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33 commits

Author SHA1 Message Date
Research Assistant
f5d056ea5d fix(skill): multi-arm discovery strategy + mandatory entry rule 
- AGENTS.md: new Section 0 mandatory entry rule with trigger phrases
- retrieval-routing.md: rewrite Ladder A as 3-arm strategy
  (retrieve body + search metadata + context --collection inventory)
- discover-papers.md: Step 2 uses multi-arm, large result handling, dedup
- find-supporting-evidence.md: retrieve as primary fulltext pass
- agent_context.py: update commands docs and rules
 2026-05-20 15:39:00 +08:00
Research Assistant
8d406913b0 docs: update AGENTS.md with skill graph structure, intent routing, bump/release, and skill deploy 2026-05-19 15:47:53 +08:00
Research Assistant
7fec54937a test(skill): align downstream docs and setup with layered skill tree 2026-05-19 14:56:40 +08:00
Research Assistant
97a2875d48 docs: reset documentation IA (readme entry pages, tutorial/troubleshooting split, AGENTS agent-only, pure command ref, maintainer guide) 
Separate audiences: README as navigation entry, getting-started as canonical tutorial,
troubleshooting as failure recovery, AGENTS as agent-only operating contract,
COMMANDS as pure reference, maintainer-guide for release/versioning/architecture.
 2026-05-16 22:47:00 +08:00
Research Assistant
3a25c02836 docs: replace git+https install URLs with pip install paperforge (PyPI) 2026-05-11 19:25:38 +08:00
Research Assistant
23fb1117a4 docs: update version reference to v1.4.18, note setup wizard fix in changelog 2026-05-10 21:53:02 +08:00
Research Assistant
de17cdf83c Revert "docs: update version reference to v1.4.18 and document setup wizard fix" 
This reverts commit f0f420dc54.
 2026-05-10 21:38:10 +08:00
Research Assistant
f0f420dc54 docs: update version reference to v1.4.18 and document setup wizard fix 2026-05-10 21:36:10 +08:00
Research Assistant
a543b611a8 docs: fix /pf-paper description — 文献问答 (Literature Q&A), not 快速摘要 2026-05-10 11:43:35 +08:00
Research Assistant
71e2fa695f fix: CI failures — stub params, ld_deep syntax, PFResult tests, setup_wizard plugin copy 
Fixes 4 CI issues:
- test_cli_worker_dispatch: add json_output param to stubs
- ld_deep.py: replace Python 3.12+ generic syntax with TypeVar
- test_e2e_cli, test_status: update assertions for PFResult envelope
- setup_wizard: skip node_modules/src dirs in plugin copy
- ci.yml: shell=bash for Windows, pin alls-green@v1.2.2
 2026-05-09 17:22:11 +08:00
Research Assistant
f6d4b54032 docs(54-002): delete pip-first docs, update README.md and AGENTS.md references 
- Delete docs/INSTALLATION.md (pip-first installation guide)
- Delete docs/setup-guide.md (detailed installation guide)
- Update README.md docs table: remove deleted file references
- Update AGENTS.md: replace deleted doc links with plugin-first install guidance
 2026-05-08 17:47:39 +08:00
Research Assistant
76df98a63d docs(merge-gate): update planning state, roadmap, and agent documentation for milestone completion 2026-05-07 21:52:31 +08:00
Research Assistant
29edb2d811 fix: overhaul install flow clarity and non-destructive incremental setup 
- 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
 2026-05-06 22:47:07 +08:00
Research Assistant
dac097c7e6 chore: cleanup stale files, update AGENTS.md, fix install wizard button crash 
- Remove root setup_wizard.py (duplicate of paperforge/setup_wizard.py)
- Remove token-usage-output.txt (runtime artifact)
- Update AGENTS.md: worker architecture, directory structure, section numbering, test count 317->462
- Fix undefined 'home' variable in plugin main.js _preCheck causing modal to silently fail
 2026-05-06 10:41:11 +08:00
Research Assistant
db476568d4 docs: add developer guide (version bump, release, i18n, pre-commit) 2026-04-30 13:33:48 +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
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
e5802f1630 docs: clarify dual-mode command invocation in AGENTS.md and README.md 
- AGENTS.md: Add /pf-sync, /pf-ocr, /pf-status to Agent command table
  with explanation of dual-mode invocation (CLI vs Agent wrapper)
- README.md: Update core commands section with all 5 /pf-* commands
  and dual-mode explanation; remove outdated worker script reference
- Remove obsolete pipeline/ directory from README structure diagram
 2026-04-25 00:37:54 +08:00
Research Assistant
ec2e91d4ac feat(update): smart update with auto-detection + Windows one-click script 
paperforge update:
- Auto-detects installation method (pip/pip-editable/git/zip)
- Routes to appropriate update strategy
- pip users: pip install --upgrade
- pip-editable users: git pull + pip install -e .
- git users: git pull
- unknown: zip download fallback

scripts/update-paperforge.ps1:
- Windows one-click update script
- Auto-detects install method
- Supports -Force (skip confirm) and -DryRun
- Clear colored output with error handling

AGENTS.md:
- Added comprehensive update section with 4 methods
- Documented auto-update and PowerShell script
 2026-04-25 00:17:54 +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
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
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
bef53fc61f docs(agents): add paperforge repair command reference 2026-04-24 01:10:06 +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
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
881457dd92 Fix configurable Lite setup paths 2026-04-23 01:44:13 +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
97426a3fe1 feat: dynamic AGENTS.md generation with custom paths in setup.py 2026-04-22 17:39:17 +08:00
Research Assistant
e5173b0e6f cleanup: remove obsolete 文献阅读.md template 
- 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
 2026-04-21 23:04:26 +08:00
Research Assistant
35b18c6b97 Initial commit: Literature workflow for medical research 2026-04-21 20:50:17 +08:00