Make basectl clean skip active runs and require explicit deletion consent

[codeforester]

Goal

Align basectl clean with the documented completed-run retention contract and Base's destructive-command safety standard.

Background

--keep-last excludes run bundles whose run.json status is running, but --older-than scans the same runs without applying that check. An old active bundle is therefore selected for deletion.

The command also performs deletion by default whenever --older-than or --keep-last is supplied. Base standards require destructive operations to be dry-run by default or require an explicit confirmation flag such as --yes.

Relevant code and docs:

• https://github.com/basefoundry/base/blob/main/cli/python/base_clean/engine.py#L28-L78
• https://github.com/basefoundry/base/blob/main/cli/python/base_clean/engine.py#L121-L174
• https://github.com/basefoundry/base/blob/main/cli/python/base_clean/engine.py#L211-L230
• https://github.com/basefoundry/base/blob/main/docs/observability.md#L157-L173
• https://github.com/basefoundry/base/blob/main/STANDARDS.md#L100-L111

Scope

• Exclude status=running bundles consistently from age and count retention.
• Make deletion dry-run by default or require --yes for real deletion.
• Provide explicit reporting for retained active bundles.
• Keep stale-run recovery separate and intentional.
• Update help, docs, tests, and completions for the chosen consent contract.

Acceptance Criteria

• --older-than never deletes a bundle whose metadata says running.
• --keep-last and --older-than use consistent completed-run semantics.
• A command without explicit deletion consent cannot remove artifacts.
• Dry-run output identifies exactly what would be removed and what active state was retained.
• Combined retention criteria remain deterministic and deduplicated.

Validation

• Focused base_clean pytest tests for running and completed bundles.
• Focused clean BATS/help/completion tests.
• Isolated-cache dry-run and consent smoke tests.
• env -u BASE_HOME ./bin/base-test
• git diff --check

Non-Goals

• Do not automatically classify an old running bundle as stale.
• Do not delete the append-only history index.
• Do not change unrelated branch/worktree pruning contracts.

Project Fields

• Status: Ready
• Priority: P2
• Area: Runtime
• Initiative: Contract Hardening
• Size: S

Agent Assignment

• Assignee: codeforester