Make temporary run retention explicit

[codeforester]

Summary

• remove the complete run tmp tree by default, including empty component parents
• expose basectl --keep-temp for explicit retention
• preserve the full temporary tree when requested and document the contract

Validation

• full Python suite: 1019 passed, 1 skipped
• full source-checkout Bats suite: 802 passed
• touched-file Pylint
• isolated CLI smoke tests for default cleanup, explicit retention, and readable bundle paths

Issue

Closes #1685

Dependency

This PR is based on #1686 and should merge after it.