Preserve pre-existing working-tree changes

The user consistently works in a repository with modified and untracked files already present, including dependency files, instructions, schemas, case artifacts, source code, and tests. Before making changes, check repository status and treat existing modifications as user-owned. Do not reset, revert, delete, overwrite, or clean unrelated files. Limit edits to files required for the task, account for overlapping changes carefully, and clearly distinguish any new modifications from the pre-existing working tree state.