote tag
  resolution
- pass UVR_R_BIN/UVR_TARGET_LIB from install-bincraft.R so the
  per-R-minor passes target their own R and library
- replace R_PKG_CACHE_DIR with UVR_CACHE_DIR/UVR_PACKAGES_DIR on the
  persistent volume, preserving the amd64-off/arm64-on split
- drop trim_pkgcache_metadata() and its test; uvr's cache does not grow
  the way pkgcache's _metadata dir did
- let uvr install system requirements from its vendored
  r-system-requirements rules, replacing pak::sysreqs_db_update()
- migrate the shiny app image, the alpine reprex and the CRAN loading
  test; ship uvr-install.sh in the build-one image
- track the uvr pin with renovate

.crow/build-all-versions.yaml

@@ -11,25 +11,25 @@ variables:
       - arm64
     default: amd64
   OS:
-    description: "Base OS image name."
+    description: 'Base OS image name.'
     options:
       - alpine
       - redhat
       - ubuntu
     default: alpine
   OS_VERSION:
-    description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)."
+    description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
     options:
-      - "3.22"
-      - "3.23"
-      - "3.24"
-      - "8"
-      - "9"
-      - "10"
-      - "jammy"
-      - "noble"
-      - "resolute"
-    default: "3.24"
+      - '3.22'
+      - '3.23'
+      - '3.24'
+      - '8'
+      - '9'
+      - '10'
+      - 'jammy'
+      - 'noble'
+      - 'resolute'
+    default: '3.24'
   R_VERSION:
     description: 'Primary R version under /opt/R.'
     options:
@@ -47,38 +47,49 @@ labels:
   platform: linux/${ARCH}
   group: rpkgs-${ARCH}
 
+# Empty UVR_CACHE_DIR/UVR_PACKAGES_DIR fall back to uvr's container-local
+# ~/.uvr defaults; amd64 deliberately does not persist them (as with the
+# pkgcache dir it replaces), arm64 does.
 matrix:
   include:
     - ARCH: amd64
-      R_PKG_CACHE_DIR: ''
+      UVR_CACHE_DIR: ''
+      UVR_PACKAGES_DIR: ''
       SPLIT_INTO: 4
       SPLIT_INDEX: 1
     - ARCH: amd64
-      R_PKG_CACHE_DIR: ''
+      UVR_CACHE_DIR: ''
+      UVR_PACKAGES_DIR: ''
       SPLIT_INTO: 4
       SPLIT_INDEX: 2
     - ARCH: amd64
-      R_PKG_CACHE_DIR: ''
+      UVR_CACHE_DIR: ''
+      UVR_PACKAGES_DIR: ''
       SPLIT_INTO: 4
       SPLIT_INDEX: 3
     - ARCH: amd64
-      R_PKG_CACHE_DIR: ''
+      UVR_CACHE_DIR: ''
+      UVR_PACKAGES_DIR: ''
       SPLIT_INTO: 4
       SPLIT_INDEX: 4
     - ARCH: arm64
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
       SPLIT_INTO: 4
       SPLIT_INDEX: 1
     - ARCH: arm64
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
       SPLIT_INTO: 4
       SPLIT_INDEX: 2
     - ARCH: arm64
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
       SPLIT_INTO: 4
       SPLIT_INDEX: 3
     - ARCH: arm64
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
       SPLIT_INTO: 4
       SPLIT_INDEX: 4
 
@@ -107,8 +118,10 @@ steps:
         from_secret: GITHUB_PAT
       # normal env vars
       GIT_USER: pat-s
-      # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
-      R_PKG_CACHE_DIR: ${R_PKG_CACHE_DIR}
+      # set the location of uvr's caches, which persist the R package
+      # dependencies needed to install the packages themselves
+      UVR_CACHE_DIR: ${UVR_CACHE_DIR}
+      UVR_PACKAGES_DIR: ${UVR_PACKAGES_DIR}
       R_LIBS_USER: /mnt/cache/R-pkgs
       CCACHE_DIR: /mnt/cache/ccache
       NCPUS: 2
@@ -116,12 +129,7 @@ steps:
       - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
     commands:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
-      # Clear churny pkgcache metadata left by a prior crashed run (the "patched"
-      # repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*).
-      # Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs. Within-run
-      # growth is bounded separately by trim_pkgcache_metadata() in build-all.R.
-      - rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
-      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
+      - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # The primary pass must not rely on build-all-versions-install-deps having
       # run on *this* agent: depends_on only orders the steps, but the cache
       # volume is per-agent, so a job landing on an agent where install-deps did