[DanielThomas]

Changes

• Use the JDK file manager for module source paths, including path lists, repeated module mappings, and multiple source roots and patterns for one module.
• When no files or modules are selected, format Java files in the supplied source directories. Generated source directories are included when supplied.
• Keep explicit file selection narrow. An explicit --module selects whole modules alongside any file operands, matching javac.
• Use source archives for import resolution without rewriting them, and never select sources from binary paths.
• Preserve syntax-only formatting for missing module dependencies, including explicit files and additional source roots.

No new options, interchange formats, documentation changes, or build-system-specific formatting logic.

Validation

• Added regression tests before the fixes; observed failures for selection expansion, multiple roots, and default directory discovery.
• ja test --all: 212 tests passed.
• Assembled the updated tool successfully.
• Tested real jig-generated argument files with no file operands: non-modular Maven, non-modular Gradle, and a Gradle module with two source roots and no --module selection. All --check invocations passed.