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Consolidate automation repository management API routes #49

@joryirving

Description

@joryirving

Mission Control currently has overlapping repository management routes with different responsibilities:

  • GET/POST /api/automation/repos — manages AutomationRepo table (automation CI/CD tracking)
  • GET/POST /api/repos — manages Repository table (issue sync tracking)
  • GET/POST /api/automation/repositories — also returns AutomationRepo data but with different shape

These routes create or manage Repository and AutomationRepo rows inconsistently. Before agents rely on Mission Control as a control plane, repo management should have one clear source of truth and one documented route family.

Acceptance criteria

  • Pick one canonical route family for tracked repository management.
  • UI uses the canonical route consistently.
  • Docs describe the canonical route.
  • Duplicate or legacy routes are removed, redirected, or clearly documented.
  • Adding a tracked repo creates the expected DB records for both automation sync and issue sync, if both are still required.
  • Removing/disabling a tracked repo behaves consistently.
  • Audit logging remains intact for repo add/remove/disable actions where applicable.
  • Existing data is not broken.
  • Add/update tests for repository add/list/remove behavior if practical.

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