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24/npm 11 Database environment with authenticated GitHub, OpenAI and Supabase access, Railway/Supabase CLI tooling, OCR runtimes, browser matrix, and unrestricted agent networking.","workspace_dir","/workspace","agent_network_access",{"_287":288,"_289":290,"_291":292,"_293":-5,"_294":-5,"_295":-5},"codex_github_direct","github_connector_id","enable_gitlab_webhooks","repos",[243],"setup",[286],"maintenance_setup",[285],"repo_map",{"_243":244},"env_vars",{"_216":217,"_218":219,"_220":221,"_222":223,"_224":225,"_226":227,"_228":229,"_230":231,"_232":233,"_234":235,"_236":237,"_238":239,"_240":239,"_241":242},"secrets",{},"secrets_with_domains","task_count",2225,"creator_id","user-meqzK8tcEkFfh4X5tXfIqXyp","share_settings","workspace","share_targets",[],1783581192.606357,"auto_setup_settings",{"_215":18},"cache_settings",{"_212":62,"_213":214},"etag","\"d700168d-0000-0200-0000-6a6b66200000\"","enable_authtranslator","enable_docker_in_docker","post_setup_cache_enabled","cache_invalidation_key","116a134b052a4c11acdc6283f01cbf55","use_auto_setup","CODEX_ENV_PYTHON_VERSION","3.12","CODEX_ENV_NODE_VERSION","20","CODEX_ENV_RUBY_VERSION","3.4.4","CODEX_ENV_RUST_VERSION","1.89.0","CODEX_ENV_GO_VERSION","1.24.3","CODEX_ENV_BUN_VERSION","1.2.14","CODEX_ENV_PHP_VERSION","8.4","CODEX_ENV_JAVA_VERSION","21","CODEX_ENV_SWIFT_VERSION","6.1","CODEX_CLOUD","1","RAG_PROVIDER_MODE","auto","NEXT_PUBLIC_DEMO_MODE","false","PLAYWRIGHT_OFFLINE_MODE","BASH_ENV","/root/.clinical-kb-codex-cloud.sh","github-1243497866",{"_45":245,"_152":246,"_247":248,"_249":171,"_250":251,"_252":253,"_254":255,"_256":257,"_258":259,"_260":261,"_262":18,"_263":62,"_264":62,"_265":18,"_266":62,"_267":62,"_268":-5,"_269":270,"_271":-5,"_58":272},"1243497866","Database","owner",{"_277":278,"_45":279,"_95":280,"_281":282,"_283":284},"repository_full_name","clone_url","https://github.com/BigSimmo/Database.git","default_branch","main","git_commits_url","https://api.github.com/repos/BigSimmo/Database/git/commits{/sha}","git_refs_url","https://api.github.com/repos/BigSimmo/Database/git/refs{/sha}","git_url","git://github.com/BigSimmo/Database.git","visibility","private","archived","allow_auto_merge","allow_merge_commit","allow_rebase_merge","allow_squash_merge","allow_update_branch","language","size",81245,"master_branch",{"_273":62,"_274":62,"_275":62,"_276":62},"admin","maintain","push","pull","login","BigSimmo",87357024,"User","avatar_url","https://avatars.githubusercontent.com/u/87357024?v=4","url","https://api.github.com/users/BigSimmo","set -Eeuo pipefail\nlog() { printf '[codex-cloud:maintenance] %s\\n' \"$*\"; }\nfail() { printf '[codex-cloud:maintenance] ERROR: %s\\n' \"$*\" >&2; exit 1; }\nrepo_root=\"$(git rev-parse --show-toplevel 2>/dev/null)\" || fail 'Run this script from the Database repository.'\ncd \"$repo_root\"\nruntime_profile=\"$HOME/.clinical-kb-codex-cloud.sh\"\n[[ -f \"$runtime_profile\" ]] || fail 'Provider runtime profile is missing; reset the environment cache.'\nsource \"$runtime_profile\"\nexpected_node_major=\"$(tr -cd '0-9' < .node-version)\"\nactual_node_version=\"$(node --version 2>/dev/null || true)\"\n[[ \"$actual_node_version\" == v\"$expected_node_major\".* ]] || fail 'Node runtime drift requires a cache reset.'\nif ! npm run check:installed-lock-parity >/dev/null 2>&1; then\n log 'Dependency drift detected; restoring package-lock.json exactly.'\n npm ci --include=dev\nfi\nnpm run check:runtime\nnpm run check:installed-lock-parity\nnpm run check:codex-cloud\ngh auth setup-git >/dev/null\ngh auth status >/dev/null\ncommand -v supabase >/dev/null 2>&1 || fail 'Supabase CLI is missing; reset the environment cache.'\nif ! command -v railway >/dev/null 2>&1; then\n npm install --global '@railway/cli@5.27.0' >/dev/null 2>&1 || log 'WARNING: Railway CLI remains unavailable; other authenticated capabilities are ready.'\nfi\nnode -e 'const k=[\"OPENAI_API_KEY\",\"NEXT_PUBLIC_SUPABASE_URL\",\"SUPABASE_PROJECT_REF\",\"SUPABASE_PROJECT_NAME\",\"NEXT_PUBLIC_SUPABASE_PUBLISHABLE_KEY\",\"SUPABASE_SERVICE_ROLE_KEY\",\"SUPABASE_SECRET_KEY\",\"SUPABASE_JWKS_URL\",\"E2E_USER_EMAIL\",\"E2E_USER_PASSWORD\",\"E2E_USER_UID\",\"RAG_EVAL_OWNER_ID\",\"RAG_QUERY_HASH_SECRET\",\"OPENAI_SAFETY_IDENTIFIER_SECRET\",\"HEALTH_DEEP_PROBE_SECRET\"]; const m=k.filter(x=>!process.env[x]); if(m.length){console.error(\"Missing provider runtime variables: \"+m.join(\", \")); process.exit(1)}'\nlog 'Maintenance complete: live provider profile and authenticated GitHub tooling are ready.'","set -Eeuo pipefail\nunset BASH_ENV\nlog() { printf '[codex-cloud:setup] %s\\n' \"$*\"; }\nfail() { printf '[codex-cloud:setup] ERROR: %s\\n' \"$*\" >&2; exit 1; }\nif ! command -v gh >/dev/null 2>&1; then\n command -v apt-get >/dev/null 2>&1 || fail 'apt-get is required to install GitHub CLI.'\n if [[ \"$(id -u)\" -eq 0 ]]; then\n apt-get update && apt-get install -y --no-install-recommends gh\n elif command -v sudo >/dev/null 2>&1; then\n sudo apt-get update && sudo apt-get install -y --no-install-recommends gh\n else\n fail 'root or sudo is required to install GitHub CLI.'\n fi\nfi\ngh --version | head -n 1\n[[ -v GH_TOKEN ]] && [[ -n \"$GH_TOKEN\" ]] || fail 'GH_TOKEN secret is required.'\nprovider_keys='OPENAI_API_KEY NEXT_PUBLIC_SUPABASE_URL SUPABASE_PROJECT_REF SUPABASE_PROJECT_NAME NEXT_PUBLIC_SUPABASE_PUBLISHABLE_KEY SUPABASE_SERVICE_ROLE_KEY SUPABASE_SECRET_KEY SUPABASE_JWKS_URL E2E_USER_EMAIL E2E_USER_PASSWORD E2E_USER_UID RAG_EVAL_OWNER_ID RAG_QUERY_HASH_SECRET OPENAI_SAFETY_IDENTIFIER_SECRET HEALTH_DEEP_PROBE_SECRET'\nfor name in $provider_keys; do\n value=\"$(printenv \"$name\" || true)\"\n [[ -n \"$value\" ]] || fail \"Required Cloud secret $name is missing.\"\ndone\nset +x\n_cloud_gh_token=\"$GH_TOKEN\"\nunset GH_TOKEN GITHUB_TOKEN\nprintf '%s' \"$_cloud_gh_token\" | gh auth login --hostname github.com --with-token >/dev/null\nunset _cloud_gh_token\ngh auth setup-git >/dev/null\nbash scripts/setup-codex-cloud.sh\nruntime_profile=\"$HOME/.clinical-kb-codex-cloud.sh\"\n{\n printf '\\n# Provider-enabled Cloud override. Generated from encrypted setup-only secrets.\\n'\n printf 'export RAG_PROVIDER_MODE=auto\\n'\n printf 'export NEXT_PUBLIC_DEMO_MODE=false\\n'\n printf 'export PLAYWRIGHT_OFFLINE_MODE=false\\n'\n printf 'unset LOCAL_NO_AUTH NEXT_PUBLIC_LOCAL_NO_AUTH\\n'\n for name in $provider_keys; do\n value=\"$(printenv \"$name\")\"\n printf 'export %s=%q\\n' \"$name\" \"$value\"\n done\n} >> \"$runtime_profile\"\nchmod 600 \"$runtime_profile\"\nsource \"$runtime_profile\"\ngh auth setup-git >/dev/null\nmkdir -p \"$HOME/.local/bin\"\ncat > \"$HOME/.local/bin/supabase\" <<'SUPABASE_WRAPPER'\n#!/usr/bin/env bash\nexec npx --yes supabase@2.109.1 \"$@\"\nSUPABASE_WRAPPER\nchmod 700 \"$HOME/.local/bin/supabase\"\nnpx --yes supabase@2.109.1 --version >/dev/null\nif npm install --global '@railway/cli@5.27.0'; then\n railway --version >/dev/null\nelse\n log 'WARNING: Railway CLI download was unavailable; provider checks remain disabled until a dedicated Railway token and reachable CLI are supplied.'\nfi\ngh auth status >/dev/null\nnode -e 'const k=[\"OPENAI_API_KEY\",\"NEXT_PUBLIC_SUPABASE_URL\",\"SUPABASE_PROJECT_REF\",\"SUPABASE_PROJECT_NAME\",\"NEXT_PUBLIC_SUPABASE_PUBLISHABLE_KEY\",\"SUPABASE_SERVICE_ROLE_KEY\",\"SUPABASE_SECRET_KEY\",\"SUPABASE_JWKS_URL\",\"E2E_USER_EMAIL\",\"E2E_USER_PASSWORD\",\"E2E_USER_UID\",\"RAG_EVAL_OWNER_ID\",\"RAG_QUERY_HASH_SECRET\",\"OPENAI_SAFETY_IDENTIFIER_SECRET\",\"HEALTH_DEEP_PROBE_SECRET\"]; const m=k.filter(x=>!process.env[x]); if(m.length){console.error(\"Missing provider runtime variables: \"+m.join(\", \")); process.exit(1)}'\nlog 'Setup complete: live provider profile, GitHub credential helper, Supabase CLI, OCR, Deno, and Playwright are ready.'","mode","on","preset_allowlist","all","allowlist_domains","","allowlist_rules","denylist_domains","safe_methods_only","number",1477,"https://github.com/BigSimmo/Database/pull/1477","state","closed","merged","mergeable","draft","title","ci: require Codex fixes to land on the PR head branch","body","### Motivation\n\n- Prevent `@codex` auto-fix replies from claiming fixes that never land by binding repair requests to the exact repository and PR head branch and refusing detached/synthetic work branches.\n- Make thread-resolution machine-verifiable so the workflow can close a thread only when a reported pushed commit is the actual PR head.\n- Strengthen the auto-resolve routing and guard so only appropriate, low-risk, auditable automatic repairs run.\n\n### Description\n\n- Updated the auto-resolve workflow `.github/workflows/codex-autofix-review-comments.yml` to embed the intended repository/PR-head into the request prompt, add machine-readable result markers (`` and ``), and validate that a reported fixed commit equals the PR head before resolving a thread. \n- Hardened the thread-resolution path to fail-closed on malformed or mismatched results and to reject ambiguous/no-op dispositions. \n- Revised repo guidance in `AGENTS.md` and `docs/codex-review-protocol.md` to require publishing fixes through the authenticated connector and to document the new result markers and verification discipline. \n- Extended the workflow guard `scripts/check-codex-autofix-workflow.mjs` to assert the new markers, routing, and verification rules. \n- Added/updated executable tests in `tests/codex-autofix-workflow.test.ts` to cover intended-branch routing, dedupe behavior, malformed results, mismatched-head refusal, and no-change dispositions. \n- Archived issue #131 in `docs/outstanding-issues.md` and updated the outstanding-issues guard where relevant.\n\n### Testing\n\n- Ran `npm run check:codex-autofix-workflow` and the guard passed. \n- Ran the focused workflow tests with `npm run test -- tests/codex-autofix-workflow.test.ts` and the updated test file passed (all included assertions green). \n- Ran repository gates: `npm run format`, `npm run check:outstanding-issues`, and `npm run verify:cheap` (dry and full local gates as part of the PR-local dry run); `verify:cheap` completed successfully (full test suite run completed: all unit tests passed with a small number skipped per environment). \n- Note: fetching the external Codex manual failed in this environment due to outbound network `ENETUNREACH`, so implementation and checks relied on the repository’s existing hardening and executable guards rather than an external docs fetch.\n\n------\n[Codex Task](https://chatgpt.com/codex/cloud/tasks/task_e_6a6b596bed788322bd395596cff73fa0)","base","head","base_sha","e26b5a1facb17863b7cbe4a83fc56963b37f3d14","head_sha","87bc83e1ec3ba781b87af7536bcb4e0a551815b8","merge_commit_sha","343a590aebf612007080d000ce5fc4c7e48d9497","comments","diff","user",{"_277":278,"_152":278,"_328":-5,"_281":282,"_45":279},"commits",5,"changed_files",7,"additions",136,"deletions",10,"email","events",[],[],"messages",[],{"_95":391,"_99":96,"_351":392},{"_95":336,"_337":338},"partial_repo_snapshot","files",[339],{"_340":341,"_342":-5,"_343":344,"_345":-5},"path","docs/codex-review-protocol.md","contents","line_range_contents",[346],"missing_reason",{"_347":348,"_349":350,"_351":352,"_353":62},"line_range_start",1,"line_range_end",50,"content",[354,292,355,292,356,292,357,358,359,360,361,362,363,364,292,365,292,366,367,368,369,370,371,292,372,292,373,374,375,376,377,378,379,292,380,292,381,382,383,384,292,385,292,386,292,387,388,389,292,390],"contains_end_of_file","# Codex Review Protocol","Use this protocol for every Codex review, audit, bug hunt, PR review, release-readiness check, and branch-cleanup review in this repository.","## Trigger and Scope","- Do not start a review opportunistically.","- Review only when the user request, `AGENTS.md` routing rules, or an explicit handoff/release workflow calls for it.","- Review the current diff, named PR, named branch, or explicitly requested area.","- Do not expand into stale branches or unrelated modules unless a confirmed defect crosses that boundary.","- Before branch or PR review, check `docs/branch-review-ledger.md` with `npm run ledger:lookup -- --scope \"\"`. It resolves the HEAD, matches abbreviated SHAs, and prints an explicit verdict. Skip unchanged completed reviews unless the user asks for a fresh pass. Do not scan the table by eye.","- Treat GitHub automatic review as one pass per pull request. A repair commit or later head does not authorize another automatic pass; require an explicit human request before re-reviewing.","- Route automatic repair only for high-risk paths, at least 10 changed non-test source files, at least 300 changed non-test source lines, or an explicit `codex-review` label. `skip-codex-review` always opts out, including when both labels are present. Small low-risk, docs-only, test-only, and generated-only changes should not receive the automatic repair request.","- Ready PRs must pass the trusted `PR policy` metadata check. It reads only the base-branch policy implementation, never executes PR code, and requires concrete verification plus risk/rollback evidence for high-risk changes.","## Review Output","- Lead with findings, ordered by severity: P0, P1, P2, then P3.","- For automatic PR reviews, emit no more than three inline findings and reserve them for P0/P1 defects. Consolidate non-blocking P2 context into one summary and omit P3 feedback.","- Each finding must include file/line evidence, trigger or failure path, expected behavior, actual risk, and the smallest proof or check that would catch it.","- If no high-confidence issue is found, say so clearly and name the highest residual risk area.","- Include checks run, checks not run, and whether any check was skipped because it could touch an API/provider.","- Keep summaries secondary to findings.","## Mutation Rules","- For a pure review request, do not edit files, stage, commit, push, post PR comments, rerun hosted CI, or call provider-backed services."," - Exception: append the completed review record to `docs/branch-review-ledger.md` so throttling state persists.","- If the user clearly asks to fix confirmed findings, make the smallest safe change and verify with local, static, or mocked checks first.","- During an automatic resolve task, work only existing unresolved Codex threads. Do not start a new review, add standalone findings, or request another review.","- After fixing or fully dispositioning a thread, start the reply with ``, then declare exactly one result: `` for a published fix or `` for a no-code disposition. The workflow closes a fixed thread only when the reported commit is the pull-request head. A local-only commit is not a fix; when publication, verification, human input, or new authorization blocks completion, use no result marker and leave the thread open with a concise reason.","- Ask before any OpenAI, Supabase, GitHub/GitLab, hosted CI, or provider-backed workflow.","- After any completed branch/PR review, append to `docs/branch-review-ledger.md` with `npm run ledger:append -- --ref --head --scope --outcome --checks `. Record the full 40-character SHA; `see PR head` and abbreviations make the record unmatchable and cause the review to run again. The ledger is append-only: never edit or delete an existing record; append a correction or superseding record (`--supersede`) instead. This ledger append is allowed even during a pure review. Do not hand-write the markdown row — hand-written rows are what produced the mojibake, wrong-width, and duplicate records the 2026-07-28 hygiene pass had to repair. Do not push a tip whose sole delta is a babysit ledger append; after merging `origin/main` into a branch that touched the ledger, run `npm run ledger:dedupe` when exact twins appear.","## Severity Guide","- P0: Data loss, security breach, production outage, or clinical safety issue likely to harm users immediately.","- P1: Broken core workflow, unsafe automation, privacy/auth failure, or repeatable defect that blocks merge/handoff.","- P2: Real defect, missing guardrail, fragile process, or test gap that should be fixed before relying on the work.","- P3: Low-risk cleanup, clarity, documentation, or future-proofing issue.","## Final merge audit","Before a protected-main merge, run the local audit from a clean PR checkout and pin the reviewed head:","```powershell","npm run audit:final-merge -- --dry-run --base-ref origin/main --head-ref HEAD --expected-head ","```","The output records the local base/head and expected merge-tree. GitHub checks, labels, review threads, fresh remote refs, and deployment health are provider reads and require explicit authorization. Once authorized, add `--providers --pr --repo BigSimmo/Database` and set `ALLOW_PROVIDER_READS=true`; the audit fails closed unless the repository's `pr-required` aggregate is present and settled successfully. After the squash merge, rerun with `--post-merge --expected-tree --health-url /api/health`; the audit compares the remote main tree and requires an HTTP success with JSON `status: \"ok\"`. The script is read-only: it never merges, pushes, reruns CI, resolves threads, or deploys.","message",[393,394,395],{"_396":49,"_49":401},{"_396":398,"_340":341,"_347":399,"_349":400},{"_396":49,"_49":397},"content_type","\n* The workflow guard and focused test suite passed. Because no files changed, I did not create an empty commit or an unnecessary follow-up pull request.\n\n**Testing**\n\n* ✅ `git diff --check d6a1473187a4c6f109c456b75bb97d02ff1951b4...HEAD`\n* ✅ `npm run check:codex-autofix-workflow` — `Codex auto-resolve workflow guard passed.`\n* ✅ `npm run test -- tests/codex-autofix-workflow.test.ts` — `Test Files 1 passed (1)` and `Tests 51 passed (51)`.\n* ✅ `git status --short --branch` — clean worktree on branch `work`.","repo_file_citation",35,38,"### Summary\n\n* No follow-up code change was needed. The checkout is already at the supplied PR head, `a32078825b667a780c5d0566cb8c1320d3efa8d4`, and the worktree remains clean.\n* The supplied comments contain no actionable review finding: CodeRabbit reported only a temporary review limit, while Supabase correctly skipped the PR because it does not change the `supabase` directory.\n* The existing PR implementation already documents the fixed-head/no-change result-marker contract and requires the reported commit to match the pull-request head before automatic thread resolution. 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You can change this behaviour in [Project Integrations Settings ↗︎](https://supabase.com/dashboard/project/sjrfecxgysukkwxsowpy/settings/integrations).\n\n
\n\nPreview Branches by Supabase.\nLearn more about [Supabase Branching ↗︎](https://supabase.com/docs/guides/platform/branching).","side","line","\n\n\n> [!WARNING]\n> ## Review limit reached\n> \n> You’ve reached a temporary PR review limit under our [Fair Usage Limits Policy](https://docs.coderabbit.ai/management/plans#fair-usage-limits-policy).
\n> Your recent review volume is higher than typical usage, so adaptive limits are currently applied.\n> \n> **Next review available in:** **11 minutes**\n> \n> Your organization has reached its usage spending cap. Adjust your spending cap in the [billing tab](https://app.coderabbit.ai/settings/billing?tab=usage&orgId=420f13a9-28c9-4ad8-9f2e-1fd2cf273b7c).\n> \n>
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How can I continue?
\n> \n> After more reviews become available, a review can be triggered using the `@coderabbitai review` command as a PR comment. Alternatively, push new commits to this PR.\n> \n> To avoid repeated limits, reduce automatic review volume by pausing incremental auto-reviews earlier, using label-based review opt-in, excluding WIP or generated PR titles, or requesting reviews manually when the PR is ready. If your team needs uninterrupted high-volume reviews, an organization admin can enable usage-based reviews.\n> \n>
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\n> \n> CodeRabbit enforces per-developer PR review limits for each organization. Most developers receive the normal plan review availability.\n> \n> For paid Pro and Pro+ PR reviews, CodeRabbit uses adaptive limits for sustained high-volume activity. When a developer's recent PR review activity reaches the 95th percentile or higher among CodeRabbit users, additional reviews become available more gradually as earlier reviews age out of the rolling window.\n> \n> Please refer [docs](https://docs.coderabbit.ai/management/plans#rate-limits) for additional details.\n> \n>
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Review details
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⚙️ Run configuration
\n> \n> **Configuration used**: Path: .coderabbit.yaml\n> \n> **Review profile**: CHILL\n> \n> **Plan**: Pro\n> \n> **Run ID**: `5a1f3d98-b1cf-49f0-9c26-ebd464700cdf`\n> \n>
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📥 Commits
\n> \n> Reviewing files that changed from the base of the PR and between d6a1473187a4c6f109c456b75bb97d02ff1951b4 and a32078825b667a780c5d0566cb8c1320d3efa8d4.\n> \n>
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📒 Files selected for processing (6)
\n> \n> * `.github/workflows/codex-autofix-review-comments.yml`\n> * `AGENTS.md`\n> * `docs/codex-review-protocol.md`\n> * `docs/outstanding-issues.md`\n> * `scripts/check-codex-autofix-workflow.mjs`\n> * `tests/codex-autofix-workflow.test.ts`\n> \n>
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