[Docs] Clarify overlay visibility semantics

[samzong]

Summary

• Rename the internal overlay field for legacy parameter hidden to DeprecatedAlias while preserving the YAML key for compatibility.
• Keep param.hidden behavior mapped to deprecated flags and cover both deprecated: true and legacy hidden: true in render tests.
• Clarify command ignore, command hidden, and parameter hidden semantics in README and architecture docs.

Verification

• go test ./internal/overlay ./internal/codegen/render
• git diff --check
• make check

Compatibility

• Existing overlays using params.<name>.hidden: true remain supported and continue to mark the flag deprecated.
• No runtime schema, catalog schema, generated command shape, auth/body/output behavior, or generated output changes.

Checklist

• Tests or focused verification cover the changed surface.
• User-facing behavior changes are documented.
• Generated output under internal/generated/, .cache/, and ad-hoc skills/<cli-name>/ directories is not committed.
• Commits are signed off when this is ready to merge.