docs: sync README command reference

[andrasbacsai]

Summary

• document the missing create, storage, preview, database env, version, init, and firewall commands
• correct stale global, environment, deployment, backup, and private-key flags
• refresh the generated command catalog required by the existing docs CI

Verification

• go run ./coolify docs llms
• go test ./cmd/...
• targeted --help checks for the corrected command trees

The full suite still hits the pre-existing TestDestinationService_CRUDAndServerPaths timeout already failing on v4.x; this PR changes documentation only.

Fixes #76

Supersedes #77.