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Fix git input handling of relative HEAD refs without branch names.
Add includes key to module configurations in v2 buf.yaml, accepting a list of directories.
If includes is specified, a proto file is considered in the module only if it is in one of the
directories specified.
If both includes and excludes keys are specified for a module, a proto file is considered
part of this module if it is contained in any of the include paths and not in any of the exclude
paths.
Allow multiple module configurations in the same v2 buf.yaml to have the same directory path.