docs: add --chain-out, --fullchain-out, --format flags (weekly audit)

[krakenhavoc]

Weekly Documentation Audit — 2026-05-12

Documentation Gaps Addressed

Certificate chain support was added to the API (app PR #79) and probe, but the CLI README.md was not updated to reflect the corresponding flags.

Gap	Fix
--chain-out flag missing from cert issue	Added to flags table
--fullchain-out flag missing from cert issue	Added to flags table
--chain-out flag missing from cert submit	Added to flags table
--fullchain-out flag missing from cert submit	Added to flags table
--format cert|chain|fullchain missing from cert download	Added to flags table
No explanation of which file to use for which server	Added Certificate chain section with output file table
CI/CD examples only showed --cert-out	Updated to include --fullchain-out
Region commands missing tier requirement	Added (Starter+) qualifier

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Files Changed

• README.md — flags tables updated, new Certificate chain section, updated CI/CD examples, Starter+ note

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Suggested Version Bump

Once the chain flags ship in a release, tag v0.2.0 — new subcommand flags constitute a minor feature addition per semver.

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Generated by Claude Code