feat(rebuild): shard the weekly rebuild and make each shard resumable

Split every OS/arch row of weekly-rebuild-missing into three shards and move
the build loop out of the inline R one-liner into local/rebuild-missing.R.

A shard re-derives its outstanding set from the bucket on every start: an
object whose ETag equals CRAN's published MD5sum is still a source fallback and
needs building. That is bincraft's check_s3_root_package() evaluated in bulk,
so a restart resumes rather than replaying thousands of per-package HEADs, and
it stays correct when a sibling shard or a process-updates run finishes work in
the meantime. No progress file, no volume, no database cursor.

Give each shard a 20h wall-clock budget so it exits cleanly instead of having
to be killed. A kill matches neither success nor failure, which is how pipeline
10910 skipped its CDN purge and left ~4600 rebuilt binaries behind stale edge
copies.

Move re-indexing and the purge into weekly-rebuild-reindex.yaml, which depends
on the rebuild and runs on success or failure. Three shards writing one slot's
PACKAGES concurrently would race: update_PACKAGES lists the live bucket, so an
early lister that uploads last publishes an index missing its siblings' work.

.crow/weekly-rebuild-missing.yaml

@@ -1,12 +1,21 @@
 # Consolidated weekly-rebuild-missing pipeline (all platforms, both arches).
-# One matrix row per OS/arch replaces the former per-platform files.
+# Three matrix rows per OS/arch, one per shard of that slot's rebuild list.
 # Routing is preserved 1:1:
 #   - cron:   each existing `weekly-rebuild-missing-<os>-<arch>` cron fires only
-#             its matching matrix row (via the per-row `cron:` name filter).
+#             its matching matrix rows (via the per-row `cron:` name filter),
+#             which is now all three shards of that slot.
 #   - manual: `weekly_rebuild_missing` dropdown, default "all" (matches the
 #             previous bare manual trigger that ran every os/arch); pick a
 #             single <os>-<arch> to run just one.
 # Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64).
+#
+# The shard picks up its own slice and re-derives what is still outstanding
+# from the bucket, so a restart resumes rather than replaying; see
+# local/rebuild-missing.R.
+#
+# Re-indexing and the CDN purge deliberately do NOT live here. Three shards
+# writing one slot's PACKAGES concurrently would race, so they moved to
+# .crow/weekly-rebuild-reindex.yaml, which depends on this pipeline.
 variables:
   # Gates this pipeline. A manual pipeline creation instantiates every file in
   # .crow/, and a declared default is applied even when the run never passed
@@ -53,74 +62,326 @@ matrix:
       ARCH: amd64
       R_VERSION: 4.5.3
       IMG: alpine:3.22
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: alpine-322
+      ARCH: amd64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.22
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: alpine-322
+      ARCH: amd64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.22
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: alpine-322
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: alpine:3.22
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: alpine-322
+      ARCH: arm64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.22
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: alpine-322
+      ARCH: arm64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.22
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: alpine-323
       ARCH: amd64
       R_VERSION: 4.5.3
       IMG: alpine:3.23
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: alpine-323
+      ARCH: amd64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.23
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: alpine-323
+      ARCH: amd64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.23
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: alpine-323
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: alpine:3.23
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: alpine-323
+      ARCH: arm64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.23
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: alpine-323
+      ARCH: arm64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.23
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: alpine-324
       ARCH: amd64
       R_VERSION: 4.5.3
       IMG: alpine:3.24
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: alpine-324
+      ARCH: amd64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.24
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: alpine-324
+      ARCH: amd64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.24
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: alpine-324
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: alpine:3.24
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: alpine-324
+      ARCH: arm64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.24
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: alpine-324
+      ARCH: arm64
+      R_VERSION: 4.5.3
+      IMG: alpine:3.24
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: redhat-8
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: redhat:8
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: redhat-8
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: redhat:8
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: redhat-8
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: redhat:8
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: redhat-8
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: redhat:8
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: redhat-8
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: redhat:8
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: redhat-8
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: redhat:8
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: redhat-9
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: redhat:9
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: redhat-9
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: redhat:9
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: redhat-9
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: redhat:9
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: redhat-9
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: redhat:9
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: redhat-9
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: redhat:9
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: redhat-9
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: redhat:9
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: redhat-10
       ARCH: amd64
       R_VERSION: 4.5.3
       IMG: redhat:10
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: redhat-10
+      ARCH: amd64
+      R_VERSION: 4.5.3
+      IMG: redhat:10
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: redhat-10
+      ARCH: amd64
+      R_VERSION: 4.5.3
+      IMG: redhat:10
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: redhat-10
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: redhat:10
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: redhat-10
+      ARCH: arm64
+      R_VERSION: 4.5.3
+      IMG: redhat:10
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: redhat-10
+      ARCH: arm64
+      R_VERSION: 4.5.3
+      IMG: redhat:10
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: ubuntu-2204
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: ubuntu:jammy
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: ubuntu-2204
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:jammy
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: ubuntu-2204
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:jammy
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: ubuntu-2204
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: ubuntu:jammy
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: ubuntu-2204
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:jammy
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: ubuntu-2204
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:jammy
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: ubuntu-2404
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: ubuntu:noble
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: ubuntu-2404
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:noble
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: ubuntu-2404
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:noble
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: ubuntu-2404
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: ubuntu:noble
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: ubuntu-2404
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:noble
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: ubuntu-2404
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:noble
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: ubuntu-2604
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: ubuntu:resolute
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: ubuntu-2604
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:resolute
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: ubuntu-2604
+      ARCH: amd64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:resolute
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
     - OS: ubuntu-2604
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: ubuntu:resolute
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 1
+    - OS: ubuntu-2604
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:resolute
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 2
+    - OS: ubuntu-2604
+      ARCH: arm64
+      R_VERSION: 4.4.3
+      IMG: ubuntu:resolute
+      SPLIT_INTO: 3
+      SPLIT_INDEX: 3
 
 steps:
   - name: 'Rebuild missing binaries'
@@ -153,6 +414,12 @@ steps:
       PLATFORM: ${OS}
       ARCH: ${ARCH}
       NCPUS: 2
+      SPLIT_INTO: ${SPLIT_INTO}
+      SPLIT_INDEX: ${SPLIT_INDEX}
+      # Wall clock after which the shard stops cleanly instead of having to be
+      # killed. A kill matches neither `success` nor `failure`, so it would skip
+      # the dependent re-index and leave rebuilt binaries behind a stale edge.
+      REBUILD_BUDGET_HOURS: 20
     commands:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
       - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
@@ -162,18 +429,7 @@ steps:
       - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
       - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2
       - /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
-      - $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, patches = 'local/patches', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1
-      # A rebuild replaces objects in place, so the slot's index still advertises
-      # the old MD5 and, for anything that had been served from source, no Built
-      # stamp. Re-index here rather than waiting for the next process-updates
-      # run, or the rebuilt binaries stay invisible to clients until then.
-      # The codename is detected from the image's /etc/os-release.
-      - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))'
-      - |
-        for RBIN in /opt/R/[0-9]*/bin/R; do
-          RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2)
-          /opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(r_minor = '$RMINOR', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" || true
-        done
+      - $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX $REBUILD_BUDGET_HOURS 2>&1
     backend_options:
       docker:
         resources:
@@ -183,25 +439,3 @@ steps:
           limits:
             memory: 18Gi
             cpu: 3000m
-
-  - name: Purge CDN cache
-    image: reg.devxy.io/docker.io/library/alpine:3.24
-    environment:
-      OTEL_R_TRACES_EXPORTER: none
-      OTEL_R_LOGS_EXPORTER: none
-      OTEL_R_METRICS_EXPORTER: none
-      BUNNYNET_API_KEY:
-        from_secret: BUNNYNET_API_KEY
-      REPO_RO_TOKEN:
-        from_secret: REPO_RO_TOKEN
-      # All hostnames on the zone share this id, so one purge covers
-      # cran.devxy.io, cran.allianceswisspass.devxy.io and cran.rpkgs.com.
-      BUNNY_PULLZONE: '3857050'
-    commands:
-      - apk add --no-cache -q bash curl git
-      - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
-      - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" "$BUNNY_PULLZONE"
-    # A rebuild that died part-way still replaced objects, and those are exactly
-    # the ones a stale edge would keep hiding, so purge either way.
-    when:
-      - status: [success, failure]