Codex/fix GitHub runners

[BigSimmo]

Summary

Verification

• npm run verify:cheap
• npm run verify:ui when UI, routing, styling, browser behavior, reduced-motion, or forced-colors behavior changed
• npm run verify:release before release or handoff confidence claims
• npm run format:check
• npm run eval:retrieval:quality (must stay 36/36) when retrieval, ranking, selection, chunking, or scoring behavior changed — CI cannot run it (needs live keys), so run it locally and paste the summary. A metadata/governance-weighting change once buried correct docs (recall 1.0→0.76) and only this eval caught it.
• npm run eval:rag -- --limit 15 + npm run eval:quality -- --rag-only when answer generation, the synthesis prompt, or answer post-processing changed (grounded-supported must not drop; citation-failure 0)
• npm run check:production-readiness when clinical workflow, privacy, environment, Supabase, source governance, or deployment behavior changed
• npm run check:deployment-readiness when deployment startup, hosting, or rollout behavior changed

Clinical Governance Preflight

Complete this section when the change touches ingestion, answer generation, search/ranking, source rendering, document access, privacy, production env, or clinical output.

• Source-backed claims still require linked source verification before clinical use
• No patient-identifiable document workflow was introduced or expanded without explicit governance approval
• Supabase target remains Clinical KB Database (sjrfecxgysukkwxsowpy)
• Service-role keys and private document access remain server-only
• Demo/synthetic content remains clearly separated from real clinical sources
• Source metadata, review status, and outdated/unknown-source behavior remain conservative
• Deployment classification/TGA SaMD impact was checked when clinical decision-support behavior changed

Notes

[coderabbitai]

Actionable comments posted: 15

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (2)

scripts/embed-registry-records.ts (1)

133-225: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Resolve the merge conflict markers in scripts/embed-registry-records.ts — keep the paginated origin/main version of listEligibleOwnerCounts; the unpaginated branch can silently truncate rows, and the file still has conflict markers elsewhere (ensureOwnerCount, main).

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/embed-registry-records.ts` around lines 133 - 225, Resolve the merge
conflict in listEligibleOwnerCounts by keeping the paginated origin/main
implementation and removing all conflict markers in
scripts/embed-registry-records.ts, including any remaining ones around
ensureOwnerCount and main. The unpaginated HEAD version can truncate owner
counts, so preserve the pageSize/range loop structure for
clinical_registry_records, medication_records, and differential_records, and
ensure the file compiles cleanly with no leftover merge artifacts.

Source: Linters/SAST tools

src/lib/rag-extractive-answer.ts (1)

293-338: 🩺 Stability & Availability | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers — file will not compile.

Conflict markers remain at Lines 293-302/316 and 323-330/335-338, and Biome fails to parse the file as a result. As with rag-routing.ts, resolving these is the point of this PR; the merge is incomplete until they are removed and a side is chosen for each hunk.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/lib/rag-extractive-answer.ts` around lines 293 - 338, Resolve the
remaining merge conflict markers in rag-extractive-answer.ts so the file parses
again and Biome can compile it. Choose the intended versions of
requiresBloodCountEvidence, asksForWithholdAction, hasBloodCountEvidence, and
hasWithholdActionEvidence, then remove all conflict markers and duplicate
branches. Make sure the final definitions are consistent with the surrounding
intent-matching logic and leave only one clean implementation per function.

Source: Learnings

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In @.github/workflows/codex-autofix-review-comments.yml:
- Around line 17-20: The workflow YAML still contains unresolved merge conflict
markers, which breaks parsing. Remove all conflict markers from the concurrency
group and embedded script blocks, then reconcile the HEAD vs origin/main content
by choosing the correct values in the workflow file. Verify the affected
sections around the concurrency group and the script content are valid
YAML/shell with no remaining <<<<<<<, =======, or >>>>>>> markers.

In `@AGENTS.md`:
- Around line 389-402: Resolve the merge conflict in AGENTS.md by collapsing the
duplicated Codex autofix workflow guidance into one canonical policy set. Keep
only one version of the instructions for codex-autofix-review-comments, making
the trigger scope, excluded event types, skip conditions, and resolve-task
behavior consistent and unambiguous, and remove the conflict markers and the
discarded branch text.

In `@docs/branch-cleanup-guide.md`:
- Around line 49-56: Resolve the merge conflict in the branch-cleanup snippet
and keep the escaped branch handling. Update the docs/branch-cleanup-guide.md
example so it uses $escapedBranch = [regex]::Escape($branch) and the
Select-String pattern references $escapedBranch instead of $branch, removing all
conflict markers. Make sure the branch lookup logic in the branch cleanup guide
remains anchored on the escaped token so the ledger row match is safe for regex
metacharacters.

In `@docs/branch-review-ledger.md`:
- Around line 21-32: The branch review ledger still contains an unresolved merge
conflict, so it is not a single canonical source for review history. Resolve the
conflict in the review-records table by removing the conflict markers and
keeping one consolidated set of rows in docs/branch-review-ledger.md, preserving
the existing entry for example/branch and the added claude/llm-pipeline-review
records so the lookup flow can rely on one clean history table.

In `@docs/rag-hybrid-findings-and-todo.md`:
- Around line 316-323: Resolve the remaining merge conflict in the post-write
evaluation note by choosing one final wording and removing the HEAD/origin/main
conflict markers from the findings document. Update the sentence in the
registry-embedding result section so it reads as a single, unambiguous
post-write evaluation summary, using the existing evaluation wording around
document_recall_at_5, content_recall_at_5, top_k_hit_rate,
force_embedding_failure_count, and failed_cases.

In `@scripts/embed-registry-records.ts`:
- Around line 120-123: Resolve the merge conflict in embed-registry-records.ts
by removing the leftover conflict markers (`<<<<<<< HEAD`, `=======`, `>>>>>>>
origin/main`) so the file parses again, and keep the `/** Ensure owner count.
*/` doc comment in the surrounding code near the affected block.
- Around line 235-238: Unresolved merge conflict markers are still present
around the script entry point; clean up the conflict in the area containing the
Main comment by removing the conflict markers and keeping the /** Main. */
documentation. Verify the surrounding top-level section in
embed-registry-records.ts is left as valid TypeScript with no leftover
HEAD/origin/main markers.

In `@src/lib/rag-extractive-answer.ts`:
- Around line 323-333: Update hasWithholdActionEvidence to match the origin/main
regex in rag-extractive-answer.ts by removing the overly permissive red|amber
and hold|held tokens from the pattern. Keep the existing function name and
surrounding logic unchanged, and use the narrower evidence terms already present
in the origin/main version so the withhold-action detection stays aligned with
the intended gating behavior.

In `@src/lib/rag-routing.ts`:
- Around line 40-45: Resolve the remaining merge conflicts in rag-routing by
removing all Git conflict markers and ensuring the file parses cleanly; the
affected areas include the clozapineBloodWithholdThresholdPattern declaration
and the other conflicted blocks throughout the module. For hunks where only
formatting or JSDoc differs, keep the intended origin/main version and delete
the markers; for the larger decision points near the later disputed sections,
choose the correct implementation consistently within the surrounding symbols
and remove all leftover conflict text.
- Around line 728-737: Keep the origin/main condition in the routing branch by
preserving the !actionableConflictOrGap gate in the table_threshold check inside
rag-routing’s decision logic; remove the merge-conflict markers and ensure the
if statement in the relevant routing path only takes the extractive route when
directTitleSupport, strongestScore >= strongRetrievalThreshold, and no
actionable conflict/gap is present, so the fallback strong route remains
reachable.

In `@src/lib/rag.ts`:
- Around line 2734-2737: Resolve the unresolved merge conflict markers in rag.ts
by removing all `<<<<<<< HEAD`, `=======`, and `>>>>>>> origin/main` blocks
around the doc-comment additions, and keep the intended comments on the affected
helpers. Make sure the merged output is clean in the sections for
`hasAdmissionCommunityLookupIntent`, `shouldReturnBeforeMemory`,
`shouldRecoverFastFailureExtractively`, and `summarizeGenerationFailureReason`,
since these parse errors in `answerQuestionWithScope` and related
routing/scoring code prevent the module from compiling.

In `@src/lib/registry-corpus.ts`:
- Around line 52-55: Remove all unresolved merge conflict markers from
registry-corpus.ts and keep only the intended code/documentation in each
conflicted block. Check the affected areas around the registry corpus embedding
logic, including the symbols and sections in this file where the conflict
markers appear, and resolve every remaining <<<<<<<, =======, and >>>>>>>
sequence so the file parses and builds cleanly.

In `@supabase/drift-manifest.json`:
- Around line 2-14: Resolve the merge conflict in drift-manifest.json so it
remains valid JSON by removing the conflict markers and keeping one clean set of
metadata. Use the newer origin/main values for generated_at and replay_seconds,
and ensure the manifest still matches what scripts/check-drift.ts and
tests/drift-detection.test.ts expect to parse.

In `@tests/rag-answer-fallback.test.ts`:
- Around line 415-421: Resolve the merge conflict in the routingReason
expectation inside the test by removing the leftover conflict markers and
keeping one valid matcher form; the issue is in the test around the
answer.routingReason assertion, and both branches are equivalent so just
preserve either formatting while deleting the <<<<<<< HEAD, =======, and >>>>>>>
origin/main lines.

In `@tests/rag-routing.test.ts`:
- Around line 186-193: Resolve the merge conflict artifacts in the rag-routing
test cases by removing all conflict markers and keeping the intended final
assertions for the clozapine FBC content and the unrelated stop wording block.
Update the affected test setup where the array/object for these expectations is
defined so the preserved content and text_rank values are valid TypeScript.
Ensure no `<<<<<<<`, `=======`, or `>>>>>>>` markers remain anywhere in the test
file so Biome can parse and run the suite.

---

Outside diff comments:
In `@scripts/embed-registry-records.ts`:
- Around line 133-225: Resolve the merge conflict in listEligibleOwnerCounts by
keeping the paginated origin/main implementation and removing all conflict
markers in scripts/embed-registry-records.ts, including any remaining ones
around ensureOwnerCount and main. The unpaginated HEAD version can truncate
owner counts, so preserve the pageSize/range loop structure for
clinical_registry_records, medication_records, and differential_records, and
ensure the file compiles cleanly with no leftover merge artifacts.

In `@src/lib/rag-extractive-answer.ts`:
- Around line 293-338: Resolve the remaining merge conflict markers in
rag-extractive-answer.ts so the file parses again and Biome can compile it.
Choose the intended versions of requiresBloodCountEvidence,
asksForWithholdAction, hasBloodCountEvidence, and hasWithholdActionEvidence,
then remove all conflict markers and duplicate branches. Make sure the final
definitions are consistent with the surrounding intent-matching logic and leave
only one clean implementation per function.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 63e657e5-afe8-4f7a-a4a8-acc24700b53e

📥 Commits

Reviewing files that changed from the base of the PR and between f4d9c4e and 983777f.

📒 Files selected for processing (16)

• .github/workflows/ci.yml
• .github/workflows/codex-autofix-review-comments.yml
• AGENTS.md
• docs/branch-cleanup-guide.md
• docs/branch-review-ledger.md
• docs/codex-review-protocol.md
• docs/rag-hybrid-findings-and-todo.md
• package.json
• scripts/embed-registry-records.ts
• src/lib/rag-extractive-answer.ts
• src/lib/rag-routing.ts
• src/lib/rag.ts
• src/lib/registry-corpus.ts
• supabase/drift-manifest.json
• tests/rag-answer-fallback.test.ts
• tests/rag-routing.test.ts

🚧 Files skipped from review as they are similar to previous changes (2)

• docs/codex-review-protocol.md
• .github/workflows/ci.yml

[coderabbitai]

Caution

Inline review comments failed to post. This is likely due to GitHub's internal server error or limits when posting large numbers of comments. If you are seeing this consistently it is likely a permissions issue. Please check "Moderation" -> "Code review limits" under your organization settings.

Actionable comments posted: 15

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (2)

scripts/embed-registry-records.ts (1)

133-225: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Resolve the merge conflict markers in scripts/embed-registry-records.ts — keep the paginated origin/main version of listEligibleOwnerCounts; the unpaginated branch can silently truncate rows, and the file still has conflict markers elsewhere (ensureOwnerCount, main).

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/embed-registry-records.ts` around lines 133 - 225, Resolve the merge
conflict in listEligibleOwnerCounts by keeping the paginated origin/main
implementation and removing all conflict markers in
scripts/embed-registry-records.ts, including any remaining ones around
ensureOwnerCount and main. The unpaginated HEAD version can truncate owner
counts, so preserve the pageSize/range loop structure for
clinical_registry_records, medication_records, and differential_records, and
ensure the file compiles cleanly with no leftover merge artifacts.

Source: Linters/SAST tools

src/lib/rag-extractive-answer.ts (1)

293-338: 🩺 Stability & Availability | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers — file will not compile.

Conflict markers remain at Lines 293-302/316 and 323-330/335-338, and Biome fails to parse the file as a result. As with rag-routing.ts, resolving these is the point of this PR; the merge is incomplete until they are removed and a side is chosen for each hunk.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/lib/rag-extractive-answer.ts` around lines 293 - 338, Resolve the
remaining merge conflict markers in rag-extractive-answer.ts so the file parses
again and Biome can compile it. Choose the intended versions of
requiresBloodCountEvidence, asksForWithholdAction, hasBloodCountEvidence, and
hasWithholdActionEvidence, then remove all conflict markers and duplicate
branches. Make sure the final definitions are consistent with the surrounding
intent-matching logic and leave only one clean implementation per function.

Source: Learnings

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In @.github/workflows/codex-autofix-review-comments.yml:
- Around line 17-20: The workflow YAML still contains unresolved merge conflict
markers, which breaks parsing. Remove all conflict markers from the concurrency
group and embedded script blocks, then reconcile the HEAD vs origin/main content
by choosing the correct values in the workflow file. Verify the affected
sections around the concurrency group and the script content are valid
YAML/shell with no remaining <<<<<<<, =======, or >>>>>>> markers.

In `@AGENTS.md`:
- Around line 389-402: Resolve the merge conflict in AGENTS.md by collapsing the
duplicated Codex autofix workflow guidance into one canonical policy set. Keep
only one version of the instructions for codex-autofix-review-comments, making
the trigger scope, excluded event types, skip conditions, and resolve-task
behavior consistent and unambiguous, and remove the conflict markers and the
discarded branch text.

In `@docs/branch-cleanup-guide.md`:
- Around line 49-56: Resolve the merge conflict in the branch-cleanup snippet
and keep the escaped branch handling. Update the docs/branch-cleanup-guide.md
example so it uses $escapedBranch = [regex]::Escape($branch) and the
Select-String pattern references $escapedBranch instead of $branch, removing all
conflict markers. Make sure the branch lookup logic in the branch cleanup guide
remains anchored on the escaped token so the ledger row match is safe for regex
metacharacters.

In `@docs/branch-review-ledger.md`:
- Around line 21-32: The branch review ledger still contains an unresolved merge
conflict, so it is not a single canonical source for review history. Resolve the
conflict in the review-records table by removing the conflict markers and
keeping one consolidated set of rows in docs/branch-review-ledger.md, preserving
the existing entry for example/branch and the added claude/llm-pipeline-review
records so the lookup flow can rely on one clean history table.

In `@docs/rag-hybrid-findings-and-todo.md`:
- Around line 316-323: Resolve the remaining merge conflict in the post-write
evaluation note by choosing one final wording and removing the HEAD/origin/main
conflict markers from the findings document. Update the sentence in the
registry-embedding result section so it reads as a single, unambiguous
post-write evaluation summary, using the existing evaluation wording around
document_recall_at_5, content_recall_at_5, top_k_hit_rate,
force_embedding_failure_count, and failed_cases.

In `@scripts/embed-registry-records.ts`:
- Around line 120-123: Resolve the merge conflict in embed-registry-records.ts
by removing the leftover conflict markers (`<<<<<<< HEAD`, `=======`, `>>>>>>>
origin/main`) so the file parses again, and keep the `/** Ensure owner count.
*/` doc comment in the surrounding code near the affected block.
- Around line 235-238: Unresolved merge conflict markers are still present
around the script entry point; clean up the conflict in the area containing the
Main comment by removing the conflict markers and keeping the /** Main. */
documentation. Verify the surrounding top-level section in
embed-registry-records.ts is left as valid TypeScript with no leftover
HEAD/origin/main markers.

In `@src/lib/rag-extractive-answer.ts`:
- Around line 323-333: Update hasWithholdActionEvidence to match the origin/main
regex in rag-extractive-answer.ts by removing the overly permissive red|amber
and hold|held tokens from the pattern. Keep the existing function name and
surrounding logic unchanged, and use the narrower evidence terms already present
in the origin/main version so the withhold-action detection stays aligned with
the intended gating behavior.

In `@src/lib/rag-routing.ts`:
- Around line 40-45: Resolve the remaining merge conflicts in rag-routing by
removing all Git conflict markers and ensuring the file parses cleanly; the
affected areas include the clozapineBloodWithholdThresholdPattern declaration
and the other conflicted blocks throughout the module. For hunks where only
formatting or JSDoc differs, keep the intended origin/main version and delete
the markers; for the larger decision points near the later disputed sections,
choose the correct implementation consistently within the surrounding symbols
and remove all leftover conflict text.
- Around line 728-737: Keep the origin/main condition in the routing branch by
preserving the !actionableConflictOrGap gate in the table_threshold check inside
rag-routing’s decision logic; remove the merge-conflict markers and ensure the
if statement in the relevant routing path only takes the extractive route when
directTitleSupport, strongestScore >= strongRetrievalThreshold, and no
actionable conflict/gap is present, so the fallback strong route remains
reachable.

In `@src/lib/rag.ts`:
- Around line 2734-2737: Resolve the unresolved merge conflict markers in rag.ts
by removing all `<<<<<<< HEAD`, `=======`, and `>>>>>>> origin/main` blocks
around the doc-comment additions, and keep the intended comments on the affected
helpers. Make sure the merged output is clean in the sections for
`hasAdmissionCommunityLookupIntent`, `shouldReturnBeforeMemory`,
`shouldRecoverFastFailureExtractively`, and `summarizeGenerationFailureReason`,
since these parse errors in `answerQuestionWithScope` and related
routing/scoring code prevent the module from compiling.

In `@src/lib/registry-corpus.ts`:
- Around line 52-55: Remove all unresolved merge conflict markers from
registry-corpus.ts and keep only the intended code/documentation in each
conflicted block. Check the affected areas around the registry corpus embedding
logic, including the symbols and sections in this file where the conflict
markers appear, and resolve every remaining <<<<<<<, =======, and >>>>>>>
sequence so the file parses and builds cleanly.

In `@supabase/drift-manifest.json`:
- Around line 2-14: Resolve the merge conflict in drift-manifest.json so it
remains valid JSON by removing the conflict markers and keeping one clean set of
metadata. Use the newer origin/main values for generated_at and replay_seconds,
and ensure the manifest still matches what scripts/check-drift.ts and
tests/drift-detection.test.ts expect to parse.

In `@tests/rag-answer-fallback.test.ts`:
- Around line 415-421: Resolve the merge conflict in the routingReason
expectation inside the test by removing the leftover conflict markers and
keeping one valid matcher form; the issue is in the test around the
answer.routingReason assertion, and both branches are equivalent so just
preserve either formatting while deleting the <<<<<<< HEAD, =======, and >>>>>>>
origin/main lines.

In `@tests/rag-routing.test.ts`:
- Around line 186-193: Resolve the merge conflict artifacts in the rag-routing
test cases by removing all conflict markers and keeping the intended final
assertions for the clozapine FBC content and the unrelated stop wording block.
Update the affected test setup where the array/object for these expectations is
defined so the preserved content and text_rank values are valid TypeScript.
Ensure no `<<<<<<<`, `=======`, or `>>>>>>>` markers remain anywhere in the test
file so Biome can parse and run the suite.

---

Outside diff comments:
In `@scripts/embed-registry-records.ts`:
- Around line 133-225: Resolve the merge conflict in listEligibleOwnerCounts by
keeping the paginated origin/main implementation and removing all conflict
markers in scripts/embed-registry-records.ts, including any remaining ones
around ensureOwnerCount and main. The unpaginated HEAD version can truncate
owner counts, so preserve the pageSize/range loop structure for
clinical_registry_records, medication_records, and differential_records, and
ensure the file compiles cleanly with no leftover merge artifacts.

In `@src/lib/rag-extractive-answer.ts`:
- Around line 293-338: Resolve the remaining merge conflict markers in
rag-extractive-answer.ts so the file parses again and Biome can compile it.
Choose the intended versions of requiresBloodCountEvidence,
asksForWithholdAction, hasBloodCountEvidence, and hasWithholdActionEvidence,
then remove all conflict markers and duplicate branches. Make sure the final
definitions are consistent with the surrounding intent-matching logic and leave
only one clean implementation per function.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 63e657e5-afe8-4f7a-a4a8-acc24700b53e

📥 Commits

Reviewing files that changed from the base of the PR and between f4d9c4e and 983777f.

📒 Files selected for processing (16)

• .github/workflows/ci.yml
• .github/workflows/codex-autofix-review-comments.yml
• AGENTS.md
• docs/branch-cleanup-guide.md
• docs/branch-review-ledger.md
• docs/codex-review-protocol.md
• docs/rag-hybrid-findings-and-todo.md
• package.json
• scripts/embed-registry-records.ts
• src/lib/rag-extractive-answer.ts
• src/lib/rag-routing.ts
• src/lib/rag.ts
• src/lib/registry-corpus.ts
• supabase/drift-manifest.json
• tests/rag-answer-fallback.test.ts
• tests/rag-routing.test.ts

🚧 Files skipped from review as they are similar to previous changes (2)

• docs/codex-review-protocol.md
• .github/workflows/ci.yml

🛑 Comments failed to post (15)

.github/workflows/codex-autofix-review-comments.yml (1)

17-20: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers left in committed YAML — workflow is broken.

Literal <<<<<<< HEAD / ======= / >>>>>>> origin/main markers remain in the concurrency group (Lines 17-20) and inside the embedded script (Lines 86-98, 100-112). actionlint and YAMLlint both report could not find expected ':' at Line 17-18, confirming the workflow YAML cannot even be parsed. This is precisely the merge-conflict issue the PR was intended to fix, per the PR objectives and the repeated "resolve the merge conflicts" requests in the comments.

Pick one side (or manually reconcile both) for each conflict block and remove the markers entirely before merge.

Example fix for the concurrency group conflict

-<<<<<<< HEAD
-  group: codex-autoresolve-${{ github.event.pull_request.number || github.event.issue.number }}-${{ github.event.pull_request.head.sha || github.event.review.id || github.event.comment.id }}
-=======
-  group: codex-autoresolve-${{ github.event.pull_request.number }}
->>>>>>> origin/main
+  group: codex-autoresolve-${{ github.event.pull_request.number || github.event.issue.number }}-${{ github.event.pull_request.head.sha || github.event.review.id || github.event.comment.id }}

Also applies to: 86-98, 100-112

🧰 Tools

🪛 actionlint (1.7.12)

[error] 17-17: could not parse as YAML: could not find expected ':'

(syntax-check)

🪛 YAMLlint (1.37.1)

[error] 18-18: syntax error: could not find expected ':'

(syntax)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In @.github/workflows/codex-autofix-review-comments.yml around lines 17 - 20,
The workflow YAML still contains unresolved merge conflict markers, which breaks
parsing. Remove all conflict markers from the concurrency group and embedded
script blocks, then reconcile the HEAD vs origin/main content by choosing the
correct values in the workflow file. Verify the affected sections around the
concurrency group and the script content are valid YAML/shell with no remaining
<<<<<<<, =======, or >>>>>>> markers.

Source: Linters/SAST tools

AGENTS.md (1)

389-402: 🎯 Functional Correctness | 🟠 Major

Remove the unresolved merge conflict here.

The section currently contains two incompatible auto-resolve policies, so the instructions are ambiguous until this is collapsed to one canonical rule set.

🧰 Tools

🪛 LanguageTool

[uncategorized] ~390-~390: The official name of this software platform is spelled with a capital “H”.
Context: ...ly by default. This repository includes `.github/workflows/codex-autofix-review-comments...

(GITHUB)

---

[uncategorized] ~396-~396: The official name of this software platform is spelled with a capital “H”.
Context: ...ly by default. This repository includes `.github/workflows/codex-autofix-review-comments...

(GITHUB)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@AGENTS.md` around lines 389 - 402, Resolve the merge conflict in AGENTS.md by
collapsing the duplicated Codex autofix workflow guidance into one canonical
policy set. Keep only one version of the instructions for
codex-autofix-review-comments, making the trigger scope, excluded event types,
skip conditions, and resolve-task behavior consistent and unambiguous, and
remove the conflict markers and the discarded branch text.

docs/branch-cleanup-guide.md (1)

49-56: 🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
set -euo pipefail

# Inspect the target file around the referenced lines with line numbers.
sed -n '1,140p' docs/branch-cleanup-guide.md | cat -n

Repository: BigSimmo/Database

Length of output: 4321

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

# Show the exact line range and surrounding context for the ledger lookup snippet.
nl -ba docs/branch-cleanup-guide.md | sed -n '35,75p'

Repository: BigSimmo/Database

Length of output: 195

---

Resolve the merge conflict and keep the escaped branch token.

The snippet still contains conflict markers. Keep $escapedBranch = [regex]::Escape($branch) so branch names with regex metacharacters don’t match the wrong ledger row.

🧰 Tools

🪛 markdownlint-cli2 (0.22.1)

[warning] 49-49: Heading style
Expected: atx; Actual: setext

(MD003, heading-style)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@docs/branch-cleanup-guide.md` around lines 49 - 56, Resolve the merge
conflict in the branch-cleanup snippet and keep the escaped branch handling.
Update the docs/branch-cleanup-guide.md example so it uses $escapedBranch =
[regex]::Escape($branch) and the Select-String pattern references $escapedBranch
instead of $branch, removing all conflict markers. Make sure the branch lookup
logic in the branch cleanup guide remains anchored on the escaped token so the
ledger row match is safe for regex metacharacters.

docs/branch-review-ledger.md (1)

21-32: 🎯 Functional Correctness | 🟠 Major

Resolve the ledger conflict before relying on it for throttling.

The review-records table is still split across two versions, so the lookup procedure no longer has one canonical history source. Collapse this to a single table before using it to suppress repeat reviews.

🧰 Tools

🪛 markdownlint-cli2 (0.22.1)

[warning] 22-22: Tables should be surrounded by blank lines

(MD058, blanks-around-tables)

---

[warning] 25-25: Table pipe style
Expected: leading_and_trailing; Actual: no_leading_or_trailing; Missing leading pipe

(MD055, table-pipe-style)

---

[warning] 25-25: Table pipe style
Expected: leading_and_trailing; Actual: no_leading_or_trailing; Missing trailing pipe

(MD055, table-pipe-style)

---

[warning] 25-25: Table column count
Expected: 6; Actual: 1; Too few cells, row will be missing data

(MD056, table-column-count)

---

[warning] 31-31: Tables should be surrounded by blank lines

(MD058, blanks-around-tables)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@docs/branch-review-ledger.md` around lines 21 - 32, The branch review ledger
still contains an unresolved merge conflict, so it is not a single canonical
source for review history. Resolve the conflict in the review-records table by
removing the conflict markers and keeping one consolidated set of rows in
docs/branch-review-ledger.md, preserving the existing entry for example/branch
and the added claude/llm-pipeline-review records so the lookup flow can rely on
one clean history table.

docs/rag-hybrid-findings-and-todo.md (1)

316-323: 📐 Maintainability & Code Quality | 🟠 Major

Finish resolving item 22.

The post-write evaluation note is still split across conflict markers, so the registry-embedding result is ambiguously documented. Collapse this to one final sentence before treating the record as complete.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@docs/rag-hybrid-findings-and-todo.md` around lines 316 - 323, Resolve the
remaining merge conflict in the post-write evaluation note by choosing one final
wording and removing the HEAD/origin/main conflict markers from the findings
document. Update the sentence in the registry-embedding result section so it
reads as a single, unambiguous post-write evaluation summary, using the existing
evaluation wording around document_recall_at_5, content_recall_at_5,
top_k_hit_rate, force_embedding_failure_count, and failed_cases.

scripts/embed-registry-records.ts (2)

120-123: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers.

Lines 120-123 still contain <<<<<<< HEAD / ======= / >>>>>>> origin/main. This is invalid TypeScript and won't parse (Biome/tsc will fail). Keep the /** Ensure owner count. */ doc comment and delete the conflict markers.

🐛 Proposed fix

-<<<<<<< HEAD
-=======
 /** Ensure owner count. */
->>>>>>> origin/main

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

/** Ensure owner count. */

🧰 Tools

🪛 Biome (2.5.1)

[error] 120-123: Expected a statement but instead found '<<<<<<< HEAD

/** Ensure owner count. */

origin/main'.

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/embed-registry-records.ts` around lines 120 - 123, Resolve the merge
conflict in embed-registry-records.ts by removing the leftover conflict markers
(`<<<<<<< HEAD`, `=======`, `>>>>>>> origin/main`) so the file parses again, and
keep the `/** Ensure owner count. */` doc comment in the surrounding code near
the affected block.

Source: Linters/SAST tools

---

235-238: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers.

Same issue at lines 235-238: keep the /** Main. */ comment and remove the conflict markers.

🐛 Proposed fix

-<<<<<<< HEAD
-=======
 /** Main. */
->>>>>>> origin/main

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

/** Main. */

🧰 Tools

🪛 Biome (2.5.1)

[error] 235-239: Expected a statement but instead found '<<<<<<< HEAD

/** Main. */

origin/main
async'.

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/embed-registry-records.ts` around lines 235 - 238, Unresolved merge
conflict markers are still present around the script entry point; clean up the
conflict in the area containing the Main comment by removing the conflict
markers and keeping the /** Main. */ documentation. Verify the surrounding
top-level section in embed-registry-records.ts is left as valid TypeScript with
no leftover HEAD/origin/main markers.

Source: Linters/SAST tools

src/lib/rag-extractive-answer.ts (1)

323-333: 🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Confirm expected evidence-gating behavior in the tests
rg -nP -C3 '(red range|amber range|withhold action|hasWithholdActionEvidence|red_result_action)' tests/

Repository: BigSimmo/Database

Length of output: 10008

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

# Show the function and its consumers around the reported lines
sed -n '300,360p' src/lib/rag-extractive-answer.ts
printf '\n---\n'
sed -n '610,660p' src/lib/rag-extractive-answer.ts

# Find direct references to hasWithholdActionEvidence and red/amber range gating
rg -n -C 2 'hasWithholdActionEvidence|red_result_action|red range|amber range|\\bhold\\b|\\bheld\\b|\\bwithhold\\b|\\bwithheld\\b|\\bwithholding\\b' src tests

Repository: BigSimmo/Database

Length of output: 24199

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

# Look for red_result_action fixtures and any evidence that "hold/held" is part of the expected gate vocabulary
rg -n -C 3 '\b(red_result_action|withhold|hold|held|red range|amber range)\b' src/lib tests | sed -n '1,260p'

printf '\n--- rag-eval-cases red_result_action block ---\n'
sed -n '160,210p' src/lib/rag-eval-cases.ts

Repository: BigSimmo/Database

Length of output: 22376

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail

# Look for test expectations or fixtures that specifically rely on "hold" or "held"
rg -n -C 2 '\bhold\b|\bheld\b' tests src/lib | sed -n '1,240p'

printf '\n--- hasWithholdActionEvidence call sites ---\n'
rg -n -C 2 'hasWithholdActionEvidence|asksForWithholdAction|red_result_action' src/lib/rag-extractive-answer.ts src/lib/rag-eval-cases.ts tests | sed -n '1,220p'

Repository: BigSimmo/Database

Length of output: 17761

---

Use the origin/main regex here. red|amber alone is too permissive, and hold|held matches the surrounding red-result gating patterns.

🧰 Tools

🪛 Biome (2.5.1)

[error] 323-323: Expected a statement but instead found '<<<<<<< HEAD'.

(parse)

---

[error] 326-326: Expected an expression for the left hand side of the === operator.

(parse)

---

[error] 326-326: Expected an expression but instead found '==='.

(parse)

---

[error] 326-326: Expected an expression but instead found '='.

(parse)

---

[error] 326-326: Invalid assignment to ======

(parse)

---

[error] 330-330: Expected an expression for the left hand side of the >>> operator.

(parse)

---

[error] 330-330: Expected an expression but instead found '>>>'.

(parse)

---

[error] 330-330: Expected an expression but instead found '>'.

(parse)

---

[error] 331-331: expected , but instead found text

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/lib/rag-extractive-answer.ts` around lines 323 - 333, Update
hasWithholdActionEvidence to match the origin/main regex in
rag-extractive-answer.ts by removing the overly permissive red|amber and
hold|held tokens from the pattern. Keep the existing function name and
surrounding logic unchanged, and use the narrower evidence terms already present
in the origin/main version so the withhold-action detection stays aligned with
the intended gating behavior.

src/lib/rag-routing.ts (2)

40-45: 🩺 Stability & Availability | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers — file will not compile.

This file still contains raw Git conflict markers (<<<<<<< HEAD, =======, >>>>>>> origin/main) at multiple locations: Lines 40-45, 260-263, 271-274, 285-288, 302-305, 313-316, 322-325, 351-354, 363/393/439, 452-455, 469-472, and 728-737. Biome confirms these break parsing. Resolving these conflicts is the stated purpose of this PR, so the merge is not actually complete.

Most of these hunks differ only in the presence of JSDoc comments (e.g. Lines 40-45 are the same regex on one vs. two lines), so keeping the origin/main side is safe there. Lines 728-737 and 363-439 require a deliberate choice (see separate note). Please remove all markers and pick the intended side for each.

🧰 Tools

🪛 Biome (2.5.1)

[error] 40-40: Expected a statement but instead found '<<<<<<< HEAD'.

(parse)

---

[error] 43-43: Expected a statement but instead found '======='.

(parse)

---

[error] 45-45: Expected a statement but instead found '>>>>>>> origin/main'.

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/lib/rag-routing.ts` around lines 40 - 45, Resolve the remaining merge
conflicts in rag-routing by removing all Git conflict markers and ensuring the
file parses cleanly; the affected areas include the
clozapineBloodWithholdThresholdPattern declaration and the other conflicted
blocks throughout the module. For hunks where only formatting or JSDoc differs,
keep the intended origin/main version and delete the markers; for the larger
decision points near the later disputed sections, choose the correct
implementation consistently within the surrounding symbols and remove all
leftover conflict text.

Source: Learnings

---

728-737: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Keep the origin/main side here (the !actionableConflictOrGap gate).

Beyond marker removal, this hunk is a semantic decision. The origin/main branch additionally gates the table_threshold extractive path on !actionableConflictOrGap, which the routing tests rely on (extractive only when no actionable conflict/gap is present; otherwise fall through to the strong route at Lines 798-818). Dropping the HEAD side keeps routing consistent with those expectations.

Proposed resolution

-<<<<<<< HEAD
-    if (queryClass === "table_threshold" && directTitleSupport && strongestScore >= strongRetrievalThreshold) {
-=======
     if (
       queryClass === "table_threshold" &&
       directTitleSupport &&
       strongestScore >= strongRetrievalThreshold &&
       !actionableConflictOrGap
     ) {
->>>>>>> origin/main

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

    if (
      queryClass === "table_threshold" &&
      directTitleSupport &&
      strongestScore >= strongRetrievalThreshold &&
      !actionableConflictOrGap
    ) {

🧰 Tools

🪛 Biome (2.5.1)

[error] 728-728: Expected a statement but instead found '<<<<<<< HEAD'.

(parse)

---

[error] 730-730: Expected a statement but instead found '======='.

(parse)

---

[error] 737-737: Expected a statement but instead found '>>>>>>> origin/main'.

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/lib/rag-routing.ts` around lines 728 - 737, Keep the origin/main
condition in the routing branch by preserving the !actionableConflictOrGap gate
in the table_threshold check inside rag-routing’s decision logic; remove the
merge-conflict markers and ensure the if statement in the relevant routing path
only takes the extractive route when directTitleSupport, strongestScore >=
strongRetrievalThreshold, and no actionable conflict/gap is present, so the
fallback strong route remains reachable.

src/lib/rag.ts (1)

2734-2737: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers left in rag.ts — file will not compile.

Literal <<<<<<< HEAD / ======= / >>>>>>> origin/main markers remain at Lines 2734-2737, 2743-2746, 2762-2765, 4690-4693, and 4713-4716 (all doc-comment insertions around hasAdmissionCommunityLookupIntent, shouldReturnBeforeMemory, shouldRecoverFastFailureExtractively, and summarizeGenerationFailureReason). Biome confirms parse errors at every one of these ranges. Since this is a core module (answerQuestionWithScope, routing/scoring helpers live here), this breaks the entire build, not just this file.

Remove the markers and keep the added doc comments (both sides are additive comments only, no logic differs) before merge.

Also applies to: 2743-2746, 2762-2765, 4690-4693, 4713-4716

🧰 Tools

🪛 Biome (2.5.1)

[error] 2734-2737: Expected a statement but instead found '<<<<<<< HEAD

/** Has admission community lookup intent. */

origin/main'.

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/lib/rag.ts` around lines 2734 - 2737, Resolve the unresolved merge
conflict markers in rag.ts by removing all `<<<<<<< HEAD`, `=======`, and
`>>>>>>> origin/main` blocks around the doc-comment additions, and keep the
intended comments on the affected helpers. Make sure the merged output is clean
in the sections for `hasAdmissionCommunityLookupIntent`,
`shouldReturnBeforeMemory`, `shouldRecoverFastFailureExtractively`, and
`summarizeGenerationFailureReason`, since these parse errors in
`answerQuestionWithScope` and related routing/scoring code prevent the module
from compiling.

Source: Linters/SAST tools

src/lib/registry-corpus.ts (1)

52-55: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers left in registry-corpus.ts — file will not compile.

Literal <<<<<<< HEAD / ======= / >>>>>>> origin/main markers remain throughout this file at Lines 52-55, 315-328, 336-360, 400-403, 408-411, 427-430, 449-452, 468-471, 495-498, and 514-524. Biome reports parse errors at essentially every one of these locations. This file implements registry corpus embedding used by production embed/re-embed flows, so a broken build here is severe.

Also applies to: 315-328, 336-360, 400-403, 408-411, 427-430, 449-452, 468-471, 495-498, 514-524

🧰 Tools

🪛 Biome (2.5.1)

[error] 52-55: Expected a statement but instead found '<<<<<<< HEAD

/** Sha256. */

origin/main'.

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/lib/registry-corpus.ts` around lines 52 - 55, Remove all unresolved merge
conflict markers from registry-corpus.ts and keep only the intended
code/documentation in each conflicted block. Check the affected areas around the
registry corpus embedding logic, including the symbols and sections in this file
where the conflict markers appear, and resolve every remaining <<<<<<<, =======,
and >>>>>>> sequence so the file parses and builds cleanly.

Source: Linters/SAST tools

supabase/drift-manifest.json (1)

2-14: 🗄️ Data Integrity & Integration | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict makes the manifest invalid JSON.

The conflict markers break JSON.parse, so every consumer (scripts/check-drift.ts, tests/drift-detection.test.ts) will throw before any comparison runs. Both sides share the same schema_sha256, so only generated_at/replay_seconds differ and the freshness test passes either way — pick one side (the newer origin/main metadata) and delete the markers.

🐛 Proposed resolution

-<<<<<<< HEAD
-  "generated_at": "2026-07-09T10:38:15.859Z",
-  "generator": "scripts/generate-drift-manifest.ts",
-  "postgres_image": "supabase/postgres:17.6.1.127",
-  "schema_sha256": "3a60bf1561142aed58e45a1cf8a9605ccc715dd7358e154c4ad9879b82be4cd5",
-  "replay_seconds": 20,
-=======
   "generated_at": "2026-07-09T11:02:02.346Z",
   "generator": "scripts/generate-drift-manifest.ts",
   "postgres_image": "supabase/postgres:17.6.1.127",
   "schema_sha256": "3a60bf1561142aed58e45a1cf8a9605ccc715dd7358e154c4ad9879b82be4cd5",
   "replay_seconds": 28,
->>>>>>> origin/main

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

  "generated_at": "2026-07-09T11:02:02.346Z",
  "generator": "scripts/generate-drift-manifest.ts",
  "postgres_image": "supabase/postgres:17.6.1.127",
  "schema_sha256": "3a60bf1561142aed58e45a1cf8a9605ccc715dd7358e154c4ad9879b82be4cd5",
  "replay_seconds": 28,

🧰 Tools

🪛 Biome (2.5.1)

[error] 2-2: unexpected character <

(parse)

---

[error] 2-2: unexpected character <

(parse)

---

[error] 2-2: unexpected character <

(parse)

---

[error] 2-2: unexpected character <

(parse)

---

[error] 2-2: unexpected character <

(parse)

---

[error] 2-2: unexpected character <

(parse)

---

[error] 2-2: unexpected character <

(parse)

---

[error] 2-2: String values must be double quoted.

(parse)

---

[error] 3-3: End of file expected

(parse)

---

[error] 3-3: End of file expected

(parse)

---

[error] 3-3: End of file expected

(parse)

---

[error] 3-3: End of file expected

(parse)

---

[error] 4-4: End of file expected

(parse)

---

[error] 4-4: End of file expected

(parse)

---

[error] 4-4: End of file expected

(parse)

---

[error] 4-4: End of file expected

(parse)

---

[error] 5-5: End of file expected

(parse)

---

[error] 5-5: End of file expected

(parse)

---

[error] 5-5: End of file expected

(parse)

---

[error] 5-5: End of file expected

(parse)

---

[error] 6-6: End of file expected

(parse)

---

[error] 6-6: End of file expected

(parse)

---

[error] 6-6: End of file expected

(parse)

---

[error] 6-6: End of file expected

(parse)

---

[error] 7-7: End of file expected

(parse)

---

[error] 7-7: End of file expected

(parse)

---

[error] 7-7: End of file expected

(parse)

---

[error] 7-8: End of file expected

(parse)

---

[error] 8-8: unexpected character =

(parse)

---

[error] 8-8: unexpected character =

(parse)

---

[error] 8-8: unexpected character =

(parse)

---

[error] 8-8: unexpected character =

(parse)

---

[error] 8-8: unexpected character =

(parse)

---

[error] 8-8: unexpected character =

(parse)

---

[error] 8-8: unexpected character =

(parse)

---

[error] 9-9: End of file expected

(parse)

---

[error] 9-9: End of file expected

(parse)

---

[error] 9-9: End of file expected

(parse)

---

[error] 9-9: End of file expected

(parse)

---

[error] 10-10: End of file expected

(parse)

---

[error] 10-10: End of file expected

(parse)

---

[error] 10-10: End of file expected

(parse)

---

[error] 10-10: End of file expected

(parse)

---

[error] 11-11: End of file expected

(parse)

---

[error] 11-11: End of file expected

(parse)

---

[error] 11-11: End of file expected

(parse)

---

[error] 11-11: End of file expected

(parse)

---

[error] 12-12: End of file expected

(parse)

---

[error] 12-12: End of file expected

(parse)

---

[error] 12-12: End of file expected

(parse)

---

[error] 12-12: End of file expected

(parse)

---

[error] 13-13: End of file expected

(parse)

---

[error] 13-13: End of file expected

(parse)

---

[error] 13-13: End of file expected

(parse)

---

[error] 13-14: End of file expected

(parse)

---

[error] 14-14: unexpected character >

(parse)

---

[error] 14-14: unexpected character >

(parse)

---

[error] 14-14: unexpected character >

(parse)

---

[error] 14-14: unexpected character >

(parse)

---

[error] 14-14: unexpected character >

(parse)

---

[error] 14-14: unexpected character >

(parse)

---

[error] 14-14: unexpected character >

(parse)

---

[error] 14-14: unexpected character /

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@supabase/drift-manifest.json` around lines 2 - 14, Resolve the merge conflict
in drift-manifest.json so it remains valid JSON by removing the conflict markers
and keeping one clean set of metadata. Use the newer origin/main values for
generated_at and replay_seconds, and ensure the manifest still matches what
scripts/check-drift.ts and tests/drift-detection.test.ts expect to parse.

Source: Linters/SAST tools

tests/rag-answer-fallback.test.ts (1)

415-421: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers left in test file — suite will not run.

Literal <<<<<<< HEAD / ======= / >>>>>>> origin/main markers remain at Lines 415-421 around the routingReason matcher. Biome confirms a parse error here. Both sides assert the same regex, just formatted differently, so resolving is trivial — but the markers must be removed for the test file to parse at all.

🧰 Tools

🪛 Biome (2.5.1)

[error] 415-416: Expected a statement but instead found '<<<<<<< HEAD
expect(answer.routingReason).toMatch(/high_confidence_extractive_retrieval|source_backed_(?:extractive|review)_fallback/)'.

(parse)

---

[error] 417-420: Expected a statement but instead found '=======
expect(answer.routingReason).toMatch(
/high_confidence_extractive_retrieval|source_backed_(?:extractive|review)_fallback/,
)'.

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@tests/rag-answer-fallback.test.ts` around lines 415 - 421, Resolve the merge
conflict in the routingReason expectation inside the test by removing the
leftover conflict markers and keeping one valid matcher form; the issue is in
the test around the answer.routingReason assertion, and both branches are
equivalent so just preserve either formatting while deleting the <<<<<<< HEAD,
=======, and >>>>>>> origin/main lines.

Source: Linters/SAST tools

tests/rag-routing.test.ts (1)

186-193: 🎯 Functional Correctness | 🔴 Critical | ⚡ Quick win

Unresolved merge conflict markers left in test file — suite will not run.

Literal <<<<<<< HEAD / ======= / >>>>>>> origin/main markers remain at Lines 186-193 (clozapine FBC content string) and Line 207 (closing marker for the "unrelated stop wording" test). Biome reports parse errors throughout this range. This breaks the entire test suite compilation, including the newly updated extractive-routing expectations described for this cohort.

Also applies to: 200-207

🧰 Tools

🪛 Biome (2.5.1)

[error] 186-186: Expected a property, a shorthand property, a getter, a setter, or a method but instead found '<<'.

(parse)

---

[error] 186-186: Expected an expression but instead found '<<'.

(parse)

---

[error] 186-186: Expected an expression but instead found '<<'.

(parse)

---

[error] 187-187: expected > but instead found content

(parse)

---

[error] 187-187: expected , but instead found :

(parse)

---

[error] 188-188: expected , but instead found ===

(parse)

---

[error] 188-188: Expected an expression but instead found '==='.

(parse)

---

[error] 188-188: Expected an expression but instead found '='.

(parse)

---

[error] 188-188: Invalid assignment to ======

(parse)

---

[error] 189-189: expected , but instead found :

(parse)

---

[error] 190-190: expected , but instead found "FBC monitoring is weekly for the first 18 weeks and then every 4 weeks if blood results are in range."

(parse)

---

[error] 191-191: expected , but instead found :

(parse)

---

[error] 192-192: expected , but instead found }

(parse)

---

[error] 192-192: expected , but instead found )

(parse)

---

[error] 193-193: Expected an identifier, an array pattern, or an object pattern but instead found ']'.

(parse)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@tests/rag-routing.test.ts` around lines 186 - 193, Resolve the merge conflict
artifacts in the rag-routing test cases by removing all conflict markers and
keeping the intended final assertions for the clozapine FBC content and the
unrelated stop wording block. Update the affected test setup where the
array/object for these expectations is defined so the preserved content and
text_rank values are valid TypeScript. Ensure no `<<<<<<<`, `=======`, or
`>>>>>>>` markers remain anywhere in the test file so Biome can parse and run
the suite.

Source: Linters/SAST tools

dom

[BigSimmo]

@copilot resolve the merge conflicts in this pull request

[Copilot]

@copilot resolve the merge conflicts in this pull request

Done. The only conflict was in scripts/check-github-action-pins.mjs — an add/add conflict on the reason string for the actions/checkout version range. Resolved by taking the main version (more descriptive wording). The merge commit is 03caef5 and node scripts/check-github-action-pins.mjs passes cleanly.