[eseiler]

Runs CI in stages behind a single required check and moves the bot, scheduled and preview workflows to GitHub App tokens and environments.

• ci.yml calls the existing ci_*.yml (now workflow_call + workflow_dispatch) in stages: Lint and License, then the Linux unit tests, then the rest. CI result is the only required CI check; the lint label is no longer used.
• ci_lint.yml checks formatting with seqan/actions/lint. lint_autofix.yml (workflow_run, calls seqan/actions/.github/workflows/lint_autofix.yml) pushes formatting fixes to the PR branch as a signed seqan-actions[bot] commit.
• ci_documentation.yml builds on pull_request and uploads the HTML; docs_preview.yml publishes it to https://seqan.github.io/docs-preview/seqan/needle// and deletes it when the PR is closed. The production deploy is a separate job in the server-deploy environment.
• Scheduled and bot workflows use seqan-pr-bot/seqan-main-bot tokens from the pr-bot/main-bot environments; cron_codechecker.yml runs in server-deploy.
• CI, documentation and the documentation deploy also run for the hibf branch, as before.

Before merging: App installations, the environments pr-bot, docs-preview, server-deploy with their secrets, and the required checks CI result and Documentation.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.05%. Comparing base (bbb3c89) to head (6542b6a).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #269   +/-   ##
=======================================
  Coverage   84.05%   84.05%           
=======================================
  Files          19       19           
  Lines        1091     1091           
  Branches      134      134           
=======================================
  Hits          917      917           
  Misses        174      174           

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