Workspace review skips staged newly added files

[acoliver]

Environment

• OCR: v1.11.1
• Mode: workspace
• Output: --audience agent --format json
• Git state: one modified tracked file and seven staged newly added files

Command

ocr review --audience agent --format json --timeout 15 --concurrency 4 --background "..."

Expected

Workspace mode reviews staged, unstaged, and untracked changes, including newly added files.

Actual

The run completed successfully but selected only the modified tracked file:

{
  "message": "Review complete: 0 finding(s) across 1 selected item(s).",
  "summary": { "files_reviewed": 1 },
  "groups": [{ "label": "src/ui_gpui/mod.rs", "files": ["src/ui_gpui/mod.rs"] }]
}

The seven staged additions were absent from manifest.coverage.selected. They included six text files and one 3,478-line Rust file, so the omission was not caused only by binary detection. The command exited 0 and stderr was empty.

git status --short immediately before the run showed:

M  src/ui_gpui/mod.rs
A  src/ui_gpui/vendor/gpui_base_selection/LICENSE-APACHE
A  src/ui_gpui/vendor/gpui_base_selection/auto_scroll.rs
A  src/ui_gpui/vendor/gpui_base_selection/global_state.rs
A  src/ui_gpui/vendor/gpui_base_selection/mod.rs
A  src/ui_gpui/vendor/gpui_base_selection/text_boundary.rs
A  src/ui_gpui/vendor/gpui_base_selection/text_selection.rs
A  src/ui_gpui/vendor/mod.rs

The run manifest reported workspace mode with resolved_base equal to HEAD.

[Parikalp-Bhardwaj]

I traced this to filterDiffs reapplying .gitignore after git collects staged changes. I am working on a focused fix that preserves tracked and staged files while still excluding ignored untracked files, with a regression test.