diff --git a/plugins/source-control/.claude-plugin/plugin.json b/plugins/source-control/.claude-plugin/plugin.json
index 9d54601b82..63ceb89d3d 100644
--- a/plugins/source-control/.claude-plugin/plugin.json
+++ b/plugins/source-control/.claude-plugin/plugin.json
@@ -1,7 +1,7 @@
 {
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "source-control",
-  "version": "0.61.2",
+  "version": "0.61.3",
   "description": "Git and GitHub delivery workflow: /commit (Conventional Commits + Co-authored-by trailer via safe heredoc mechanics), /pull-request (prep, create, CI monitoring, review-comment triage, merge, CI-log fetch), /babysit-prs (self-pacing fleet loop, safe by default; opt-in worker/autopilot tiers add gate-checked merge and thread resolution behind a deterministic Python engine), /babysit-loop (the loop-lane merge lane: a standing or drain loop that invokes babysit-prs per cycle, configured through repo-scoped babysit_loop_* keys on the layered source-control.md seam, with merge authority human-only until the target repo's tracked config adopts the lane, a gate-proven C2-mechanical baseline once adopted, and standing merge-rung raises binding from the team-tracked layer only, with one named exception, where an invocation line explicitly typing both the autopilot tier keyword and the dedicated raise argument --merge c3-this-run widens that single invocation's merge authority up to C3 behind a fresh independent frontier-tier resolver, while C4-structural and C5-untrusted-provenance stay unconditionally human-merge), /worktree (create, status, cleanup, audit for parallel-session isolation), /setup (check the effective commit-subject / PR-title convention merged across its config layers and the babysit-prs config, or apply, which interviews the repo and writes the convention config to a chosen layer), and /resolve-conflicts (intent-first merge/rebase conflict resolution with a semantic-conflict sweep, never --abort). The commit-subject / PR-title convention is configurable via a source-control.md config written by a re-runnable setup skill, layered across a ~/.claude user-global file, the tracked team file, and a gitignored .claude/source-control.local.md personal overlay merged per key; Conventional Commits is the default when no convention is declared.",
   "author": {
     "name": "Melodic Software",
diff --git a/plugins/source-control/CHANGELOG.md b/plugins/source-control/CHANGELOG.md
index d9907a7b36..5c8c91531b 100644
--- a/plugins/source-control/CHANGELOG.md
+++ b/plugins/source-control/CHANGELOG.md
@@ -3,6 +3,13 @@
 All notable changes to the `source-control` plugin are documented here. Format follows
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); this plugin uses semantic versioning.
 
+## [0.61.3] - 2026-09-27
+
+### Fixed
+
+- The PR-body linkage gates (`pr-body-linkage-gate.sh`, `pr-linkage-mcp-gate.sh`) agree with the `pr-contract` step again (melodic-software/ci-workflows#544). A `Refs: #N` or `Relates to: #N` line of its own (optional `owner/repo`, up to three spaces of indent) counts as linkage, so a PR that references an issue it must not close is no longer told to add a closing keyword. A closing keyword with a disclaimer among the five words before it (`not`, `never`, `no`, `without`, `deliberately`, `intentionally`, or an `n't` contraction, after the last `.!?;,`) is blocked as a negated closing reference, even beside valid linkage, because GitHub's parser still closes the issue on merge. The closing keyword is matched one line at a time, as CI does. The block messages use CI's wording and the remedy names the `Refs:` marker.
+- A body line starting with a lowercase `t` is no longer masked as indented code, and a tab-indented line now is. The validator's regex spelled the tab as `\t`, which a bash regex reads as a literal `t`, so a line such as "this PR closes #5", or a `## Fix` section whose text began with "t", was dropped from the scan.
+
 ## [0.61.2] - 2026-09-27
 
 ### Changed
diff --git a/plugins/source-control/hooks/pr-body-linkage-gate.sh b/plugins/source-control/hooks/pr-body-linkage-gate.sh
index a0e55004b4..51bdf9acfb 100755
--- a/plugins/source-control/hooks/pr-body-linkage-gate.sh
+++ b/plugins/source-control/hooks/pr-body-linkage-gate.sh
@@ -19,7 +19,10 @@
 # then an unterminated `<!--` swallowing the rest — both, in that order,
 # exactly as the validator does), the body must carry
 #   (a) a native closing keyword (`Closes/Fixes/Resolves #N`, including
-#       `owner/repo#N`) OR the literal `No linked issue` / `No related issue:`;
+#       `owner/repo#N`), a non-closing `Refs: #N` / `Relates to: #N` marker on
+#       its own line, OR the literal `No linked issue` / `No related issue:`;
+#       and no negated closing reference (`does not close #N`) anywhere, which
+#       GitHub's negation-blind parser would still close on merge;
 #   (b) four present AND non-empty contract sections — `## Summary`, `## Fix`,
 #       `## Verification`, `## Related` — where a DEEPER heading (`### …`) is
 #       that section's content, not its terminator.
@@ -290,7 +293,7 @@ block() {
   for p in "$@"; do echo "  - $p" >&2; done
   echo "Gate: ${GATE_FILE#"$REPO_ROOT/"} (its pr-contract step)." >&2
   echo "Add to the body:" >&2
-  echo "  Closes #<issue>      (or the literal line: No linked issue)" >&2
+  echo "  Closes #<issue>      (or on its own line: Refs: #<issue> to link without closing, or No linked issue)" >&2
   echo "  ## Summary" >&2
   echo "  <what and why>" >&2
   echo "  ## Fix" >&2
diff --git a/plugins/source-control/hooks/pr-body-linkage-gate.test.sh b/plugins/source-control/hooks/pr-body-linkage-gate.test.sh
index b633eec651..cc51250ff5 100755
--- a/plugins/source-control/hooks/pr-body-linkage-gate.test.sh
+++ b/plugins/source-control/hooks/pr-body-linkage-gate.test.sh
@@ -155,6 +155,10 @@ assert_block "a ## Fix that exists only inside a fenced sample is not the sectio
 assert_block "a ## Fix that exists only as indented code is not the section" "$GATED" "gh pr create -t T --body-file indented-fix.md"
 assert_block "a ## Fix that exists only in an inline span is not the section" "$GATED" "gh pr create -t T --body-file inline-fix.md"
 assert_allow "a real ## Fix is not hidden by a later fenced sample" "$GATED" "gh pr create -t T --body-file real-plus-fenced-fix.md"
+printf '%s\n' $'Closes #5\n\n## Summary\n\nx\n\n## Fix\n\n\tonly tab-indented code\n\n## Verification\n\nx\n\n## Related\n\n- x' >"$GATED/tab-indented-fix.md"
+assert_block "a tab-indented line is code, leaving ## Fix empty" "$GATED" "gh pr create -t T --body-file tab-indented-fix.md"
+assert_allow "a line starting with a lowercase t is not code" "$GATED" \
+  "$(gh_body $'this PR closes #5\n\n## Summary\n\nx\n\n## Fix\n\nthe change\n\n## Verification\n\nx\n\n## Related\n\n- x')"
 # On a line of unmatched, strictly-increasing backtick-run lengths, the
 # pair-after-collect scan must not rescan the remainder from each opener
 # (superlinear): it must finish quickly and still fail-closed on a missing
@@ -218,6 +222,61 @@ assert_allow "No linked issue marker accepted" "$GATED" \
 assert_allow "No related issue: marker accepted" "$GATED" \
   "$(gh_body $'No related issue: drift sweep'"$SECTIONS")"
 
+# Non-closing marker (ci-workflows#544): a `Refs:` / `Relates to:` line of its
+# own is linkage; anything else on that line, or no colon, is not.
+assert_allow "Refs: #N on its own line accepted" "$GATED" \
+  "$(gh_body $'Refs: #1234'"$SECTIONS")"
+assert_allow "Relates to: #N on its own line accepted" "$GATED" \
+  "$(gh_body $'Relates to: #1234'"$SECTIONS")"
+assert_allow "Refs: owner/repo#N accepted" "$GATED" \
+  "$(gh_body $'Refs: melodic-software/standards#5'"$SECTIONS")"
+assert_allow "Refs: marker indented three spaces accepted" "$GATED" \
+  "$(gh_body $'   REFS:  #5  '"$SECTIONS")"
+assert_block "Refs: marker with trailing prose is not linkage" "$GATED" \
+  "$(gh_body $'Refs: #5 for context'"$SECTIONS")"
+assert_block "Refs #N without a colon is not linkage" "$GATED" \
+  "$(gh_body $'Refs #5'"$SECTIONS")"
+assert_block "a closing keyword split across lines is not linkage" "$GATED" \
+  "$(gh_body $'Closes\n#5'"$SECTIONS")"
+
+# Negated closers: GitHub's parser ignores the negation and closes the issue
+# anyway, so CI fails them even beside valid linkage.
+assert_block "negated closer blocks" "$GATED" \
+  "$(gh_body $'This does not close #5.'"$SECTIONS")"
+assert_block "negated closer blocks even beside a Refs: marker" "$GATED" \
+  "$(gh_body $'Refs: #5\n\nThis PR deliberately never fixes #5.'"$SECTIONS")"
+assert_block "negated closer blocks even beside a real closing keyword" "$GATED" \
+  "$(gh_body $'Closes #4\n\nThis is not meant to resolve #5 here.'"$SECTIONS")"
+printf '%s\n' "Refs: #5"$'\n\n'"This doesn't close #5.$SECTIONS" >"$GATED/negated-apostrophe.md"
+assert_block "an n't contraction negates a closer" "$GATED" \
+  "gh pr create -t T --body-file negated-apostrophe.md"
+printf '%s\n' "Refs: #5"$'\n\n'$'This doesn\xe2\x80\x99t close #5.'"$SECTIONS" >"$GATED/negated-typographic.md"
+assert_block "a typographic-apostrophe contraction negates a closer" "$GATED" \
+  "gh pr create -t T --body-file negated-typographic.md"
+assert_allow "\"not only\" is affirmative" "$GATED" \
+  "$(gh_body $'This not only closes #5 but more.'"$SECTIONS")"
+assert_allow "a negation before the last comma does not reach the closer" "$GATED" \
+  "$(gh_body $'Not a draft, closes #5'"$SECTIONS")"
+assert_allow "a negation more than five words back does not reach the closer" "$GATED" \
+  "$(gh_body $'Not one two three four five closes #5'"$SECTIONS")"
+printf '%s\n' $'Closes #4\n\nThe template example `does not close #5` is shown.'"$SECTIONS" >"$GATED/negated-inline.md"
+assert_allow "a negated closer inside inline code is masked" "$GATED" \
+  "gh pr create -t T --body-file negated-inline.md"
+
+run "$GATED" "$(gh_body $'This does not close #5. We never fix #6.\nIt does not close #5 either.'"$SECTIONS")"
+if [[ "$ERR" == *'Negated closing reference ("close #5" (trigger "not"), "fix #6" (trigger "never")).'* &&
+  "$ERR" == *'Missing a native closing keyword (Closes/Fixes/Resolves #N). If this PR references an issue it must not close, put "Refs: #N"'* ]]; then
+  ok "negated-closer message lists each distinct closer once with its trigger, beside the missing-linkage message"
+else
+  fail "negated-closer or missing-linkage message wrong: $ERR"
+fi
+run "$GATED" "$(gh_body "$NO_KEYWORD")"
+if [[ "$ERR" == *'"Refs: #N" (or "Relates to: #N")'* && "$ERR" == *'Refs: #<issue>'* && "$ERR" != *'Negated'* ]]; then
+  ok "missing-linkage message and remedy name the Refs: marker"
+else
+  fail "missing-linkage message or remedy lacks the Refs: marker: $ERR"
+fi
+
 # Word boundaries: JavaScript's \b makes both of these non-matches, so a body
 # carrying only one of them must still block.
 assert_block "trailing word char after #N is not a match" "$GATED" \
diff --git a/plugins/source-control/hooks/pr-linkage-mcp-gate.sh b/plugins/source-control/hooks/pr-linkage-mcp-gate.sh
index 6226f2d06c..99fa4ae403 100755
--- a/plugins/source-control/hooks/pr-linkage-mcp-gate.sh
+++ b/plugins/source-control/hooks/pr-linkage-mcp-gate.sh
@@ -20,7 +20,10 @@
 # stripping HTML comments (terminated spans, then an unterminated `<!--`
 # swallowing the rest), the body must carry
 #   (a) a native closing keyword (`Closes/Fixes/Resolves #N`, including
-#       `owner/repo#N`) OR the literal `No linked issue` / `No related issue:`;
+#       `owner/repo#N`), a non-closing `Refs: #N` / `Relates to: #N` marker on
+#       its own line, OR the literal `No linked issue` / `No related issue:`;
+#       and no negated closing reference (`does not close #N`) anywhere, which
+#       GitHub's negation-blind parser would still close on merge;
 #   (b) four present AND non-empty contract sections — `## Summary`, `## Fix`,
 #       `## Verification`, `## Related` — where a DEEPER heading (`### ...`)
 #       is that section's content, not its terminator.
@@ -293,7 +296,7 @@ echo "BLOCKED: PR body fails this repo's PR-contract check." >&2
 for p in "${LINKAGE_PROBLEMS[@]}"; do echo "  - $p" >&2; done
 echo "Gate: ${GATE_FILE#"$REPO_ROOT/"} (its pr-contract step)." >&2
 echo "Add to the body:" >&2
-echo "  Closes #<issue>      (or the literal line: No linked issue)" >&2
+echo "  Closes #<issue>      (or on its own line: Refs: #<issue> to link without closing, or No linked issue)" >&2
 echo "  ## Summary" >&2
 echo "  <what and why>" >&2
 echo "  ## Fix" >&2
diff --git a/plugins/source-control/hooks/pr-linkage-mcp-gate.test.sh b/plugins/source-control/hooks/pr-linkage-mcp-gate.test.sh
index 612ccc8c03..e5e3e35d73 100755
--- a/plugins/source-control/hooks/pr-linkage-mcp-gate.test.sh
+++ b/plugins/source-control/hooks/pr-linkage-mcp-gate.test.sh
@@ -111,6 +111,8 @@ run 2 "markers only inside HTML comments block" "$(payload "$GATED" $CREATE $OWN
 run 2 "bare 'Closes #' with no number blocks" "$(payload "$GATED" $CREATE $OWNER $REPO "$BARE_HASH")"
 run 0 "deeper heading is section content" "$(payload "$GATED" $CREATE $OWNER $REPO "$DEEP_HEADING")"
 run 0 "owner/repo#N keyword form passes" "$(payload "$GATED" $CREATE $OWNER $REPO "$CROSS_REPO")"
+run 0 "Refs: #N non-closing marker passes" "$(payload "$GATED" $CREATE $OWNER $REPO $'Refs: #12'"$SECTIONS")"
+run 2 "negated closer blocks beside a Refs: marker" "$(payload "$GATED" $CREATE $OWNER $REPO $'Refs: #12\n\nThis does not close #12.'"$SECTIONS")"
 run 2 "create with no body field blocks (empty body)" "$(payload "$GATED" $CREATE $OWNER $REPO)"
 run 0 "update with no body field passes" "$(payload "$GATED" $UPDATE $OWNER $REPO)"
 run 2 "update with bad body blocks" "$(payload "$GATED" $UPDATE $OWNER $REPO "$NO_RELATED")"
diff --git a/plugins/source-control/hooks/pr-linkage-validator.sh b/plugins/source-control/hooks/pr-linkage-validator.sh
index da117e876e..cb0e8716e9 100644
--- a/plugins/source-control/hooks/pr-linkage-validator.sh
+++ b/plugins/source-control/hooks/pr-linkage-validator.sh
@@ -143,18 +143,88 @@ trim_to() {
   printf -v "$__plv_dest" '%s' "$s"
 }
 
-# The validator's regexes, transcribed to POSIX ERE. JavaScript's `\b` has no
-# ERE equivalent, so the probe is wrapped in newlines and the boundary is spelled
-# as an explicit non-word character on each side — `#12abc` and `unclosed #5`
-# stay non-matches, exactly as `\b` makes them. Matched against a lower-cased
-# probe in place of the `i` flag.
-KEYWORD_ERE='[^a-z0-9_](close[sd]?|fix(es|ed)?|resolve[sd]?)[[:space:]]*:?[[:space:]]*([a-z0-9_.-]+/[a-z0-9_.-]+)?#[0-9]+[^a-z0-9_]'
+# The pr-contract analyzer's linkage patterns (`scan_line` and the `no-issue`
+# test in ci-workflows .github/actions/pr-contract/run.sh), transcribed to POSIX
+# ERE and matched against lower-cased text in place of `tolower`. The closing
+# keyword and the non-closing marker are matched one line at a time, as CI
+# does; the no-issue phrase is matched over the whole body, wrapped in newlines
+# so the explicit non-word boundary also holds at either end.
+CLOSING_ERE='(close[sd]?|fix(es|ed)?|resolve[sd]?)[[:blank:]]*:?[[:blank:]]*([a-z0-9_.-]+/[a-z0-9_.-]+)?#[0-9]+'
+NON_CLOSING_ERE='^ {0,3}(refs|relates[[:blank:]]+to):[[:blank:]]*([a-z0-9_.-]+/[a-z0-9_.-]+)?#[0-9]+[[:blank:]]*$'
 NO_ISSUE_ERE='[^a-z0-9_]no (linked|related) issue[^a-z0-9_]'
+_PLV_WORD_ERE="[A-Za-z][A-Za-z']*"
 
-has_linkage() {
-  local probe
-  probe=$'\n'"${1,,}"$'\n'
-  [[ "$probe" =~ $KEYWORD_ERE || "$probe" =~ $NO_ISSUE_ERE ]]
+# CI's `negation_trigger`: the first disclaimer word among the last five words
+# between the previous `.!?;,` and the keyword, into <dest>; empty when there is
+# none. A typographic apostrophe (U+2019) counts as a straight one, and "not
+# only" is affirmative.
+negation_trigger_to() {
+  local __plv_dest="$1" tail="${2##*[.!?;,]}" lower n first i
+  local -a words=()
+  printf -v "$__plv_dest" '%s' ""
+  tail="${tail//$'\xe2\x80\x99'/\'}"
+  while [[ "$tail" =~ $_PLV_WORD_ERE ]]; do
+    words+=("${BASH_REMATCH[0]}")
+    tail="${tail#*"${BASH_REMATCH[0]}"}"
+  done
+  n=${#words[@]}
+  first=0
+  ((n > 5)) && first=$((n - 5))
+  for ((i = first; i < n; i++)); do
+    lower="${words[i],,}"
+    [[ "$lower" == not ]] && ((i + 1 < n)) && [[ "${words[i + 1],,}" == only ]] && continue
+    case "$lower" in
+    not | never | no | without | deliberately | intentionally | *"n't")
+      printf -v "$__plv_dest" '%s' "${words[i]}"
+      return 0
+      ;;
+    *) ;;
+    esac
+  done
+}
+
+# Scan the masked body for linkage. Returns 0 when it carries an un-negated
+# closing keyword, a non-closing `Refs:` / `Relates to:` marker on its own line,
+# or a no-issue opt-out. Fills LINKAGE_NEGATED with one `"<text>" (trigger
+# "<word>")` entry per distinct negated closing reference, in first-seen order.
+# A negated closer never counts as linkage, and CI fails it even when valid
+# linkage exists elsewhere, because GitHub's parser still closes the issue.
+LINKAGE_NEGATED=()
+scan_linkage() {
+  local line lower chunk m pre start len off before after text _plv_trigger i found=1
+  local -A negated_seen=()
+  LINKAGE_NEGATED=()
+  linkage::split_lines "$1"
+  for ((i = 0; i < ${#LINKAGE_LINES[@]}; i++)); do
+    line="${LINKAGE_LINES[i]}"
+    lower="${line,,}"
+    [[ "$lower" =~ $NON_CLOSING_ERE ]] && found=0
+    off=0
+    while chunk="${lower:off}" && [[ "$chunk" =~ $CLOSING_ERE ]]; do
+      m="${BASH_REMATCH[0]}"
+      # The leftmost match is also the first occurrence of its own text.
+      pre="${chunk%%"$m"*}"
+      start=$((off + ${#pre}))
+      len=${#m}
+      off=$((start + len))
+      before=""
+      ((start > 0)) && before="${lower:start-1:1}"
+      after="${lower:off:1}"
+      [[ "$before" == [a-z0-9_] || "$after" == [a-z0-9_] ]] && continue
+      text="${line:start:len}"
+      negation_trigger_to _plv_trigger "${line:0:start}"
+      if [[ -z "$_plv_trigger" ]]; then
+        found=0
+        continue
+      fi
+      [[ -n "${negated_seen[$text]:-}" ]] && continue
+      negated_seen[$text]=1
+      LINKAGE_NEGATED+=("\"${text}\" (trigger \"${_plv_trigger}\")")
+    done
+  done
+  ((found == 0)) && return 0
+  lower=$'\n'"${1,,}"$'\n'
+  [[ "$lower" =~ $NO_ISSUE_ERE ]]
 }
 
 # The four contract sections the pinned ci-workflows reusable requires
@@ -246,7 +316,8 @@ mask_markdown_code_to() {
         continue
       fi
     fi
-    if [[ "$rest" =~ ^(\ {4}|\t) ]]; then
+    # A glob, not `=~ ^(\ {4}|\t)`: in a bash regex `\t` is a literal `t`.
+    if [[ "$rest" == "    "* || "$rest" == $'\t'* ]]; then
       out+=$'\n'
       continue
     fi
@@ -318,8 +389,8 @@ mask_markdown_code_to() {
 }
 
 # Aggregate verdict: strip comments, mask Markdown code (CI does both before
-# any heading or keyword scan), then the closing-keyword half plus every
-# required section. Fills the global LINKAGE_PROBLEMS array with one line per
+# any heading or keyword scan), then every required section plus the linkage
+# half: a negated closing reference, and missing linkage. Fills the global LINKAGE_PROBLEMS array with one line per
 # problem so the author sees the full set in one pass; returns 0 when the body
 # passes (array empty), 1 otherwise. The consuming hook owns what a failure
 # DOES — block message, telemetry, exit code.
@@ -328,6 +399,7 @@ linkage::problems() {
   # `_plv_`-prefixed per the DEST-NAME CONTRACT above: an out-variable named
   # `body`, `out`, or `line` would be captured by the callee's own local.
   local _plv_stripped="" _plv_body="" _plv_content="" heading
+  local _plv_linked=0 _plv_negated=""
   strip_html_comments_to _plv_stripped "$1"
   mask_markdown_code_to _plv_body "$_plv_stripped"
   LINKAGE_PROBLEMS=()
@@ -339,8 +411,14 @@ linkage::problems() {
       LINKAGE_PROBLEMS+=("Missing a \"## ${heading}\" section.")
     fi
   done
-  has_linkage "$_plv_body" ||
-    LINKAGE_PROBLEMS+=('Missing a native closing keyword (Closes/Fixes/Resolves #N) and no "No linked issue" marker.')
+  # shellcheck disable=SC2310  # the exit IS the verdict: linkage present or not
+  scan_linkage "$_plv_body" || _plv_linked=1
+  ((${#LINKAGE_NEGATED[@]} == 0)) || {
+    printf -v _plv_negated '%s, ' "${LINKAGE_NEGATED[@]}"
+    LINKAGE_PROBLEMS+=("Negated closing reference (${_plv_negated%, }). GitHub's linkage parser ignores the surrounding words, so this still registers a closing reference and still auto-closes the issue when this PR merges. Remove the closing keyword and use \"Refs: #N\" (or \"Relates to: #N\") on its own line instead.")
+  }
+  ((_plv_linked == 0)) ||
+    LINKAGE_PROBLEMS+=('Missing a native closing keyword (Closes/Fixes/Resolves #N). If this PR references an issue it must not close, put "Refs: #N" (or "Relates to: #N") on its own line. If it relates to no GitHub issue at all, state "No linked issue" (or "No related issue:") in the body instead.')
   : >"$_PR_LINKAGE_SPLIT_FILE"
   ((${#LINKAGE_PROBLEMS[@]} == 0))
 }