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

local/build-all.R

@@ -27,7 +27,9 @@ package_cache_files <- c(
   "/mnt/cache/packages/s3_cache.rds"
 )
 if (!all(file.exists(package_cache_files))) {
-  message("Package snapshot missing from cache; recomputing via packages-to-build.R")
+  message(
+    "Package snapshot missing from cache; recomputing via packages-to-build.R"
+  )
   dir.create("/mnt/cache/packages", showWarnings = FALSE, recursive = TRUE)
   save_rds_atomic <- function(obj, path) {
     tmp <- paste0(path, ".tmp.", Sys.getpid())
@@ -36,7 +38,10 @@ if (!all(file.exists(package_cache_files))) {
   }
   source(file.path("local", "packages-to-build.R"))
   save_rds_atomic(pkgs, "/mnt/cache/packages/pkgs_to_build.rds")
-  save_rds_atomic(pkgs[r_minor_sensitive == TRUE], "/mnt/cache/packages/r_minor_sensitive_pkgs.rds")
+  save_rds_atomic(
+    pkgs[r_minor_sensitive == TRUE],
+    "/mnt/cache/packages/r_minor_sensitive_pkgs.rds"
+  )
   message("Package snapshot recomputed.")
 }
 
@@ -112,20 +117,22 @@ built <- DBI::dbGetQuery(
 )
 DBI::dbDisconnect(con)
 before <- nrow(chunk)
-chunk <- chunk[!paste(chunk$Package, chunk$Version) %in% paste(built$name, built$tag), ]
-sprintf("Skipped %d already-attempted package versions; %d remaining for this job", before - nrow(chunk), nrow(chunk))
+chunk <- chunk[
+  !paste(chunk$Package, chunk$Version) %in% paste(built$name, built$tag),
+]
+sprintf(
+  "Skipped %d already-attempted package versions; %d remaining for this job",
+  before - nrow(chunk),
+  nrow(chunk)
+)
 
 # Read pre-computed S3 listing from install-deps step
 # This avoids loading s3fs/reticulate/Python in the build container,
-# saving significant memory for pak subprocess forks
+# saving significant memory for the dependency-installer subprocesses
 s3_cache <- readRDS("/mnt/cache/packages/s3_cache.rds")
 sprintf("S3 cache: %s files", length(s3_cache))
 
 n <- nrow(chunk)
-# Every `trim_every` packages, bound the pkgcache _metadata dir so a full-platform
-# run does not accumulate thousands of ~70 MB snapshots and fill the host disk.
-# No-op on amd64 (R_PKG_CACHE_DIR is empty / cache not persisted).
-trim_every <- 25L
 mapply(
   function(pkg, ver, sens, i) {
     cat(sprintf("[%d/%d] %s_%s (r_minor_sensitive=%s)\n", i, n, pkg, ver, sens))
@@ -151,12 +158,6 @@ mapply(
       upload = TRUE,
       store_build_metadata = TRUE
     )
-    if (i %% trim_every == 0L) {
-      removed <- trim_pkgcache_metadata()
-      if (removed > 0L) {
-        cat(sprintf("  [pkgcache trim] removed %d stale _metadata entries\n", removed))
-      }
-    }
   },
   chunk$Package,
   chunk$Version,