Git changed-file listings now include submodule changes and root commits

What

A submodule is a git repository nested inside another one. Two helpers that Claude Code uses to find changed files now pass --ignore-submodules=none to git, so changes to submodules are listed.

• The helper that lists files changed across commits used --name-only. It now uses --raw --no-abbrev and reads git's raw output. It also adds -c log.diffMerges=separate -c log.showRoot=true. Root commits, meaning the first commit in a repository, and submodule changes are now included.
• The helper that lists changed files in a diff also adds --ignore-submodules=none. A diff.ignoreSubmodules setting in your own git config can no longer hide changed files from this check.

Why

These checks can no longer silently miss a repository's first commit or a submodule update, whatever your personal git settings say.