Simplify early public Bash helper APIs

[codeforester]

Context

Claude's latest review called out several compatibility or duplicate public
surfaces that are more confusing than useful while base-bash-libs is still new.
Base is currently the only consumer, so we do not need to preserve backward
compatibility for helpers that have not been adopted externally.

Scope

• Remove the duplicate str_in_array helper and keep list_contains as the
  canonical array-membership predicate.
• Remove the bare run stdlib alias so BATS users do not inherit a surprising
  symbol from the library.
• Remove std_run_with_timeout and direct callers to std_run --timeout.
• Tighten docs/tests around canonical list and command-runner APIs.
• Add or adjust tests so list_remove explicitly documents and verifies
  all-match removal.

Validation

• Focused BATS suites for touched libraries.
• Full ./tests/validate.sh.