Config: Flatten .herb.yml structure and add rule-level patterns

[marcoroth]

This pull request restructures the .herb.yml schema to use a flat structure for linter and formatter file patterns, moving from the nested files.patterns/exclude/extensions format to a simpler files.include/exclude format.

The change also introduces new include, exclude, and only options for rule-level configuration, allowing rules to specify additional file patterns in an additive manner similar to tool-level includes.

The rule pattern system now supports three distinct configuration options with clear precedence rules. When only is specified, it restricts the rule to those specific patterns and ignores any include settings. When only is absent but include is present, the rule applies only to files matching the include patterns. The exclude option is always applied regardless of other pattern settings.