fix(abi): prune the objects recorded broken, not every risky package (#211)

## Why

A dry run of the prune on `ubuntu-2404-amd64` (pipeline 12494):

```
Dry run: 3013 object(s) left in place. Re-run with --apply to delete.
```

3013 objects on one slot. The recorded verdicts say roughly **230** of that slot's objects actually fail `dyn.load()` anywhere.

The gap is the selector: the prune used `abi_cache_risky_packages()`, the source classifier, which calls **93%** of compiled packages risky where the binaries' own symbols say **4.3%**. Applying it would have deleted ~2800 working binaries and turned each into a source fallback for every client that cannot be routed by R minor.

This is the same mistake #129 fixed in the index writer. The prune was written before the per-object verdicts existed (#200, before #128/#129) and was never brought forward.

## What changed

- Selection comes from `abi_flat_safety`, every `NOT safe` row for the slot regardless of which minor it fails under, since the flat object is served to clients on all of them.
- Matching is by **object**, `<package>_<version>`, not by package name. A package can have a safe flat binary at one version and an unsafe one at another; the old code deleted both.
- The explicit `[pkg ...]` override is unchanged in behaviour and still matches by package name, which is what you want when naming a package by hand.
- The refusal guard moves with the selector. An empty result now means the slot's flat-safety backfill never ran — the exact state rhel8 was found in today — and pruning nothing while reporting success would have hidden it.

## Not changed

Still a dry run unless `PRUNE_APPLY=yes`, and still refuses to delete an object whose package CRAN no longer ships, since there would be no source to fall back to.

## Ordering note

A prune converts each deleted binary into a source fallback. bincraft #131 fixes source fallbacks of *archived* versions being advertised as binaries, which breaks `uvr` outright. That should land before any large prune, or this will manufacture new instances of it.

Reviewed-on: #211

.crow/prune-stale-flat-binaries.yaml

@@ -1,11 +1,18 @@
-# Remove flat-slot binaries belonging to ABI-risky packages, then re-index.
+# Remove flat-slot binaries recorded unable to load under some R minor, then
+# re-index.
 #
-# `upload_single_binary()` writes an ABI-risky package only to the per-minor
+# The list comes from `abi_flat_safety`, so it names the objects the binaries
-# slot, so a risky package should have no flat binary at all. Packages built
+# themselves report as broken, not the ones a source heuristic suspects. That
-# before they were classified risky still do, and the flat slot is what every
+# distinction is the whole cost of the operation: the heuristic calls 93% of
-# client that cannot be routed by R minor receives. That binary was built under
+# compiled packages risky and would delete roughly 3000 objects per slot to fix
-# whichever R was primary at the time, so it dies at load under any minor that
+# about 230.
-# dropped a symbol it uses:
+#
+# `upload_single_binary()` has written a non-portable package only to the
+# per-minor slot since v5.3.0, so this is a one-time cleanup of what was
+# uploaded before that. The flat slot is what every client that cannot be
+# routed by R minor receives, and such a binary was built under whichever R was
+# primary at the time, so it dies at load under any minor that dropped a symbol
+# it uses:
 #
 #   base64enc.so: undefined symbol: SETLENGTH
 #

local/prune-stale-flat-binaries.R

@@ -1,14 +1,23 @@
-### Remove flat-slot binaries of packages that are ABI-risky.
+### Remove flat-slot binaries recorded as unable to load under some R minor.
 #
 # Usage:
 #   Rscript local/prune-stale-flat-binaries.R <arch> <codename> [--apply] [pkg ...]
 #
-# `upload_single_binary()` writes an ABI-risky package only to the per-minor
+# The list comes from `abi_flat_safety`, written by the flat-safety backfill
-# slot, never to the flat one, so a risky package should have no flat binary at
+# from the binaries' own symbols, so it names exactly the objects that fail at
-# all. Packages built before they were classified risky still do, and the flat
+# dyn.load() somewhere. It deliberately does *not* use
-# slot is what every client that cannot be routed by R minor receives. That
+# `abi_cache_risky_packages()`: that source heuristic calls 93% of compiled
-# binary was built under whichever R was primary at the time, so it fails at
+# packages risky where the binaries say 4.3%, and pruning on it would delete
-# load under any minor that dropped a symbol it uses:
+# roughly 3000 working objects per slot to fix about 230 broken ones. Selecting
+# per object rather than per package is the same correction #129 made to the
+# index writer.
+#
+# `upload_single_binary()` has written a non-portable package only to the
+# per-minor slot since v5.3.0, so this is a one-time cleanup of objects
+# uploaded before that, not a recurring sweep. The flat slot is what every
+# client that cannot be routed by R minor receives, and such a binary was built
+# under whichever R was primary at the time, so it fails at load under any
+# minor that dropped a symbol it uses:
 #
 #   base64enc.so: undefined symbol: SETLENGTH
 #
@@ -60,27 +69,57 @@ flat_files <- relative[is_flat]
 flat_pkg <- sub("_.*$", "", flat_files)
 
 if (length(explicit) > 0L) {
-  risky <- explicit
+  doomed <- flat_files[flat_pkg %in% explicit]
-  cat(sprintf("Restricted to %d named package(s)\n", length(risky)))
+  cat(sprintf(
+    "%s/%s: %d flat binaries, %d belong to the %d named package(s)\n",
+    arch,
+    codename,
+    length(flat_files),
+    length(doomed),
+    length(explicit)
+  ))
 } else {
-  risky <- bincraft:::abi_cache_risky_packages()
+  con <- DBI::dbConnect(
-  cat(sprintf("Classifier cache reports %d risky package(s)\n", length(risky)))
+    RPostgres::Postgres(),
-  if (length(risky) == 0L) {
+    dbname = "build_metadata",
+    host = "r-binaries.devxy.io",
+    port = 15432L,
+    user = "rpkgs",
+    password = Sys.getenv("PGPASS"),
+    sslmode = "require"
+  )
+  on.exit(try(DBI::dbDisconnect(con), silent = TRUE), add = TRUE)
+
+  # Every recorded-unsafe row, whichever minor it fails under: the flat object
+  # is served to clients on all of them, so one failing minor condemns it.
+  rows <- DBI::dbGetQuery(
+    con,
+    paste0(
+      "SELECT package, version FROM abi_flat_safety ",
+      "WHERE NOT safe AND codename = $1 AND arch = $2"
+    ),
+    params = list(codename, arch)
+  )
+  if (nrow(rows) == 0L) {
     stop(
-      "The classifier cache returned nothing. Refusing to proceed: an empty risky set here is indistinguishable from an unreachable cache, and would silently prune nothing while reporting success.", # nolint
+      "No unsafe objects are recorded for this slot. Refusing to proceed: that is indistinguishable from a slot whose flat-safety backfill never ran, and pruning nothing while reporting success would hide it.", # nolint
       call. = FALSE
     )
   }
-}
 
-doomed <- flat_files[flat_pkg %in% risky]
+  # Match the object, not the package. A package can have a safe flat binary at
-cat(sprintf(
+  # one version and an unsafe one at another, and deleting both would throw
-  "%s/%s: %d flat binaries, %d belong to ABI-risky packages\n",
+  # away a working binary.
+  unsafe_objects <- sprintf("%s_%s", rows$package, rows$version)
+  doomed <- flat_files[sub("\\.tar\\.gz$", "", flat_files) %in% unsafe_objects]
+  cat(sprintf(
+    "%s/%s: %d flat binaries, %d recorded unable to load under some R minor\n",
     arch,
     codename,
     length(flat_files),
     length(doomed)
-))
+  ))
+}
 
 # Never remove the last artifact of a package. The source fallback republishes
 # the CRAN source under this key, but only for packages CRAN still ships, so