{
  "id": "doctolib-worktrees/631d371b",
  "slug": "631d371b",
  "title": "Session: 631d371b — 2026-05-04",
  "type": "source",
  "project": "doctolib-worktrees",
  "date": "2026-05-04",
  "started": "2026-05-04T15:27:03.247000+00:00",
  "ended": "2026-05-05T12:05:20.906000+00:00",
  "model": "claude-sonnet-4-6",
  "cwd": "/Users/USER/workspace/doctolib/worktrees",
  "git_branch": "HEAD",
  "permission_mode": "acceptEdits",
  "user_messages": 1,
  "tool_calls": 25,
  "tools_used": [
    "Bash"
  ],
  "is_subagent": false,
  "wikilinks_out": [],
  "body_text": "Project: doctolib-worktrees · Branch: HEAD · Mode: acceptEdits · Model: claude-sonnet-4-6\n\nStats: 1 user messages, 25 tool calls, tools used: Bash.\n\nConversation\n\nTurn 1 — User\n\nupdate the code from the PR https://github.com/doctolib/doctolib/pull/241176 with the latest version on master branch, push it, and then run the ci tests with \"dctl ci test --pr 241176\"\n\nTurn 1 — Assistant\n\nLet me start by exploring the repository structure to understand the setup.\n\nTools used:\n\n- Bash: ls /Users/USER/workspace/doctolib/worktrees\n\nTools used:\n\n- Bash: ls /Users/USER/workspace/doctolib/\n\nTool results:\n\n  → result (ok): cleanup-merged-worktrees.sh\ndoctolib\ntreatment-plan\n\nTool results:\n\n  → result (ok): actions\nbilleo-engine\nc3-rest-api-guidelines\ndocto-crypt\ndoctoboot\ndoctolib\ndoctolib-pr-review.skill\ndoctolib-pro-desktop\ngithub-workspaces\nkube\nmisc\noxygen\nprompts\nsoftware-design-training\nterraform-aws-secrets\nterraform-infra\ntest-failures\nti-client\ntreatment-plan\nunified-healthcare-data-platform-infra\nupfront\nwaiting-room\nworktrees\n\nTools used:\n\n- Bash: ls /Users/USER/workspace/doctolib/worktrees/doctolib\n\nTool results:\n\n  → result (ok): fhir-2089\nFHIR-2091-nhr-document-list-pagination\nFHIR-2166-fix-nhr-mock-status-visibility\nfhir-2169\nfhir-2181\nFHIR-2184\nfhir-2189_class-code-label-map\nfhir-2190_improve-filter-panel-ui\nfhir-2199-dmp-validation-page\nfhir-2209_fix-patient-ins-env-transformation\nfhir-2216_fix-nhr-date-columns-and-document-type\nfhir-2221_display-last-dmp-access-date\nfhir-2222_add-visible-to-all-filter\nfhir-2223_fix-column-widths-dmp\nFHIR-2224\nfhir-2235_expand-document-category-filter-type-codes\n\nTools used:\n\n- Bash: cd /Users/USER/workspace/doctolib/doctolib && git worktree list\n\nTool results:\n\n  → result (ok): /Users/USER/workspace/doctolib/doctolib                                                                07ad53f66fc1 [master]\n/Users/USER/workspace/doctolib/worktrees/doctolib/fhir-2089                                            9c01fcf036d7 (detached HEAD)\n/Users/USER/workspace/doctolib/worktrees/doctolib/FHIR-2091-nhr-document-list-pagination               0729f7b7bbaa [FHIR-2091-nhr-document-list-pagination]\n/Users/USER/workspace/doctolib/worktrees/doctolib/FHIR-2166-fix-nhr-mock-status-visibi\n…(truncated, 2122 more chars)\n\nNow let me find the branch for PR #241176.\n\nTools used:\n\n- Bash: cd /Users/USER/workspace/doctolib/doctolib && gh pr view 241176 --json headRefName,baseRefName,title,state 2>&1\n\nTool results:\n\n  → result (ok): {\"baseRefName\":\"master\",\"headRefName\":\"fhir-2222_add-visible-to-all-filter\",\"state\":\"OPEN\",\"title\":\"fix(fhir-2222): add Visible to all option to DMP NHR document visibility filter\"}\nShell cwd was reset to /Users/USER/workspace/doctolib/worktrees\n\nThe PR branch is fhir-2222_add-visible-to-all-filter. Let me check its current state and how far it's behind master.\n\nTools used:\n\n- Bash: cd /Users/USER/workspace/doctolib/worktrees/doctolib/fhir-2222_add-visible-to-all-filter && git status && git log --oneline -5\n\nTools used:\n\n- Bash: cd /Users/USER/workspace/doctolib/doctolib && git fetch origin master --quiet && git log --oneline -5 origin/master\n\nTool results:\n\n  → result (ok): On branch fhir-2222_add-visible-to-all-filter\nYour branch is up to date with 'origin/fhir-2222_add-visible-to-all-filter'.\n\nIt took 3.00 seconds to enumerate untracked files.\nSee 'git help status' for information on how to improve this.\n\nnothing to commit, working tree clean\n4359daceb259 refactor(fhir-2222): change visibleToAll to union bitmask model\n080c4457547a fix(fhir-2222): handle visibleToAll in mock filter and close test gaps\ncb4ab8289db2 fix(fhir-2222): add visibleToAll filter to DMP NH\n…(truncated, 220 more chars)\n\nTool results:\n\n  → result (ok): 2c6ba5702bc7 chore(deps): update dependency @doctolib/clinical-notes to ^2.22.1 (#241904)\n8f9306cad2a7 fix(APE-3910): Remove unneeded RT UpdateSessionBillingDataField (#241770)\nedc219d8da50 chore(VIBE-1534): add patient.crm_patient_campaign_sender_jobs to pg_no_seqscan check_tables (#237900)\ndf1ffc018d76 fix(CFS-1335): handle duplicate Phrase job name on workflow retry (#241856)\nf76759b50654 feat(DOPE-5385): renovate config for tpf-prescription-forms-commons (#241900)\nShell cwd was reset to /Use\n…(truncated, 36 more chars)\n\nTools used:\n\n- Bash: cd /Users/USER/workspace/doctolib/worktrees/doctolib/fhir-2222_add-visible-to-all-filter && git rev-list --count HEAD..origin/master\n\nTool results:\n\n  → result (ok): 562\n\nThe branch is 562 commits behind master. I'll merge master into the PR branch now.\n\n★ Insight ─────────────────────────────────────\n- Merging master into a feature branch (rather than rebasing) is safer for open PRs because it preserves the existing commit history — a rebase would rewrite SHAs and force-push, which can confuse reviewers who already reviewed the old commits.\n- Git's three-way merge algorithm finds a common ancestor and applies diverged changes from both sides, creating a merge commit that ties both histories together.\n─────────────────────────────────────────────────\n\nTools used:\n\n- Bash: git merge origin/master --no-edit 2>&1\n\nTool results:\n\n  → result (ERROR): Exit code 128\nerror: Unable to create '/Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock': File exists.\n\nAnother git process seems to be running in this repository, or the lock file may be stale\nfatal: Unable to write index.\n\nTools used:\n\n- Bash: rm /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock && git merge origin/master --no-edit 2>&1\n\nTool results:\n\n  → result (ERROR): Exit code 128\nerror: Unable to create '/Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock': File exists.\n\nAnother git process seems to be running in this repository, or the lock file may be stale\nfatal: Unable to write index.\n\nTools used:\n\n- Bash: ls -la /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/\n\nTool results:\n\n  → result (ok): drwxr-xr-x clertonra staff 320 B  Mon May  4 17:34:09 2026 .\ndrwxr-xr-x clertonra staff 576 B  Mon May  4 16:45:21 2026 ..\n.rw-r--r-- clertonra staff 432 B  Wed Apr 29 09:55:26 2026 COMMIT_EDITMSG\n.rw-r--r-- clertonra staff   6 B  Tue Apr 28 16:04:50 2026 commondir\n.rw-r--r-- clertonra staff  96 B  Tue Apr 28 16:04:50 2026 gitdir\n.rw-r--r-- clertonra staff  25 B  Tue Apr 28 16:04:50 2026 HEAD\n.rw-r--r-- clertonra staff  14 MB Wed Apr 29 09:55:26 2026 index\n.rw-r--r-- clertonra staff   0 B  Mon M\n…(truncated, 162 more chars)\n\nTools used:\n\n- Bash: rm /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock\n\nTool results:\n\n  → result (ok): (Bash completed with no output)\n\nTools used:\n\n- Bash: git merge origin/master --no-edit 2>&1\n\nTool results:\n\n  → result (ERROR): Exit code 128\nerror: Unable to create '/Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock': File exists.\n\nAnother git process seems to be running in this repository, or the lock file may be stale\nfatal: Unable to write index.\n\nThe lock keeps regenerating. Let me check if there's an active git process.\n\nTools used:\n\n- Bash: pgrep -a git 2>/dev/null | head -20\n\nTool results:\n\n  → result (ok): 11781\n16757\n21624\n23065\n32273\n71290\n78697\n78701\n78702\n89903\n92418\n\nTools used:\n\n- Bash: ps aux | grep git | grep -v grep | head -20\n\nTool results:\n\n  → result (ok): <persisted-output>\nOutput too large (733.1KB). Full output saved to: /Users/USER/.claude/projects/-Users-clertonra-workspace-doctolib-worktrees/a00cc540-43f8-419b-9cad-c21c42432c7e/tool-results/b18rjl5x9.txt\n\nPreview (first 2KB):\nclertonra        78739  75.6  0.1 442541888  41424 s000  R+    5:34PM   0:02.40 git -C /Users/USER/workspace/doctolib/worktrees/doctolib/fhir-2222_add-visible-to-all-filter status --porcelain=v2 --branch --untracked-files=all\nroot               579  42.0  0.1 418843072 \n…(truncated, 1184 more chars)\n\nA git status process is running in that worktree. Let me wait for it and run the merge with the explicit path.\n\nTools used:\n\n- Bash: sleep 5 && ls /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock 2>/dev/null && echo \"lock still exists\" || echo \"lock cleared\"\n\nTool results:\n\n  → result (ok): /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock\nlock still exists\n\nTools used:\n\n- Bash: ps aux | grep \"git.*fhir-2222\" | grep -v grep\n\nTool results:\n\n  → result (ok): (Bash completed with no output)\n\nThe process finished but left a stale lock. Let me remove it and run the merge.\n\nTools used:\n\n- Bash: rm /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock && git merge origin/master --no-edit 2>&1\n\nTool results:\n\n  → result (ERROR): Exit code 128\nerror: Unable to create '/Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock': File exists.\n\nAnother git process seems to be running in this repository, or the lock file may be stale\nfatal: Unable to write index.\n\nThe zsh gitstatus daemon keeps recreating the lock. Let me run rm and merge atomically in a single Bash call.\n\nTools used:\n\n- Bash: rm -f /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock; git -C /Users/USER/workspace/doctolib/worktrees/doctolib/fhir-2222_add-visible-to\n…(truncated, 46 more chars)\n\nTool results:\n\n  → result (ERROR): Exit code 128\nerror: Unable to create '/Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock': File exists.\n\nAnother git process seems to be running in this repository, or the lock file may be stale\nfatal: Unable to write index.\n\nTools used:\n\n- Bash: lsof /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock 2>/dev/null || echo \"file not open by any process\"\n\nTool results:\n\n  → result (ok): file not open by any process\n\nTools used:\n\n- Bash: stat /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock\n\nTool results:\n\n  → result (ok): 16777234 324402469 -rw-r--r-- 1 clertonra staff 0 0 \"May  4 17:35:24 2026\" \"May  4 17:35:24 2026\" \"May  4 17:35:24 2026\" \"May  4 17:35:24 2026\" 4096 0 0 /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock\n\nThe lock is stale but something recreates it each time. Let me check if a hook is interfering.\n\nTools used:\n\n- Bash: cat /Users/USER/.claude/settings.json | python3 -c \"import json,sys; d=json.load(sys.stdin); print(json.dumps(d.get('hooks', {}), indent=2))\" 2>/dev/null || echo \"no hooks or file not found\"\n\nTool results:\n\n  → result (ok): {\n  \"Stop\": [\n    {\n      \"hooks\": [\n        {\n          \"type\": \"command\",\n          \"command\": \"~/.claude/hooks/langfuse-publisher.sh\"\n        }\n      ]\n    }\n  ]\n}\n\nTools used:\n\n- Bash: kill $(pgrep -f \"gitstatusd-darwin-arm64\") 2>/dev/null; sleep 1; rm -f /Users/USER/workspace/doctolib/doctolib/.git/worktrees/fhir-2222_add-visible-to-all-filter/index.lock; git -C /Users/clerton\n…(truncated, 111 more chars)\n\nTool results:\n\n  → result (ok): <persisted-output>\nOutput too large (2.5MB). Full output saved to: /Users/USER/.claude/projects/-Users-clertonra-workspace-doctolib-worktrees/a00cc540-43f8-419b-9cad-c21c42432c7e/tool-results/b0kry0jxf.txt\n\nPreview (first 2KB):\nAuto-merging packages/@doctolib/national-health-records/src/variants/dmp/factories/filtersFactory.ts\nMerge made by the 'ort' strategy.\n .billeo-version                                    |     2 +-\n .cherry/freemium.ts                                |     5 +-\n .../migrat\n…(truncated, 1749 more chars)\n\nThe merge succeeded. Now let me push the updated branch.\n\nTools used:\n\n- Bash: git -C /Users/USER/workspace/doctolib/worktrees/doctolib/fhir-2222_add-visible-to-all-filter push origin fhir-2222_add-visible-to-all-filter 2>&1\n\nTool results:\n\n  → result (ok): To https://github.com/doctolib/doctolib.git\n   4359daceb259..fa7900ff6e95  fhir-2222_add-visible-to-all-filter -> fhir-2222_add-visible-to-all-filter\n\nBranch pushed successfully. Now let me run the CI tests.\n\nTools used:\n\n- Bash: dctl ci test --pr 241176 2>&1\n\nTool results:\n\n  → result (ok): ✓ Workflow triggered\n✓ Triggered workflow available at https://github.com/doctolib/doctolib/actions/runs/25328624564?pr=241176\n\nAll done. Here's what happened:\n\n1. Merged master — the branch fhir-2222_add-visible-to-all-filter was 562 commits behind master. Killed stale gitstatus daemon locks and ran git merge origin/master --no-edit using the ORT strategy (no conflicts).\n2. Pushed — the updated branch is now at fa7900ff6e95.\n3. CI triggered — workflow is running at the GitHub Actions link above.\n\n★ Insight ─────────────────────────────────────\n- The index.lock race condition was caused by the zsh gitstatus daemon (used by powerlevel10k/oh-my-zsh prompt themes) — it continuously polls open directories for git status and holds the index lock briefly, conflicting with any manual git write operation.\n- Killing the daemon temporarily is safe; it auto-restarts when the next shell prompt renders.\n─────────────────────────────────────────────────",
  "sha256": "17d578736800066d",
  "source_url": "sessions/doctolib-worktrees/2026-05-04T15-27-doctolib-worktrees-631d371b.html"
}