Make temporary run data opt-in and remove empty tmp scaffolding

[codeforester]

Goal

Make temporary run data disappear by default and preserve it only when explicitly requested.

Scope

• Remove the complete run tmp/ tree, including empty component parents, after cleanup.
• Preserve the complete tree only when --keep-temp (or the documented explicit retention setting) is requested.
• Expose the retention control consistently through the basectl command surface.
• Define the behavior for successful and failed runs and update cache-layout, CLI, and observability documentation.

Acceptance criteria

• Default successful and failed runs leave no tmp/ directory behind.
• Explicit retention preserves temporary files and all required parent directories.
• Run metadata and the primary log remain available regardless of temp retention.
• Focused tests and the full Base validation suite pass.