Propagate global flags to query subcommands

[longlho]

Summary

• propagate top-level -C/--directory and -c/--config into doctor/query subcommands when they do not provide local overrides
• add a query e2e regression that uses an ignored broken symlink to prove the global config is applied before link-following discovery

Tests

• rustup run 1.93.0 cargo fmt --check
• bazel test //crates/codescythe_cli:codescythe_cli_e2e_test --test_filter=cli_quer --test_output=errors
• bazel test //crates/codescythe_cli:codescythe_cli_test //crates/codescythe_cli:codescythe_cli_e2e_test --test_output=errors