fix(source-control): emit in_reply_to_id for threaded inline PR review replies

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": "0.26.10",
+  "version": "0.26.11",
   "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 merge-rung raises binding from the team-tracked layer only), /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 — interview the repo and write 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",

plugins/source-control/CHANGELOG.md

@@ -3,6 +3,22 @@
 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.
 
+## [0.26.11]
+
+### Fixed
+
+- **`fetch-all-pr-comments.sh` now emits `in_reply_to_id` for inline review comments (#587).** The
+  script's unified schema never projected the GitHub REST field that marks an inline review comment
+  as a threaded reply, so any caller reading the script's own output saw the key absent (surfacing as
+  `None`/`null` in downstream tooling) even for comments GraphQL confirmed were properly threaded
+  replies. Reproduced against live PR #563 data: the raw `pulls/<pr>/comments` response correctly
+  carries `in_reply_to_id` on reply comments — the script's `jq` projection for the inline surface
+  simply dropped it. Added `in_reply_to_id: .in_reply_to_id` to the inline mapping (sourced from the
+  same raw field GraphQL cross-checks against) and `in_reply_to_id: null` to the general/review
+  mappings, which have no reply-parent concept on their surfaces. Additive schema change — existing
+  consumers that don't read the new key are unaffected. Regression-tested with a threaded-reply
+  fixture.
+
 ## [0.26.10]
 
 ### Changed

plugins/source-control/scripts/fetch-all-pr-comments.sh

@@ -8,7 +8,19 @@
 #   3. Inline review comments (line-anchored on the diff)
 #
 # Output: unified JSON array sorted by creation date. Each object:
-#   {"id":N,"type":"general|review|inline","author":"login","body":"...","path":"...","line":N,"created_at":"ISO"}
+#   {"id":N,"type":"general|review|inline","author":"login","body":"...","path":"...","line":N,"created_at":"ISO","in_reply_to_id":N|null}
+#
+# in_reply_to_id is populated ONLY for type "inline" (the only GitHub REST
+# surface that threads via this field — general/review comments have no
+# reply-parent concept and always carry null). GitHub sets it to the id of
+# the THREAD-OPENING comment, not the immediately-preceding reply: every
+# reply in a thread carries the same in_reply_to_id (empirically verified
+# against live review-thread data — every referenced parent in that set was
+# itself a root comment), so grouping by `in_reply_to_id // id` recovers
+# thread membership directly. This does not change the documented REST
+# cross-check in reference/review-discipline.md / skills/pull-request/SKILL.md
+# — this script's schema was the only thing missing the field; the raw API
+# was always correct.
 #
 # Usage:
 #   fetch-all-pr-comments.sh <pr-number>
@@ -39,7 +51,7 @@ set -uo pipefail # -e omitted: gh api failures explicitly guarded with || { exit
 PR_NUMBER=""
 
 usage() {
-  sed -n '2,27p' "${BASH_SOURCE[0]}" | sed 's/^# \{0,1\}//'
+  sed -n '2,39p' "${BASH_SOURCE[0]}" | sed 's/^# \{0,1\}//'
   exit 0
 }
 
@@ -127,7 +139,8 @@ if ! GENERAL=$(printf '%s' "$GENERAL_RAW" | jq -c '
       body: .body,
       path: null,
       line: null,
-      created_at: .created_at
+      created_at: .created_at,
+      in_reply_to_id: null
     }
 ' 2>/dev/null); then
   printf 'fetch-all-pr-comments: jq failed parsing issues/%s/comments response\n' "$PR_NUMBER" >&2
@@ -151,7 +164,8 @@ if ! REVIEWS=$(printf '%s' "$REVIEWS_RAW" | jq -c '
       body: .body,
       path: null,
       line: null,
-      created_at: (.submitted_at // .created_at)
+      created_at: (.submitted_at // .created_at),
+      in_reply_to_id: null
     }
 ' 2>/dev/null); then
   printf 'fetch-all-pr-comments: jq failed parsing pulls/%s/reviews response\n' "$PR_NUMBER" >&2
@@ -174,7 +188,8 @@ if ! INLINE=$(printf '%s' "$INLINE_RAW" | jq -c '
       body: .body,
       path: .path,
       line: (.line // .original_line),
-      created_at: .created_at
+      created_at: .created_at,
+      in_reply_to_id: .in_reply_to_id
     }
 ' 2>/dev/null); then
   printf 'fetch-all-pr-comments: jq failed parsing pulls/%s/comments response\n' "$PR_NUMBER" >&2

plugins/source-control/scripts/fetch-all-pr-comments.test.sh

@@ -68,15 +68,17 @@ cat >"$FIXTURE_INLINE" <<'JSON'
     "path": "src/Auth.cs",
     "line": 42,
     "original_line": null,
+    "in_reply_to_id": null,
     "created_at": "2026-05-20T09:30:00Z"
   },
   {
     "id": 3002,
-    "user": {"login": "codex[bot]"},
+    "user": {"login": "kyle-sexton"},
     "body": "Stale count reference",
     "path": "src/Counter.cs",
     "line": null,
     "original_line": 15,
+    "in_reply_to_id": 3001,
     "created_at": "2026-05-20T12:00:00Z"
   }
 ]
@@ -158,6 +160,23 @@ assert_eq "inline comments have path" "2" "$inline_with_path"
 fallback_line=$(printf '%s' "$out" | jq '[.[] | select(.id == 3002)] | .[0].line')
 assert_eq "original_line fallback" "15" "$fallback_line"
 
+# Case 6a: a top-level inline comment reports in_reply_to_id null (regression
+# guard for #587 — the field must be sourced from the raw API response, not
+# silently dropped by the jq projection)
+top_level_reply_id=$(printf '%s' "$out" | jq '[.[] | select(.id == 3001)] | .[0].in_reply_to_id')
+assert_eq "top-level inline comment has null in_reply_to_id" "null" "$top_level_reply_id"
+
+# Case 6b: a threaded inline reply reports the true parent id
+threaded_reply_id=$(printf '%s' "$out" | jq '[.[] | select(.id == 3002)] | .[0].in_reply_to_id')
+assert_eq "threaded inline reply reports parent id" "3001" "$threaded_reply_id"
+
+# Case 6c: general and review comments (no reply-parent concept) carry null
+general_reply_id=$(printf '%s' "$out" | jq '[.[] | select(.id == 1001)] | .[0].in_reply_to_id')
+assert_eq "general comment has null in_reply_to_id" "null" "$general_reply_id"
+
+review_reply_id=$(printf '%s' "$out" | jq '[.[] | select(.id == 2001)] | .[0].in_reply_to_id')
+assert_eq "review comment has null in_reply_to_id" "null" "$review_reply_id"
+
 # Case 7: gh api failure exits 2
 FAIL_STUB="$TEST_TMPDIR/bin-fail/gh"
 mkdir -p "$TEST_TMPDIR/bin-fail"