Add custom_data in formats_override

[kunitoki]

This pull request adds robust support for per-format and per-output custom_data overrides in the configuration system, allowing users to specify format-specific or output-specific template variables that are deeply merged over global custom_data. The implementation introduces a new custom_data field to FormatOverrideConfig, ensures correct merging logic, and provides comprehensive documentation and tests for the new behavior.

Configuration and Merging Enhancements

• Added a custom_data field to FormatOverrideConfig and ensured it is parsed, defaulted to {} if absent or null, and deeply merged with the global custom_data when generating for a specific format or output. The merging logic is exposed as merge_yaml_dicts, replacing the previous _merge_yaml_dicts function and updating all usages to the new name. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13]

Documentation Updates

• Updated docs/input-file-reference.md to document the new custom_data behavior, including deep merging semantics and YAML examples for global, per-format, and per-output overrides. [1] [2]

Testing Improvements

• Added extensive tests to verify correct parsing, merging, and defaulting of custom_data in both global and format/output-specific contexts, including deep merge scenarios and CLI integration. [1] [2] [3]

Minor Test and Import Cleanups

• Added necessary imports in test files and removed redundant ones to support new test cases and maintain clarity. [1] [2] [3] [4]

Other Test Enhancements

• Improved assertions in existing tests to ensure output files remain unchanged on breaking changes. [1] [2]