feat: align Base with base-cli 0.4.0

[codeforester]

Summary

• Pin Base development checks to base-cli==0.4.0.
• Use the public base_cli.runtime.RuntimeLayout contract.
• Translate expected user configuration failures to base_cli.ConfigurationError.
• Accept Click-compatible equals-form options in delegated GitHub project parsing.
• Refresh Base framework documentation and compatibility tests for the 0.4 API boundary.

Dependency order

This PR depends on base-cli release PR #100 being merged and base-cli==0.4.0 being published to PyPI.

Validation

• Base Python suite: 944 passed, 1 skipped, 248 subtests.
• The suite passes against the installed base-cli 0.4.0 wheel in an isolated environment.
• Source-checkout targeted tests and documentation checks pass.

Note

The broader BATS suite still exposes a pre-existing Base/base-bash-libs symbol mismatch (base_bash_libs_require_version versus base_require_version); that is outside this PR.

[codeforester]

Superseded by the issue-backed canonical alignment PR #1876 so the repository branch-policy check can validate the train.