chore: remove repos from integrations.settings column for github and github-nango integrations (CM-1005)

[themarolt]

Note

Medium Risk
Touches GitHub/GitHub-Nango onboarding/mapping and worker stream execution paths and includes a data migration that mutates production integration settings; regressions could break repo selection or syncing if hydration/stripping logic is incomplete.

Overview
GitHub repo configuration is moved out of integrations.settings. A new migration backs up integrations.settings then removes orgs[].repos plus top-level repos/unavailableRepos for github/github-nango integrations (excluding status='mapping').

API/workers now hydrate repos from public.repositories for compatibility. Backend IntegrationRepository._populateRelations repopulates settings.orgs[].repos (and settings.nangoMapping for github-nango) from DB rows, while DAL adds helpers like getReposForGithubIntegration, getReposGroupedByOrg, populateGithubSettingsWithRepos, and stripReposFromGithubSettings.

GitHub mapping/onboarding flow is updated to rely on repositories rows. mapGithubRepos/mapUnifiedRepositories propagate forkedFrom via a map built from the repositories table (or settings on first run), strip repos from settings after writing DB rows, and delay triggering the run-worker until after transaction commit; progress/monitoring and nango worker logic is updated to read desired repos from the repositories table instead of settings.

Small related changes. GitHub integration stream code avoids writing repos back into settings (only persists unavailableRepos), types mark repo fields as deprecated/optional, the LF integration list computes useGitHubNango based on existing integrations/team-user, and the repo CLI gains reset-and-restart plus improved help output.

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