From 0a58b88cd604d3af05077a670380bdfa0e5e0759 Mon Sep 17 00:00:00 2001
From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com>
Date: Mon, 7 Sep 2026 03:48:39 +0100
Subject: [PATCH 1/5] fix(ci): gate current Hypatia SARIF and preserve baseline
 validation

---
 .github/workflows/hypatia-scan-reusable.yml | 41 ++++++++++++++++++---
 scripts/tests/hypatia-blocking-gate-test.sh | 41 +++++++++++++++++++++
 2 files changed, 77 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/hypatia-scan-reusable.yml b/.github/workflows/hypatia-scan-reusable.yml
index bc486448f..388fd7b2c 100644
--- a/.github/workflows/hypatia-scan-reusable.yml
+++ b/.github/workflows/hypatia-scan-reusable.yml
@@ -7,7 +7,7 @@ on:
   workflow_call:
     inputs:
       block-on-high:
-        description: Refuse any high or critical finding, without requiring a baseline
+        description: Refuse current high or critical findings after validated baseline filtering; no baseline is required
         type: boolean
         required: false
         default: false
@@ -246,7 +246,7 @@ jobs:
           retention-days: 90
 
       - name: Gate on baseline (blocking when a baseline is committed)
-        if: steps.scan.outputs.findings_count > 0
+        if: '!inputs.block-on-high && steps.scan.outputs.findings_count > 0'
         run: |
           # Wave-8 gate promotion: when the calling repo commits a
           # .hypatia-baseline.json (schema: .machine_readable/hypatia-baseline.
@@ -271,12 +271,43 @@ jobs:
         if: inputs.block-on-high
         run: |
           set -euo pipefail
-          count=$(jq '[.[] | select(.severity == "high" or .severity == "critical")] | length' hypatia-findings.json)
+          # Use the scanner's authoritative SARIF projection, after the same
+          # baseline filter used for the Security tab. Raw JSON also contains
+          # code_scanning_alerts: historical GitHub alert summaries, including
+          # alerts fixed by this PR that cannot close until it reaches main.
+          # Hypatia already excludes those meta-rules in its SARIF renderer.
+          # Counting them here creates a circular merge dependency. Raw JSON
+          # remains in the artifact for the fleet's historical-debt review.
+          # Validate a present baseline even when there are no current errors.
+          # Advisory mode validates without gating historical meta-findings;
+          # the final filtered SARIF below supplies the blocking decision.
+          if [ -f .hypatia-baseline.json ]; then
+            if [ ! -f scripts/apply-baseline.sh ]; then
+              echo "::error::A committed baseline requires scripts/apply-baseline.sh"
+              exit 2
+            fi
+            bash scripts/apply-baseline.sh hypatia-findings.relativized.json .hypatia-baseline.json advisory >/dev/null
+          fi
+          # Missing/truncated output must never become a clean security gate.
+          if ! jq -se '
+            length == 1 and (.[0] |
+              .version == "2.1.0" and (.runs | type == "array" and length > 0) and
+              all(.runs[];
+                .tool.driver.name == "Hypatia" and
+                (.results | type == "array") and
+                all(.results[];
+                  type == "object" and (.ruleId | type == "string" and length > 0) and
+                  (.level as $level | ["error", "warning", "note", "none"] | index($level) != null))))
+          ' hypatia.sarif >/dev/null; then
+            echo "::error::Hypatia did not produce one valid SARIF findings document"
+            exit 2
+          fi
+          count=$(jq '[.runs[].results[] | select(.level == "error")] | length' hypatia.sarif)
           if [ "$count" -gt 0 ]; then
-            echo "::error::Hypatia found $count high or critical finding(s); see the scan artifact"
+            echo "::error::Hypatia found $count current high or critical finding(s); see the SARIF artifact"
             exit 1
           fi
-          echo "Hypatia blocking gate: no high or critical findings"
+          echo "Hypatia blocking gate: no current high or critical findings after baseline filtering"
 
       - name: Check for critical issues (ADVISORY — does not gate)
         if: '!inputs.block-on-high && steps.scan.outputs.critical > 0'
diff --git a/scripts/tests/hypatia-blocking-gate-test.sh b/scripts/tests/hypatia-blocking-gate-test.sh
index 7d383e73f..b52063a8b 100755
--- a/scripts/tests/hypatia-blocking-gate-test.sh
+++ b/scripts/tests/hypatia-blocking-gate-test.sh
@@ -25,6 +25,13 @@ check() {
     printf '%s' "$payload" > hypatia-findings.json
   fi
   if bash validate.sh >result.log 2>&1; then
+    # Fixture for the authoritative renderer's severity projection. The
+    # separate controls below exercise malformed SARIF and historical echoes.
+    jq '{version:"2.1.0", runs:[{tool:{driver:{name:"Hypatia"}}, results:
+      [.[] | {ruleId:"hypatia/control/planted", level:
+        (if .severity == "critical" or .severity == "high" then "error"
+         elif .severity == "medium" then "warning" else "note" end)}]}]}' \
+      hypatia-findings.json > hypatia.sarif
     if bash gate.sh >>result.log 2>&1; then actual=0; else actual=$?; fi
   else
     actual=$?
@@ -48,3 +55,37 @@ check 'null is not a findings array' 2 'null'
 check 'unknown severity refuses' 2 '[{"severity":"unknown"}]'
 check 'missing severity refuses' 2 '[{}]'
 check 'multiple JSON documents refuse' 2 '[] []'
+
+sarif_check() {
+  local name=$1 expected=$2 payload=$3 actual
+  if [[ "$payload" = MISSING ]]; then
+    rm -f hypatia.sarif
+  else
+    printf '%s' "$payload" > hypatia.sarif
+  fi
+  if bash gate.sh >result.log 2>&1; then actual=0; else actual=$?; fi
+  if [[ "$actual" -ne "$expected" ]]; then
+    printf 'FAIL: %s: expected %s, got %s\n' "$name" "$expected" "$actual"
+    cat result.log
+    exit 1
+  fi
+  printf 'PASS: %s\n' "$name"
+}
+clean='{"version":"2.1.0","runs":[{"tool":{"driver":{"name":"Hypatia"}},"results":[]}]}'
+printf '%s' '[{"rule_module":"code_scanning_alerts","type":"CSA003","severity":"high"}]' > hypatia-findings.json
+sarif_check 'historical echo does not block a clean current scan' 0 "$clean"
+sarif_check 'missing SARIF refuses' 2 MISSING
+sarif_check 'empty SARIF refuses' 2 ''
+sarif_check 'truncated SARIF refuses' 2 '{"version":'
+sarif_check 'multiple SARIF documents refuse' 2 "$clean $clean"
+sarif_check 'empty runs refuse' 2 '{"version":"2.1.0","runs":[]}'
+sarif_check 'missing results refuse' 2 '{"version":"2.1.0","runs":[{"tool":{"driver":{"name":"Hypatia"}}}]}'
+sarif_check 'unknown result level refuses' 2 '{"version":"2.1.0","runs":[{"tool":{"driver":{"name":"Hypatia"}},"results":[{"ruleId":"control","level":"unknown"}]}]}'
+printf '%s' '[]' > .hypatia-baseline.json
+sarif_check 'baseline without validator refuses' 2 "$clean"
+mkdir scripts
+cp "$repo/scripts/apply-baseline.sh" scripts/apply-baseline.sh
+printf '%s' '[]' > hypatia-findings.relativized.json
+sarif_check 'valid baseline accepted' 0 "$clean"
+printf '%s' '{}' > .hypatia-baseline.json
+sarif_check 'malformed baseline refuses even without findings' 2 "$clean"

From 3bc7de609f3fea6ddb5d584010e7568fba40686f Mon Sep 17 00:00:00 2001
From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com>
Date: Mon, 7 Sep 2026 03:56:16 +0100
Subject: [PATCH 2/5] fix(ci): require evidence that baseline filtering
 completed

---
 .github/workflows/hypatia-scan-reusable.yml   |   7 +++++++
 scripts/filter-sarif-by-baseline.sh           | Bin 4619 -> 4765 bytes
 .../tests/filter-sarif-by-baseline-test.sh    |  16 ++++++++++++++++
 scripts/tests/hypatia-blocking-gate-test.sh   |   2 ++
 4 files changed, 25 insertions(+)

diff --git a/.github/workflows/hypatia-scan-reusable.yml b/.github/workflows/hypatia-scan-reusable.yml
index 388fd7b2c..08db03550 100644
--- a/.github/workflows/hypatia-scan-reusable.yml
+++ b/.github/workflows/hypatia-scan-reusable.yml
@@ -182,6 +182,7 @@ jobs:
           sparse-checkout-cone-mode: false
 
       - name: Filter SARIF through the baseline before upload
+        id: filter_baseline
         if: always()
         run: |
           # ⚠ WITHOUT THIS, ACKNOWLEDGING A FINDING DOES NOT UNBLOCK ANYTHING.
@@ -269,6 +270,8 @@ jobs:
       - name: Block high and critical findings when requested
         id: blocking-findings
         if: inputs.block-on-high
+        env:
+          HYPATIA_BASELINE_FILTERED: ${{ steps.filter_baseline.outputs.filtered }}
         run: |
           set -euo pipefail
           # Use the scanner's authoritative SARIF projection, after the same
@@ -287,6 +290,10 @@ jobs:
               exit 2
             fi
             bash scripts/apply-baseline.sh hypatia-findings.relativized.json .hypatia-baseline.json advisory >/dev/null
+            if [ "${HYPATIA_BASELINE_FILTERED:-}" != "true" ]; then
+              echo "::error::Baseline validation passed but SARIF filtering did not complete"
+              exit 2
+            fi
           fi
           # Missing/truncated output must never become a clean security gate.
           if ! jq -se '
diff --git a/scripts/filter-sarif-by-baseline.sh b/scripts/filter-sarif-by-baseline.sh
index 98d61b2df1b36d5be7e6f62faf4fa22614b4e01c..406cf28b5aca8c27dca2a0a9a2d3acbbdd7dc4ce 100755
GIT binary patch
delta 154
zcmeBHnX9_t5|2x?f^L<9l1jC^XNX6rQ@np@NI+<am2Rz)LaahfjY4X2M!tf2T4qj3
iYEf#6ZAnpSs=9)m9Z(07hRtVq>{&giVNz&_5*GlV?k`*b

delta 16
XcmbQM+O4wT63^s)+}xYhdG%NUH-rU&

diff --git a/scripts/tests/filter-sarif-by-baseline-test.sh b/scripts/tests/filter-sarif-by-baseline-test.sh
index 1a67fdbff..aa0bf07ef 100755
--- a/scripts/tests/filter-sarif-by-baseline-test.sh
+++ b/scripts/tests/filter-sarif-by-baseline-test.sh
@@ -93,5 +93,21 @@ echo '[{"severity":"low","rule_module":"code_safety","type":"unwrap_without_chec
 bash "$S" "$T/in.sarif" "$T/f.json" "$T/b.json" "$T/out.sarif" >/dev/null 2>&1
 ck "an empty SARIF survives filtering" 0 "$(count "$T/out.sarif")"
 
+# The blocking workflow needs affirmative evidence that filtering completed.
+export GITHUB_OUTPUT="$T/filter-output"
+: > "$GITHUB_OUTPUT"
+mk_sarif; mk_findings
+bash "$S" "$T/in.sarif" "$T/f.json" "$T/b.json" "$T/out.sarif" > "$T/filter.log" 2>&1
+ck "successful filtering is reported" 'filtered=true' "$(cat "$GITHUB_OUTPUT")"
+: > "$GITHUB_OUTPUT"
+bash "$S" "$T/in.sarif" "$T/f.json" "$T/bad.json" "$T/out.sarif" > "$T/filter.log" 2>&1
+ck "invalid baseline cannot report filtering success" '' "$(cat "$GITHUB_OUTPUT")"
+: > "$GITHUB_OUTPUT"
+APPLY_BASELINE="$T/missing-validator" bash "$S" "$T/in.sarif" "$T/f.json" "$T/b.json" "$T/out.sarif" > "$T/filter.log" 2>&1
+ck "missing validator cannot report filtering success" '' "$(cat "$GITHUB_OUTPUT")"
+: > "$GITHUB_OUTPUT"
+bash "$S" "$T/in.sarif" "$T/empty.json" "$T/b.json" "$T/out.sarif" > "$T/filter.log" 2>&1
+ck "completed zero-match filtering is reported" 'filtered=true' "$(cat "$GITHUB_OUTPUT")"
+
 printf '\n  %d passed, %d failed\n' "$pass" "$fail"
 [ "$fail" -eq 0 ]
diff --git a/scripts/tests/hypatia-blocking-gate-test.sh b/scripts/tests/hypatia-blocking-gate-test.sh
index b52063a8b..031a9f78d 100755
--- a/scripts/tests/hypatia-blocking-gate-test.sh
+++ b/scripts/tests/hypatia-blocking-gate-test.sh
@@ -86,6 +86,8 @@ sarif_check 'baseline without validator refuses' 2 "$clean"
 mkdir scripts
 cp "$repo/scripts/apply-baseline.sh" scripts/apply-baseline.sh
 printf '%s' '[]' > hypatia-findings.relativized.json
+sarif_check 'unconfirmed baseline filtering refuses' 2 "$clean"
+export HYPATIA_BASELINE_FILTERED=true
 sarif_check 'valid baseline accepted' 0 "$clean"
 printf '%s' '{}' > .hypatia-baseline.json
 sarif_check 'malformed baseline refuses even without findings' 2 "$clean"

From 3c3acc19951b39c8ffe68b917aae4cc2e5b232e5 Mon Sep 17 00:00:00 2001
From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com>
Date: Mon, 7 Sep 2026 08:46:15 +0100
Subject: [PATCH 3/5] Pin the SARIF filter to the audited compatible revision

---
 .github/workflows/hypatia-scan-reusable.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/hypatia-scan-reusable.yml b/.github/workflows/hypatia-scan-reusable.yml
index 08db03550..5fc5b453f 100644
--- a/.github/workflows/hypatia-scan-reusable.yml
+++ b/.github/workflows/hypatia-scan-reusable.yml
@@ -175,7 +175,9 @@ jobs:
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           repository: hyperpolymath/standards
-          ref: main
+          # This revision includes the filter's successful-completion output.
+          # Keep the helper immutable and compatible with the strict gate.
+          ref: 3bc7de609f3fea6ddb5d584010e7568fba40686f
           path: .standards-checkout
           sparse-checkout: |
             scripts

From 6b0bfce648cf9b306693cea0af0bd5f6fc9fea0f Mon Sep 17 00:00:00 2001
From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com>
Date: Mon, 7 Sep 2026 09:34:43 +0100
Subject: [PATCH 4/5] Match baseline globs literally and reject invalid gate
 configuration

---
 scripts/apply-baseline.sh            | 22 +++++++++++++++----
 scripts/tests/apply-baseline-test.sh | 33 +++++++++++++++++++++++++---
 2 files changed, 48 insertions(+), 7 deletions(-)

diff --git a/scripts/apply-baseline.sh b/scripts/apply-baseline.sh
index 0916c7bfc..72c1568df 100755
--- a/scripts/apply-baseline.sh
+++ b/scripts/apply-baseline.sh
@@ -39,6 +39,14 @@ FINDINGS_FILE="${1:-}"
 BASELINE_FILE="${2:-}"
 MODE="${3:-advisory}"
 BLOCKING_THRESHOLD="${BLOCKING_THRESHOLD:-high}"
+case "$MODE" in
+  advisory|blocking) ;;
+  *) echo "error: invalid baseline mode: $MODE" >&2; exit 2 ;;
+esac
+case "$BLOCKING_THRESHOLD" in
+  info|low|medium|high|critical) ;;
+  *) echo "error: invalid blocking threshold: $BLOCKING_THRESHOLD" >&2; exit 2 ;;
+esac
 TODAY="$(date -u +%Y-%m-%d)"
 
 if [[ -z "$FINDINGS_FILE" || -z "$BASELINE_FILE" ]]; then
@@ -152,6 +160,15 @@ EXPIRED_COUNT=$((EXPIRED_COUNT - ACTIVE_COUNT))
 ANNOTATED="$(jq -n \
   --argjson findings "$FINDINGS_JSON" \
   --argjson baseline "$ACTIVE_BASELINE" '
+  # Tokenise the two supported wildcards; every other character is literal.
+  # No sentinel substitution: a real filename may contain DOUBLESTAR.
+  def glob_regex:
+    [scan("\\*\\*|\\*|[^*]")
+     | if . == "**" then ".*"
+       elif . == "*" then "[^/]*"
+       elif inside(".\\+?^$()[]{}|") then "\\" + .
+       else . end]
+    | "\\A" + join("") + "\\z";
   # Two captures are essential here:
   #   `f as $finding` — without this, references like `f.file` inside the
   #   select() get re-evaluated against the current baseline entry (the
@@ -177,10 +194,7 @@ ANNOTATED="$(jq -n \
             | $pat != null
             and ($finding.file | test(
               $pat
-              | gsub("\\*\\*"; "DOUBLESTAR")
-              | gsub("\\*"; "[^/]*")
-              | gsub("DOUBLESTAR"; ".*")
-              | "^" + . + "$"
+              | glob_regex
             ))
           )
         )
diff --git a/scripts/tests/apply-baseline-test.sh b/scripts/tests/apply-baseline-test.sh
index 3bf2f87f6..dc5a1c13b 100755
--- a/scripts/tests/apply-baseline-test.sh
+++ b/scripts/tests/apply-baseline-test.sh
@@ -15,7 +15,7 @@
 set -euo pipefail
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
-APPLY="$SCRIPT_DIR/../apply-baseline.sh"
+APPLY="${APPLY_BASELINE_TARGET:-$SCRIPT_DIR/../apply-baseline.sh}"
 WORK="$(mktemp -d)"
 trap 'rm -rf "$WORK"' EXIT
 
@@ -25,7 +25,7 @@ fail=0
 assert_status() {
   local label="$1" findings="$2" baseline="$3" expected="$4"
   local got
-  got=$("$APPLY" "$findings" "$baseline" advisory 2>/dev/null \
+  got=$(bash "$APPLY" "$findings" "$baseline" advisory \
     | jq -r '"\(.findings_suppressed | length),\(.findings_kept | length)"')
   if [ "$got" = "$expected" ]; then
     echo "PASS: $label  (suppressed,kept=$got)"
@@ -98,7 +98,7 @@ assert_status "hyphenated HYP-S009 rule type is valid and matches" \
 cat > "$WORK/baseline6-invalid.json" <<'EOF'
 [{"severity":"medium","rule_module":"implementation_inside_canon","type":"HYP--S009","file":"spec/Cargo.toml"}]
 EOF
-if "$APPLY" "$WORK/findings6.json" "$WORK/baseline6-invalid.json" advisory >/dev/null 2>&1; then
+if bash "$APPLY" "$WORK/findings6.json" "$WORK/baseline6-invalid.json" advisory >/dev/null 2>&1; then
   echo "FAIL: malformed HYP--S009 rule type was accepted"
   fail=$((fail + 1))
 else
@@ -106,6 +106,33 @@ else
   pass=$((pass + 1))
 fi
 
+# Regex metacharacters and the former sentinel must remain literal glob text.
+for literal in 'src/foo.rs' 'src/a+b(1)[2]{x}^$?.rs' 'src/DOUBLESTAR.rs'; do
+  jq -n --arg file "$literal" '[{severity:"high",rule_module:"cicd_rules",type:"banned_language_file",file:$file}]' > "$WORK/literal.json"
+  jq -n --arg pattern "$literal" '[{severity:"high",rule_module:"cicd_rules",type:"banned_language_file",file_pattern:$pattern}]' > "$WORK/literal-baseline.json"
+  assert_status "literal glob matches itself: $literal" "$WORK/literal.json" "$WORK/literal-baseline.json" "1,0"
+done
+jq -n '[{severity:"high",rule_module:"cicd_rules",type:"banned_language_file",file_pattern:"src/foo.rs"}]' > "$WORK/literal-baseline.json"
+for unrelated in 'src/fooXrs' $'src/foo.rs\nother'; do
+  jq -n --arg file "$unrelated" '[{severity:"high",rule_module:"cicd_rules",type:"banned_language_file",file:$file}]' > "$WORK/unrelated.json"
+  assert_status "literal glob rejects unrelated path" "$WORK/unrelated.json" "$WORK/literal-baseline.json" "0,1"
+done
+
+assert_invalid_option() {
+  local label="$1" mode="$2" threshold="$3" status=0
+  BLOCKING_THRESHOLD="$threshold" bash "$APPLY" "$WORK/findings1.json" "$WORK/empty.json" "$mode" > "$WORK/invalid.out" 2> "$WORK/invalid.err" || status=$?
+  if [ "$status" -eq 2 ]; then
+    echo "PASS: $label rejected as invalid configuration"
+    pass=$((pass + 1))
+  else
+    echo "FAIL: $label returned $status (expected 2)"
+    cat "$WORK/invalid.err"
+    fail=$((fail + 1))
+  fi
+}
+assert_invalid_option "invalid mode" bypass high
+assert_invalid_option "invalid threshold" blocking nonsense
+
 echo
 echo "Total: $pass passed, $fail failed"
 [ "$fail" -eq 0 ]

From 469605210e767ee94d1c7a9c13cb6a1d0a78cad1 Mon Sep 17 00:00:00 2001
From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com>
Date: Mon, 7 Sep 2026 09:36:14 +0100
Subject: [PATCH 5/5] Pin shared SARIF filter to validated literal baseline
 matcher

---
 .github/workflows/hypatia-scan-reusable.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/hypatia-scan-reusable.yml b/.github/workflows/hypatia-scan-reusable.yml
index 5fc5b453f..913d0fc2d 100644
--- a/.github/workflows/hypatia-scan-reusable.yml
+++ b/.github/workflows/hypatia-scan-reusable.yml
@@ -175,9 +175,9 @@ jobs:
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           repository: hyperpolymath/standards
-          # This revision includes the filter's successful-completion output.
+          # Includes the filter's completion output and literal-glob matching.
           # Keep the helper immutable and compatible with the strict gate.
-          ref: 3bc7de609f3fea6ddb5d584010e7568fba40686f
+          ref: 6b0bfce648cf9b306693cea0af0bd5f6fc9fea0f
           path: .standards-checkout
           sparse-checkout: |
             scripts