Clear warning-level ShellCheck findings in non-test Bash code

[codeforester]

Problem

Warning-level ShellCheck on non-test Bash code still reports a small set of cleanup items:

• cli/bash/commands/basectl/subcommands/onboard.sh: indirect read warning around prompt response storage.
• lib/shell/base_platform_tools.sh: direct PATH="" mutation warning.
• lib/shell/bash_profile and lib/shell/bashrc: missing ShellCheck shell directives.
• pass-by-name helper false positives in export_context.sh, gh.sh, and repo.sh need either targeted annotations or local naming cleanup.

These are lower-risk than the structural issues, but clearing them makes future Bash review output more useful.

Scope

• Resolve or annotate the warning-level ShellCheck findings that are intentional.
• Avoid behavior changes beyond the minimal cleanup needed.
• Keep broad refactors out of this issue.

Acceptance Criteria

• Warning-level ShellCheck output is clean or contains only documented intentional exceptions.
• Focused command tests continue to pass for touched files.
• No user-visible CLI behavior changes unless explicitly covered by tests.