- 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
- Add Path Resolution section to AGENTS.md with BBT format table,
wikilink rules, junction setup instructions, and multi-attachment handling
- Update Library Record frontmatter example with new fields:
pdf_path (wikilink), bbt_path_raw, zotero_storage_key, attachment_count,
supplementary, path_error
- Add ADR-011: Zotero Path Normalization Strategy documenting D-01 through D-08
- Fix dead links in ARCHITECTURE.md and planning research files
- Add scripts/consistency_audit.py with 4 automated checks
- Check 1: No old command names in active code/docs
- Check 2: No paperforge_lite references in Python code
- Check 3: No dead internal links in markdown
- Check 4: Command docs have required sections
Fix violations found by audit:
- Update paperforge/ocr_diagnostics.py error messages to use new commands
- Update pipeline/worker/literature_pipeline.py generated content to use /pf-deep
- Update scripts/welcome.py to recommend /pf-deep
- Update skills/literature-qa/prompt_deep_subagent.md title to /pf-deep
- Update skills/literature-qa/scripts/ld_deep.py docstrings to /pf-deep
- Fix dead links in docs/COMMANDS.md and command/*.md
- Update AGENTS.md migration section to reference MIGRATION-v1.2.md
- Update paperforge/cli.py module docstring to use current commands
- Delete templates/文献阅读.md (frontmatter is hardcoded in pipeline)
- Remove template deployment from setup.py
- Update README.md and AGENTS.md references
