Guard mutation runs against differential under-selection

The default differential run can select fewer covered sites than exist after a
function is added or removed, forcing a manual --mutate-all rerun. Add
mutate-file.sh (auto-reruns when Selected < Covered) and clean-builds.sh
(removes worker-copy bloat), and document them plus the intrinsic upper-bound
Gherkin survivors in the architect cheat-sheet.

By specifier.

docs/architect-startup.md

@@ -20,11 +20,13 @@ the last run. If you add tests to kill survivors but the SOURCE is unchanged, a
 plain re-run reports `Killed: 0, Survived: 0, Uncovered: 0` and silently skips
 the survivors.
 
-**Always pass `--mutate-all` when re-running mutation on a file that already has
-a manifest** (especially right after adding hardening tests). New files (no
-manifest) run fully on the first pass.
-
-Canonical invocation (run from the component dir so `npm test` works):
+Prefer `swarmforge/scripts/mutate-file.sh`, which detects differential
+under-selection automatically (`Selected < Covered`) and reruns once with
+`--mutate-all`. Run it from the component directory:
+```bash
+../swarmforge/scripts/mutate-file.sh src/<file>.js --max-workers 8
+```
+Manual fallback when you must run the binary directly:
 ```bash
 node ../psf-memo-client/node_modules/mutate4javascript/bin/mutate4javascript.js \
   src/<file>.js --max-workers 8 --mutate-all
@@ -44,6 +46,14 @@ bb gherkin-mutator \
 Parse survivors with a small python one-liner over `d['results']` (filter
 `Status == 'survived'`).
 
+### Equivalent upper-bound survivors (no project filter hook)
+APS `gherkin-mutator` exposes no project-specific mutation-filter hook, so
+upper-bound steps such as `the store was read at most <max_entries> entries`
+leave survivors when the bound is mutated upward (a larger bound can never
+fail). Treat these as intrinsic equivalents, document them in the review
+summary, and do not chase them. Prefer exact counts or independently-tied
+fixture values when a bound must itself be mutatable.
+
 ## Long runs
 - Mutation and gherkin-mutator runs take 60-180s each. Use `--max-workers 8` /
   `--workers 8` and `--status-interval` so progress is visible.
@@ -56,8 +66,7 @@ Stale `tmp/acceptance` (LevelDB dirs) and `target/mutation-workers` can bloat to
 hang. `architect-startup.sh` now flags any of these over 100MB as `[FAIL]`.
 Clean them before any mutation run:
 ```bash
-rm -rf psf-memo-db/tmp/acceptance psf-memo-db/target/mutation-workers \
-       psf-memo-client/tmp/acceptance psf-memo-client/target/mutation-workers
+swarmforge/scripts/clean-builds.sh
 ```
 This cut a notifications-query mutation run from 20+ minutes to ~2 minutes.
 

swarmforge/scripts/clean-builds.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+# Remove gitignored build directories that bloat mutate4javascript worker
+# copies and make mutation runs appear to hang.
+#
+# Usage: clean-builds.sh
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
+
+for component in psf-memo-client psf-memo-db psf-memo-indexer; do
+  rm -rf "$ROOT/$component/tmp/acceptance" \
+         "$ROOT/$component/target/mutation-workers"
+done
+
+echo "clean-builds: removed tmp/acceptance and target/mutation-workers for all components"

swarmforge/scripts/mutate-file.sh

@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+# Run mutate4javascript on one source file and guard against silent
+# differential under-selection.
+#
+# The default differential run can select fewer covered mutations than exist
+# after a function is added or removed. When Selected < Covered, this wrapper
+# reruns once with --mutate-all so new mutations are not skipped.
+#
+# Run from the component directory (so the tool's `npm test` baseline works):
+#   swarmforge/scripts/mutate-file.sh src/<file>.js [options...]
+set -uo pipefail
+
+if [ "$#" -lt 1 ]; then
+  echo "usage: mutate-file.sh <source-file.js> [mutate4javascript options...]" >&2
+  exit 2
+fi
+
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
+BIN="${MUTATE4JS_BIN:-$ROOT/psf-memo-client/node_modules/mutate4javascript/bin/mutate4javascript.js}"
+
+if [ ! -f "$BIN" ]; then
+  echo "mutate-file: cannot find mutate4javascript at $BIN" >&2
+  exit 1
+fi
+
+SOURCE="$1"
+shift
+
+already_all=0
+for arg in "$@"; do
+  [ "$arg" = "--mutate-all" ] && already_all=1
+done
+
+mkdir -p "$ROOT/tmp"
+OUT="$(mktemp "$ROOT/tmp/mutate-file.XXXXXX")"
+trap 'rm -f "$OUT"' EXIT
+
+node "$BIN" "$SOURCE" "$@" 2>&1 | tee "$OUT"
+status=${PIPESTATUS[0]}
+
+if [ "$already_all" -eq 0 ]; then
+  covered="$(grep -oE 'Covered mutation sites: [0-9]+' "$OUT" | grep -oE '[0-9]+' | tail -1)"
+  selected="$(grep -oE 'Selected mutation sites: [0-9]+' "$OUT" | grep -oE '[0-9]+' | tail -1)"
+  if [ -n "${covered:-}" ] && [ -n "${selected:-}" ] && [ "$selected" -lt "$covered" ]; then
+    echo "" >&2
+    echo "mutate-file: selected $selected of $covered covered sites (differential under-selection); rerunning with --mutate-all" >&2
+    node "$BIN" "$SOURCE" "$@" --mutate-all
+    status=$?
+  fi
+fi
+
+exit "$status"