- Replace all bare 'paperforge setup' with 'paperforge setup --headless'
- Rewrite Section 3 of setup-guide.md to describe headless-only workflow
- Update command reference table at Section 7.1 to use --headless
- Update INSTALLATION.md setup command and Better BibTeX section
- Move Better BibTeX auto-export to post-install step (exports dir created by setup)
- Clarify wizard overview: show resources_dir/literature_dir/control_dir hierarchy
- Fix post-install flow order: BBT export → enable plugin → dashboard → sync
- Split do_ocr and analyze marks into separate steps (OCR before deep-reading)
- Mark all literature flags via Base views, not manual file editing
- Make installer incremental: preserve existing files, only create missing ones
- Remove destructive junction/link deletion in TUI wizard
- Merge .env instead of overwriting; skip overwrite for AGENTS.md, docs, plugin
- Update TUI, headless, and plugin completion output to match corrected flow
- Add regression test for non-destructive setup behavior