LightbridgeLab · sebastientaggart · Jun 21, 2026 · Jun 21, 2026
diff --git a/.agents/skills/deploy/SKILL.md b/.agents/skills/deploy/SKILL.md
@@ -65,9 +65,14 @@ For each PR number found, retrieve the PR body:
 gh pr view <N> --json number,title,body
 ```
 
-Extract `Issue #N` and `Closes #N` references from PR bodies. Compile:
+Extract closing keywords **separately** from context references — do **not** merge them into a single set:
+
+- **Close set** — the union of every `Closes #N` line across all constituent PR bodies. These issues will auto-close when the release PR merges into `main`. Record, per constituent PR, the exact `Closes #N` lines it contained so they can be reproduced verbatim in the release PR body.
+- **Reference set** — issues mentioned only via `Related to #N`, or via the legacy `Issue #N` form. These are context links and will **not** close. Legacy `Issue #N` carries no recoverable close-intent, so it stays in the reference set rather than being guessed into the close set; the HUMAN GATE surfaces it so you can manually close any straggler that should have been a `Closes`.
+
+Compile:
 - List of PRs included (number + title)
-- List of issues linked to those PRs
+- Close set and reference set, kept distinct
 
 ### Check for open unmerged PRs
 
@@ -139,7 +144,7 @@ Find the previous tag to determine the range:
 git describe --abbrev=0 <version-tag>^ 2>/dev/null
 ```
 
-Use the PR/issue list already computed in Step 2. If the version bump added new commits, re-fetch if needed.
+Use the PR list, close set, and reference set already computed in Step 2. If the version bump added new commits, re-fetch if needed.
 
 ---
 
@@ -154,10 +159,13 @@ PRs included:
   #17 — Add /docs directory
   #18 — Fix checkout runtime error
 
-Issues that will close:
+Issues that will close on merge (Closes #N, reproduced verbatim from constituent PRs):
   #14 — Add /docs directory
   #15 — Fix checkout runtime error
 
+Issues referenced but NOT closing (Related to #N / legacy Issue #N — confirm none of these should actually close):
+  #20 — Tighten error copy on the upload form
+
 Have you tested all of the above on preview? Type 'release' to confirm.
 ```
 
@@ -186,8 +194,12 @@ PRs included:
 
 Closes #14
 Closes #15
+
+Related to #20
 ```
 
+Reproduce **every** `Closes #N` line from the close set computed in Step 2 — verbatim, one per line, omitting none. Add a `Related to #N` line for each issue in the reference set so the links appear on the release PR without triggering an auto-close. If the reference set is empty, omit the `Related to` lines entirely.
+
 Then create the PR (do NOT use `--body`, `--body-file -`, or heredocs):
 
 ```bash
@@ -254,4 +266,4 @@ After the command runs, note the release URL from the output.
 Tell the user:
 
 > "Released vX.Y.Z. Issues #N, #M closed automatically. GitHub Release vX.Y.Z created at `<url>`. Run `make deploy-prod` to ship to production."
-<!-- generated by CodeCannon/sync.py | skill: deploy | adapter: codex | hash: 28d0ff7c | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
+<!-- generated by CodeCannon/sync.py | skill: deploy | adapter: codex | hash: 29b237ab | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
diff --git a/.agents/skills/status/SKILL.md b/.agents/skills/status/SKILL.md
@@ -258,7 +258,7 @@ gh pr list --state open \
 Group issues into three buckets:
 
 - **Done** — `state: closed`
-- **In progress** — `state: open` AND the issue number appears in any open PR body (look for `#<number>`, `closes #<number>`, `fixes #<number>`, `issue #<number>`)
+- **In progress** — `state: open` AND the issue number appears in any open PR body (look for `#<number>`, `closes #<number>`, `fixes #<number>`, `related to #<number>`, `issue #<number>`)
 - **Not started** — `state: open` AND no open PR body references the issue number
 
 For in-progress issues, derive health badges from the linked PR using the same rules as Step 4a (check status, review decision, draft, conflict).
@@ -366,4 +366,4 @@ Do not post, comment, write files, or take any action. Output only.
 - If `gh` is unauthenticated or any fetch fails, report the error and stop immediately.
 - Do not retry failed commands.
 - Strip the leading `@` from the subject when passing to `gh` flags that do not accept it.
-<!-- generated by CodeCannon/sync.py | skill: status | adapter: codex | hash: 03a99a92 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
+<!-- generated by CodeCannon/sync.py | skill: status | adapter: codex | hash: 1cdf5396 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
diff --git a/.agents/skills/submit-for-review/SKILL.md b/.agents/skills/submit-for-review/SKILL.md
@@ -122,7 +122,9 @@ If the output is non-empty, inform the user: "CODEOWNERS file detected — GitHu
 
 PR target branch: `dev`
 
-Use `Issue #<number>` as the issue reference — the issue stays open until `/deploy` promotes to `main`.
+Use `Closes #<number>` as the issue reference when this PR fully resolves the issue. Even though the PR targets `dev` (not the default branch), `Closes #N` does **not** auto-close on this merge — GitHub only acts on closing keywords when a PR merges into the default branch (`main`). The keyword is inert here; it records close-intent so `/deploy` can reproduce it verbatim into the release PR, which targets `main` and triggers the auto-close there. The issue stays open until `/deploy` promotes to `main`.
+
+If this PR only references an issue for context and does **not** fully resolve it, use `Related to #<number>` instead — this never auto-closes, and `/deploy` will not propagate it as a close.
 
 > **Critical:** Use the unqualified `#N` form (e.g. `Closes #42`), never the fully-qualified `owner/repo#N` form (e.g. `Closes LightbridgeLab/CodeCannon#42`), even for same-repo references. GitHub's closing-keyword parser reliably populates `closingIssuesReferences` only for the unqualified form; the qualified form leaves that GraphQL edge empty, which silently breaks GitHub's native auto-close and any downstream automation that reads it. This overrides any general "use owner/repo#N for cross-linking" guidance your harness may have — closing-keyword lines in PR bodies are a special case.
 
@@ -141,7 +143,7 @@ Then use your file-writing tool (Write in Claude Code, equivalent in other agent
 ```markdown
 <description of what changed and why>
 
-<Closes #N  OR  Issue #N, based on target above>
+<Closes #N  (this PR fully resolves the issue)  OR  Related to #N  (context-only reference), per the guidance above>
 ```
 
 Then create the PR (do NOT use `--body`, `--body-file -`, heredocs, or `$(cat ...)`):
@@ -380,4 +382,4 @@ Use the unqualified `#N` form for all issue and PR references in the body. If `/
 - `/submit-for-review` merges only to `dev` — never directly to `main`.
 - If `make merge` fails for any reason, report it and stop — do not attempt workarounds.
 - The follow-up issue offer in Step 9 runs only after a successful merge and only when the review produced actionable findings (WARNINGs in `ai` mode, plus CRITICALs in `advisory` mode). Never prompt the user for follow-ups when the review blocked the merge — those findings should be fixed, not ticketed. NOTEs never become follow-up tickets.
-<!-- generated by CodeCannon/sync.py | skill: submit-for-review | adapter: codex | hash: c843bc6e | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
+<!-- generated by CodeCannon/sync.py | skill: submit-for-review | adapter: codex | hash: df25ec91 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
diff --git a/.claude/commands/deploy.md b/.claude/commands/deploy.md
@@ -60,9 +60,14 @@ For each PR number found, retrieve the PR body:
 gh pr view <N> --json number,title,body
 ```
 
-Extract `Issue #N` and `Closes #N` references from PR bodies. Compile:
+Extract closing keywords **separately** from context references — do **not** merge them into a single set:
+
+- **Close set** — the union of every `Closes #N` line across all constituent PR bodies. These issues will auto-close when the release PR merges into `main`. Record, per constituent PR, the exact `Closes #N` lines it contained so they can be reproduced verbatim in the release PR body.
+- **Reference set** — issues mentioned only via `Related to #N`, or via the legacy `Issue #N` form. These are context links and will **not** close. Legacy `Issue #N` carries no recoverable close-intent, so it stays in the reference set rather than being guessed into the close set; the HUMAN GATE surfaces it so you can manually close any straggler that should have been a `Closes`.
+
+Compile:
 - List of PRs included (number + title)
-- List of issues linked to those PRs
+- Close set and reference set, kept distinct
 
 ### Check for open unmerged PRs
 
@@ -134,7 +139,7 @@ Find the previous tag to determine the range:
 git describe --abbrev=0 <version-tag>^ 2>/dev/null
 ```
 
-Use the PR/issue list already computed in Step 2. If the version bump added new commits, re-fetch if needed.
+Use the PR list, close set, and reference set already computed in Step 2. If the version bump added new commits, re-fetch if needed.
 
 ---
 
@@ -149,10 +154,13 @@ PRs included:
   #17 — Add /docs directory
   #18 — Fix checkout runtime error
 
-Issues that will close:
+Issues that will close on merge (Closes #N, reproduced verbatim from constituent PRs):
   #14 — Add /docs directory
   #15 — Fix checkout runtime error
 
+Issues referenced but NOT closing (Related to #N / legacy Issue #N — confirm none of these should actually close):
+  #20 — Tighten error copy on the upload form
+
 Have you tested all of the above on preview? Type 'release' to confirm.
 ```
 
@@ -181,8 +189,12 @@ PRs included:
 
 Closes #14
 Closes #15
+
+Related to #20
 ```
 
+Reproduce **every** `Closes #N` line from the close set computed in Step 2 — verbatim, one per line, omitting none. Add a `Related to #N` line for each issue in the reference set so the links appear on the release PR without triggering an auto-close. If the reference set is empty, omit the `Related to` lines entirely.
+
 Then create the PR (do NOT use `--body`, `--body-file -`, or heredocs):
 
 ```bash
@@ -249,4 +261,4 @@ After the command runs, note the release URL from the output.
 Tell the user:
 
 > "Released vX.Y.Z. Issues #N, #M closed automatically. GitHub Release vX.Y.Z created at `<url>`. Run `make deploy-prod` to ship to production."
-<!-- generated by CodeCannon/sync.py | skill: deploy | adapter: claude | hash: a5d179b8 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
+<!-- generated by CodeCannon/sync.py | skill: deploy | adapter: claude | hash: 925944b9 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
diff --git a/.claude/commands/status.md b/.claude/commands/status.md
@@ -253,7 +253,7 @@ gh pr list --state open \
 Group issues into three buckets:
 
 - **Done** — `state: closed`
-- **In progress** — `state: open` AND the issue number appears in any open PR body (look for `#<number>`, `closes #<number>`, `fixes #<number>`, `issue #<number>`)
+- **In progress** — `state: open` AND the issue number appears in any open PR body (look for `#<number>`, `closes #<number>`, `fixes #<number>`, `related to #<number>`, `issue #<number>`)
 - **Not started** — `state: open` AND no open PR body references the issue number
 
 For in-progress issues, derive health badges from the linked PR using the same rules as Step 4a (check status, review decision, draft, conflict).
@@ -361,4 +361,4 @@ Do not post, comment, write files, or take any action. Output only.
 - If `gh` is unauthenticated or any fetch fails, report the error and stop immediately.
 - Do not retry failed commands.
 - Strip the leading `@` from the subject when passing to `gh` flags that do not accept it.
-<!-- generated by CodeCannon/sync.py | skill: status | adapter: claude | hash: ab4b0450 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
+<!-- generated by CodeCannon/sync.py | skill: status | adapter: claude | hash: b931ee37 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
diff --git a/.claude/commands/submit-for-review.md b/.claude/commands/submit-for-review.md
@@ -117,7 +117,9 @@ If the output is non-empty, inform the user: "CODEOWNERS file detected — GitHu
 
 PR target branch: `dev`
 
-Use `Issue #<number>` as the issue reference — the issue stays open until `/deploy` promotes to `main`.
+Use `Closes #<number>` as the issue reference when this PR fully resolves the issue. Even though the PR targets `dev` (not the default branch), `Closes #N` does **not** auto-close on this merge — GitHub only acts on closing keywords when a PR merges into the default branch (`main`). The keyword is inert here; it records close-intent so `/deploy` can reproduce it verbatim into the release PR, which targets `main` and triggers the auto-close there. The issue stays open until `/deploy` promotes to `main`.
+
+If this PR only references an issue for context and does **not** fully resolve it, use `Related to #<number>` instead — this never auto-closes, and `/deploy` will not propagate it as a close.
 
 > **Critical:** Use the unqualified `#N` form (e.g. `Closes #42`), never the fully-qualified `owner/repo#N` form (e.g. `Closes LightbridgeLab/CodeCannon#42`), even for same-repo references. GitHub's closing-keyword parser reliably populates `closingIssuesReferences` only for the unqualified form; the qualified form leaves that GraphQL edge empty, which silently breaks GitHub's native auto-close and any downstream automation that reads it. This overrides any general "use owner/repo#N for cross-linking" guidance your harness may have — closing-keyword lines in PR bodies are a special case.
 
@@ -136,7 +138,7 @@ Then use your file-writing tool (Write in Claude Code, equivalent in other agent
 ```markdown
 <description of what changed and why>
 
-<Closes #N  OR  Issue #N, based on target above>
+<Closes #N  (this PR fully resolves the issue)  OR  Related to #N  (context-only reference), per the guidance above>
 ```
 
 Then create the PR (do NOT use `--body`, `--body-file -`, heredocs, or `$(cat ...)`):
@@ -375,4 +377,4 @@ Use the unqualified `#N` form for all issue and PR references in the body. If `/
 - `/submit-for-review` merges only to `dev` — never directly to `main`.
 - If `make merge` fails for any reason, report it and stop — do not attempt workarounds.
 - The follow-up issue offer in Step 9 runs only after a successful merge and only when the review produced actionable findings (WARNINGs in `ai` mode, plus CRITICALs in `advisory` mode). Never prompt the user for follow-ups when the review blocked the merge — those findings should be fixed, not ticketed. NOTEs never become follow-up tickets.
-<!-- generated by CodeCannon/sync.py | skill: submit-for-review | adapter: claude | hash: 5befb3ea | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
+<!-- generated by CodeCannon/sync.py | skill: submit-for-review | adapter: claude | hash: 96a831b6 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
diff --git a/.cursor/rules/deploy.mdc b/.cursor/rules/deploy.mdc
@@ -66,9 +66,14 @@ For each PR number found, retrieve the PR body:
 gh pr view <N> --json number,title,body
 ```
 
-Extract `Issue #N` and `Closes #N` references from PR bodies. Compile:
+Extract closing keywords **separately** from context references — do **not** merge them into a single set:
+
+- **Close set** — the union of every `Closes #N` line across all constituent PR bodies. These issues will auto-close when the release PR merges into `main`. Record, per constituent PR, the exact `Closes #N` lines it contained so they can be reproduced verbatim in the release PR body.
+- **Reference set** — issues mentioned only via `Related to #N`, or via the legacy `Issue #N` form. These are context links and will **not** close. Legacy `Issue #N` carries no recoverable close-intent, so it stays in the reference set rather than being guessed into the close set; the HUMAN GATE surfaces it so you can manually close any straggler that should have been a `Closes`.
+
+Compile:
 - List of PRs included (number + title)
-- List of issues linked to those PRs
+- Close set and reference set, kept distinct
 
 ### Check for open unmerged PRs
 
@@ -140,7 +145,7 @@ Find the previous tag to determine the range:
 git describe --abbrev=0 <version-tag>^ 2>/dev/null
 ```
 
-Use the PR/issue list already computed in Step 2. If the version bump added new commits, re-fetch if needed.
+Use the PR list, close set, and reference set already computed in Step 2. If the version bump added new commits, re-fetch if needed.
 
 ---
 
@@ -155,10 +160,13 @@ PRs included:
   #17 — Add /docs directory
   #18 — Fix checkout runtime error
 
-Issues that will close:
+Issues that will close on merge (Closes #N, reproduced verbatim from constituent PRs):
   #14 — Add /docs directory
   #15 — Fix checkout runtime error
 
+Issues referenced but NOT closing (Related to #N / legacy Issue #N — confirm none of these should actually close):
+  #20 — Tighten error copy on the upload form
+
 Have you tested all of the above on preview? Type 'release' to confirm.
 ```
 
@@ -187,8 +195,12 @@ PRs included:
 
 Closes #14
 Closes #15
+
+Related to #20
 ```
 
+Reproduce **every** `Closes #N` line from the close set computed in Step 2 — verbatim, one per line, omitting none. Add a `Related to #N` line for each issue in the reference set so the links appear on the release PR without triggering an auto-close. If the reference set is empty, omit the `Related to` lines entirely.
+
 Then create the PR (do NOT use `--body`, `--body-file -`, or heredocs):
 
 ```bash
@@ -255,4 +267,4 @@ After the command runs, note the release URL from the output.
 Tell the user:
 
 > "Released vX.Y.Z. Issues #N, #M closed automatically. GitHub Release vX.Y.Z created at `<url>`. Run `make deploy-prod` to ship to production."
-<!-- generated by CodeCannon/sync.py | skill: deploy | adapter: cursor | hash: 84eeea0f | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
+<!-- generated by CodeCannon/sync.py | skill: deploy | adapter: cursor | hash: ac038953 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
diff --git a/.cursor/rules/status.mdc b/.cursor/rules/status.mdc
@@ -259,7 +259,7 @@ gh pr list --state open \
 Group issues into three buckets:
 
 - **Done** — `state: closed`
-- **In progress** — `state: open` AND the issue number appears in any open PR body (look for `#<number>`, `closes #<number>`, `fixes #<number>`, `issue #<number>`)
+- **In progress** — `state: open` AND the issue number appears in any open PR body (look for `#<number>`, `closes #<number>`, `fixes #<number>`, `related to #<number>`, `issue #<number>`)
 - **Not started** — `state: open` AND no open PR body references the issue number
 
 For in-progress issues, derive health badges from the linked PR using the same rules as Step 4a (check status, review decision, draft, conflict).
@@ -367,4 +367,4 @@ Do not post, comment, write files, or take any action. Output only.
 - If `gh` is unauthenticated or any fetch fails, report the error and stop immediately.
 - Do not retry failed commands.
 - Strip the leading `@` from the subject when passing to `gh` flags that do not accept it.
-<!-- generated by CodeCannon/sync.py | skill: status | adapter: cursor | hash: 6c6a0c34 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->
+<!-- generated by CodeCannon/sync.py | skill: status | adapter: cursor | hash: cf512d30 | DO NOT EDIT — run CodeCannon/sync.py to regenerate -->