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34 commits

Author SHA1 Message Date
Research Assistant
2d28ae841d docs: Zotero data dir — auto-detect first, always let user override 2026-04-28 14:33:35 +08:00
Research Assistant
71efe2b5f4 docs: rewrite AI setup guide — ask ALL params, explain dirs, promote BBT JSON export 2026-04-28 14:33:35 +08:00
Research Assistant
2ca557bb9e feat: headless setup mode, Obsidian plugin, AI agent install guide (v1.4.2) 2026-04-28 14:33:35 +08:00
Research Assistant
ebc4fdeb00 chore: rename PaperForge Lite -> PaperForge across 27 files 2026-04-28 01:25:51 +08:00
Research Assistant
bcd0934117 docs: sync all doc references — README, INSTALLATION.md, AGENTS.md for v1.4.1 pip-first flow 2026-04-28 01:06:58 +08:00
Research Assistant
0a47a6e2ed docs: add comprehensive setup and usage guide 2026-04-28 01:03:23 +08:00
Research Assistant
f650797054 docs: pf-deep skill refactoring implementation plan 2026-04-28 00:11:56 +08:00
Research Assistant
c4390f4124 docs: pf-deep skill refactoring design (atoms/molecules/compounds) 2026-04-27 23:56:55 +08:00
Research Assistant
67a52a898a fix: VaultStep.__init__ missing step_id and checker in super() call 2026-04-27 19:49:36 +08:00
Research Assistant
78bf95b818 docs(18-documentation-ux-polish): add ADR-012/013 and update AGENTS.md command table 
- Add ADR-012 (Shared Utilities Extraction) and ADR-013 (Dual-Output Logging)
- Add command mapping table to AGENTS.md Section 1
- Add --verbose and auto_analyze_after_ocr notes to Section 5
- Add --verbose variants to all CLI examples in Section 8
- Add chart-reading INDEX.md cross-reference
- Update Section 11 with v1.4 migration guide link
 2026-04-27 18:06:03 +08:00
Research Assistant
729ce990c7 docs(18-documentation-ux-polish): create MIGRATION-v1.4.md and fix README orphaned lines 
- Create docs/MIGRATION-v1.4.md following v1.2 template structure
- Document all v1.3-to-v1.4 changes: dual-output logging, retry, pre-commit, auto_analyze_after_ocr
- Remove orphaned legacy code lines 102-104 from README.md
- Verify no other rendering issues in doc audit
 2026-04-27 18:05:58 +08:00
Research Assistant
13e548df04 docs(11-01): update AGENTS.md and ARCHITECTURE.md for path normalization 
- 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
 2026-04-24 20:45:18 +08:00
Research Assistant
f0d2fa1978 docs(phase-10): add consistency checklist 
- Add docs/CONSISTENCY-CHECKLIST.md for manual soft-constraint review
- Covers terminology, commands, cross-references, version references
- Includes style, branding, and platform notes verification
 2026-04-24 18:06:55 +08:00
Research Assistant
abab8df3f5 feat(phase-10): add consistency audit script 
- 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
 2026-04-24 18:06:35 +08:00
Research Assistant
5aeacaecbd docs(phase-10): add COMMANDS.md master reference 
- Add master command reference with Agent/CLI matrix
- Include quick reference, workflow reference, platform notes
- Link to all per-command docs and AGENTS.md
 2026-04-24 17:51:42 +08:00
Research Assistant
4c3fe53351 docs(phase-10): add MIGRATION-v1.2.md 
- Complete migration guide from v1.1 to v1.2
- Covers all breaking changes: package rename, CLI unification, Agent namespace change
- 7 step-by-step migration instructions with copy-pasteable commands
- Import path changes for custom scripts
- 3 rollback options with state compatibility notes
- 9 FAQ entries covering common upgrade issues
- Quick reference card for old vs new commands
- Cross-references to ARCHITECTURE.md, COMMANDS.md, AGENTS.md
 2026-04-24 17:41:05 +08:00
Research Assistant
f1e52b1f43 docs(phase-10): add ARCHITECTURE.md with ADR records 
- System Overview: two-layer design (Worker + Agent)
- Data Flow: ASCII diagram with 6-stage pipeline
- Directory Structure: 5 core directories with rationale table
- Commands Package: registry pattern explanation + code examples
- 10 ADRs covering decisions from Phases 1-9
- Extension Points: guide for new CLI commands, Agent commands, platforms
 2026-04-24 17:36:49 +08:00
Research Assistant
62ec89441c docs(09-command-unification): update user-facing docs for unified commands 
- Replace paperforge selection-sync/index-refresh with paperforge sync
- Replace paperforge ocr run with paperforge ocr
- Replace /LD-deep, /LD-paper with /pf-deep, /pf-paper
- Add v1.1 -> v1.2 command migration table to AGENTS.md
- Update README.md, docs/INSTALLATION.md, docs/setup-guide.md
 2026-04-24 16:56:39 +08:00
Research Assistant
3ac9b8a323 docs(phase-9): update all markdown references to paperforge 
- Updated 91 files: paperforge_lite → paperforge
- Includes: AGENTS.md, README.md, docs/, command/, skills/, .planning/
- Preserved historical records in Phase 1 artifacts
 2026-04-24 16:15:38 +08:00
Research Assistant
6052c823e6 Add run_repair() function for three-way OCR state divergence repair 2026-04-24 00:02:32 +08:00
Research Assistant
1d8478ce9c fix(wizard): auto-run pip install -e . and improve UX flow 
- setup_wizard.py: _deploy() now calls pip install -e <repo_root> automatically
- DoneStep: removes manual 'pip install -e .' instruction (wizard handles it)
- README.md: removes separate pip install -r requirements.txt step
- docs/INSTALLATION.md: same pip install simplification
- pyproject.toml: add pytest ignore for nested sandbox vault
- tests/sandbox/: remove old vault/ (replaced by 00_TestVault/)
- tests/sandbox/README.md: update flow, wizard handles pip install
 2026-04-23 20:49:10 +08:00
Research Assistant
b9f06ccad3 feat: complete PaperForge Lite v1.0 release hardening (5 phases, 28 reqs, 145 tests) 2026-04-23 20:15:20 +08:00
Research Assistant
51d35d6999 feat(01-04): replace unresolved path-token commands with stable paperforge commands 
- command/lp-*.md: replace python <system_dir>/... with paperforge status|selection-sync|index-refresh|ocr run; add fallback legacy command section
- command/ld-deep.md: update queue preflight to 'paperforge deep-reading'; add paperforge paths --json for variable resolution
- README.md: update core commands section to show paperforge first, legacy as fallback
- docs/INSTALLATION.md: add paperforge paths/status as primary verification
- docs/setup-guide.md: replace python pipeline/worker/... with paperforge selection-sync/index-refresh
- setup_wizard.py DoneStep: add pip install -e . and paperforge commands as primary next steps

All 15 tests in tests/test_command_docs.py pass.
 2026-04-23 11:40:24 +08:00
Research Assistant
881457dd92 Fix configurable Lite setup paths 2026-04-23 01:44:13 +08:00
Research Assistant
fd7ccb53fc fix: unify PaddleOCR env var names to match pipeline expectations (API_TOKEN/JOB_URL) 2026-04-23 00:57:48 +08:00
Research Assistant
d72bf76f08 docs: update README and INSTALLATION for wizard-based setup 2026-04-22 23:36:26 +08:00
Research Assistant
89374cb35f remove: all 科研读图指南 and Template references from project 2026-04-22 23:20:49 +08:00
Research Assistant
c607dd0441 rename: LiteraturePipeline -> PaperForge in all paths and references 2026-04-22 22:10:16 +08:00
Research Assistant
cea8046c30 feat: rewrite setup wizard as step-by-step guide with screenshots 2026-04-22 20:20:45 +08:00
Research Assistant
eafbab7594 feat: add TUI setup wizard and setup guide 
- Add setup_wizard.py: Textual TUI with checklist + guide
  - Detects: Python, Vault structure, Zotero, Better BibTeX, JSON exports
  - Blocked guide until all checks pass
  - Open local docs/setup-guide.md from TUI
- Add docs/setup-guide.md: Detailed text-based setup instructions
  - Menu path diagrams for Zotero/BBT configuration
  - JSON-to-Base relationship explanation
  - FAQ section
- Integrate 'wizard' command into literature_pipeline.py
 2026-04-22 19:28:52 +08:00
Research Assistant
f3b79cd678 docs: remove outdated audit and modular design docs 2026-04-21 23:56:45 +08:00
Research Assistant
b68804f89d docs: add modular installation architecture design 2026-04-21 22:12:48 +08:00
PaperForge Assistant
9cadab68ad fix(setup): resolve all audit findings 2026-04-21 22:10:40 +08:00
Research Assistant
35b18c6b97 Initial commit: Literature workflow for medical research 2026-04-21 20:50:17 +08:00