Covers get_file_contents, get_dir_contents, get_repository_tree,
create_or_update_file, delete_file — all verified working with the
current write:issue/write:repository token scope.
check-manifests.sh requires all paths declared in plugin.json to exist.
Adds empty hook and MCP server stubs matching kyberforge convention.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>