Make command history user-facing while retaining internal trace

[codeforester]

Summary

• record one primary user-facing history row per public basectl invocation
• retain delegated Python/helper rows as linked internal trace records
• hide internal rows by default and expose them with basectl history --include-internal
• preserve project, root, manifest, and child log metadata for project-targeting commands

Validation

• ./bin/base-test — 1005 passed, 1 skipped
• focused history/completion Bats — 42 passed
• focused pylint and git diff --check

Fixes #1671