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DETAILED CONFLICT FILE LISTING - PR #29
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Total: 115 conflicted files organized by resolution priority and category

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CRITICAL - MUST RESOLVE FIRST (5 files)
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CORE APPLICATION:
  1. apps/api/src/api/main.py
     - Type: add/add (different router imports and initialization logic)
     - Feature branch: workos_oauth_router, file_router, orchestrator_ws_router, financial_router
     - Develop branch: search_router, participant_router, monitoring_router
     - Resolution: Union approach (merge both router sets)

CONFIGURATION:
  2. apps/api/pyproject.toml
     - Type: add/add (dependency version conflicts)
     - Key conflicts:
       a) pydantic: extras=["email"] vs no extras
       b) pytest: 8.0.0 vs 7.4.3
       c) workos: feature branch only
     - Resolution: Keep feature branch versions where more recent

  3. apps/api/src/config/settings.py
     - Type: add/add (configuration options)
     - Resolution: Merge both configurations (keep comprehensive version)

AUTHENTICATION:
  4. apps/api/src/adapters/auth/authentication-manager.ts
     - Type: add/add (implementation conflicts)
     - Feature branch: _tokenCache (private), encryption methods
     - Develop branch: tokenCache (public), different implementation
     - Resolution: Code review required, merge both improvements

DEPENDENCIES:
  5. requirements.txt
     - Type: add/add (Python dependencies)
     - Resolution: Align with pyproject.toml decisions

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HIGH PRIORITY - CORE BACKENDS (60 files)
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API ADAPTERS (10 files):
  6. apps/api/src/adapters/base/adapter.ts
  7. apps/api/src/adapters/core/box-adapter.ts
  8. apps/api/src/adapters/core/membrane-adapter.ts
  9. apps/api/src/adapters/core/plaid-adapter.ts
  10. apps/api/src/adapters/core/quickbooks-adapter.ts
  11. apps/api/src/adapters/index.ts
  12. apps/api/src/adapters/registry/adapter-registry.ts
  13. apps/api/src/adapters/sync/sync-engine.ts
  14. apps/api/src/models/optimization/CostOptimizer.ts
  15. apps/api/src/models/orchestrator/EnsembleStrategy.ts

  Resolution Strategy: Compare implementations, keep both improvements
  Expected outcome: Consolidated adapter layer

API SERVICES (14 files):
  16. apps/api/src/api/services/activity_service.py
  17. apps/api/src/api/services/conversation_service.py
  18. apps/api/src/api/services/graph_context_service.py
  19. apps/api/src/api/services/message_service.py
  20. apps/api/src/api/services/participant_service.py
  21. apps/api/src/api/services/search_service.py
  22. apps/api/tests/api/services/test_conversation_service.py
  23. apps/api/tests/api/services/test_message_service.py
  24. apps/api/tests/api/services/test_participant_service.py
  25. apps/api/tests/api/services/test_search_service.py
  26. apps/api/tests/auth/test_identity_sync.py
  27. apps/api/src/auth/models/workos_models.py
  28. apps/api/src/auth/sync_scheduler.py
  29. apps/api/src/orchestrator/state.py

  Resolution Strategy: Merge service methods (likely non-overlapping)
  Expected outcome: Complete service layer

API ROUTERS (11 files):
  30. apps/api/src/api/routers/__init__.py
  31. apps/api/src/api/routers/activity_router.py
  32. apps/api/src/api/routers/conversation_router.py
  33. apps/api/src/api/routers/enhancement_router.py
  34. apps/api/src/api/routers/graph_context_router.py
  35. apps/api/src/api/routers/invitation_router.py
  36. apps/api/src/api/routers/message_router.py
  37. apps/api/src/api/routers/participant_router.py
  38. apps/api/src/api/routers/search_router.py
  39. apps/api/src/api/routers/webhooks_router.py
  40. apps/api/src/api/routes/oauth_clients.py

  Resolution Strategy: Consolidate endpoint definitions
  Expected outcome: Full API route coverage

API MODELS (11 files):
  41. apps/api/src/api/models/__init__.py
  42. apps/api/src/api/models/activity.py
  43. apps/api/src/api/models/common.py
  44. apps/api/src/api/models/conversation.py
  45. apps/api/src/api/models/multi_modal.py
  46. apps/api/src/api/models/participant.py
  47. apps/api/src/api/models/query.py
  48. apps/api/src/api/models/search.py
  49. apps/api/tests/api/models/ (if any)
  50. apps/api/src/models/orchestrator/MultiModalOrchestrator.ts
  51. apps/api/src/models/tracking/ModelPerformanceTracker.ts

  Resolution Strategy: Compare model definitions, consolidate
  Expected outcome: Unified data models

API MIDDLEWARE (2 files):
  52. apps/api/src/api/middleware/__init__.py
  53. apps/api/src/api/middleware/permissions.py

  Resolution Strategy: Merge middleware components
  Expected outcome: Complete middleware stack

OTHER BACKEND FILES (14 files):
  54. apps/api/src/security/key_vault_service.py
  55. apps/api/tests/api/middleware/test_permissions.py
  56. apps/api/tests/api/routers/__init__.py
  57. apps/api/tests/api/routers/test_activity_router.py
  58. apps/api/tests/api/routers/test_conversation_router.py
  59. apps/api/tests/api/routers/test_invitation_router.py
  60. apps/api/tests/api/routers/test_message_router.py
  61. apps/api/tests/api/routers/test_participant_router.py
  62. apps/api/tests/api/routers/test_search_router.py
  63. apps/api/tests/api/routers/test_websocket_router.py
  64. apps/api/tests/auth/test_admin_service.py
  65. apps/api/tests/auth/test_session_validation.py

  Resolution Strategy: Standard merge or use test strategy decision
  Expected outcome: Complete test coverage

INTEGRATION TESTS (7 files):
  66. apps/api/tests/integration/test_multi_user_collaboration.py
  67. apps/api/tests/integration/test_orchestrator_singleton.py
  68. apps/api/tests/integration/test_performance.py
  69. apps/api/tests/integration/test_state_isolation.py
  70. apps/api/tests/integration/test_thread_safety.py
  71. apps/api/tests/integration/test_websocket_subscription.py
  72. apps/api/tests/recovery/test_recovery.sh

  Resolution Strategy: Keep both test suites
  Expected outcome: Comprehensive integration tests

OTHER TEST FILES (6 files):
  73. apps/api/tests/test_activity_service.py
  74. apps/api/tests/test_cli_debug_window.py
  75. apps/api/tests/test_cli_e2e.py
  76. apps/api/tests/test_get_current_user.py
  77. apps/api/tests/test_jwt_validation.py
  78. apps/api/tests/verify_jwt_endpoint.py

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MEDIUM PRIORITY - FRONTEND (24 files)
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COMPONENTS:
  79. apps/frontend/file-ingestion-ui/src/App.tsx
  80. apps/frontend/file-ingestion-ui/src/components/ArchiesBrainPage.tsx
  81. apps/frontend/file-ingestion-ui/src/components/Dashboard.tsx
  82. apps/frontend/file-ingestion-ui/src/components/DataPreview.tsx
  83. apps/frontend/file-ingestion-ui/src/components/FileList.tsx
  84. apps/frontend/file-ingestion-ui/src/components/FileUpload.tsx
  85. apps/frontend/file-ingestion-ui/src/components/FinancialPage.tsx
  86. apps/frontend/file-ingestion-ui/src/components/FinancialUploadCard.tsx
  87. apps/frontend/file-ingestion-ui/src/components/shared/Navigation.tsx

  Resolution Strategy: Compare implementations, merge best practices
  Expected outcome: Complete UI component library

CONFIGURATION & BUILD:
  88. apps/frontend/file-ingestion-ui/package.json
  89. apps/frontend/file-ingestion-ui/vite.config.ts

  Resolution Strategy: Merge dependency specs, use newer stable versions
  Expected outcome: Working build configuration

STYLES:
  90. apps/frontend/file-ingestion-ui/src/styles/ArchiesBrain.css
  91. apps/frontend/file-ingestion-ui/src/styles/Dashboard.css

  Resolution Strategy: Union of both style definitions
  Expected outcome: Complete styling

NODE MODULES (14 conflicted symlinks/binaries - HANDLED SEPARATELY):
  92-105. apps/frontend/file-ingestion-ui/node_modules/.bin/* (various)
  106-119. apps/frontend/file-ingestion-ui/node_modules/[packages]~origin_develop

  Resolution Strategy: DELETE all node_modules conflicts
  Post-merge action: Run npm install --legacy-peer-deps

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LOW PRIORITY - INFRASTRUCTURE (16 files)
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DATABASE MIGRATIONS:
  120. infrastructure/database/manual-migrations/008_identity_sync_audit.sql
  121. infrastructure/database/manual-migrations/010_conversation_participants.sql
  122. infrastructure/database/manual-migrations/011_conversations_enhancement.sql
  123. infrastructure/database/manual-migrations/012_activity_feed.sql
  124. infrastructure/database/manual-migrations/012_participants_and_invitations.sql
  125. infrastructure/database/migrations/versions/002_graph_contextual_references.py

  Resolution Strategy: Keep both migrations (ordering may need adjustment)
  Expected outcome: Complete schema version history

RECOVERY SCRIPTS:
  126. apps/api/tests/recovery/README.md
  127. apps/api/tests/recovery/validate_clean_state.sh
  128. apps/api/tests/recovery/validate_post_cherry_pick.sh

  Resolution Strategy: Merge documentation and scripts
  Expected outcome: Complete recovery procedures

BUILD ARTIFACTS & DEPENDENCIES:
  129. node_modules/.pnpm/zustand@4.5.7.../middleware.js
  130. node_modules/@types/node/* (deleted vs modified)

  Resolution Strategy: DELETE, regenerate via npm install
  Expected outcome: Clean dependencies

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SUMMARY BY RESOLUTION EFFORT
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EASY (Can use ours/theirs) - 20-25 files:
  - All node_modules/* conflicts
  - Some test files
  - Some infrastructure scripts
  Action: git checkout --ours apps/frontend/file-ingestion-ui/node_modules/*

MEDIUM (Requires review) - 40-50 files:
  - API Models
  - API Services
  - Frontend components
  - Database migrations
  Action: Compare both versions, consolidate

COMPLEX (Needs careful merge) - 40-50 files:
  - API Routers
  - API Adapters
  - Core application files
  - Authentication
  - Configuration
  Action: Deep code review, test after

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FILE ORGANIZATION ISSUE (CRITICAL)
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STRUCTURAL CONFLICT: Directory Location Mismatch

Feature branch uses: src/api/[middleware|models|routers|services]
Develop branch uses: apps/api/src/api/[middleware|models|routers|services]

Affected files (40+):
  - src/api/middleware/__init__.py
  - src/api/middleware/permissions.py
  - src/api/models/activity.py
  - src/api/models/participant.py
  - src/api/models/search.py
  - src/api/routers/activity_router.py
  - src/api/routers/conversation_router.py
  - src/api/routers/graph_context_router.py
  - src/api/routers/invitation_router.py
  - src/api/routers/message_router.py
  - src/api/routers/participant_router.py
  - src/api/routers/search_router.py
  - src/api/services/[various]
  ... and more

DECISION REQUIRED: 
  Which structure is canonical?
  - Option A: src/api/... (feature branch)
  - Option B: apps/api/src/api/... (develop branch, more appropriate for monorepo)

RECOMMENDATION: Option B (apps/api/src/api/) follows monorepo best practices

RESOLUTION ACTION:
  1. Clarify decision with architectural lead
  2. Move all files to canonical location
  3. Update all import statements
  4. Verify build succeeds
  5. Run import validation

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END OF DETAILED CONFLICT LISTING
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