Research Assistant
abab8df3f5
feat(phase-10): add consistency audit script
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- 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
45de80da5d
refactor(phase-9): update all Python imports to paperforge
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- Updated 35 files: from paperforge_lite.* → from paperforge.*
- Verified: pytest passes (172 passed, 2 skipped)
2026-04-24 16:15:30 +08:00
Research Assistant
500d268db7
feat(01-03): wire validate_setup.py to shared resolver
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- load_config now tries paperforge_lite.config.load_vault_config first,
falls back to legacy JSON parsing for pre-01-03 installs
- resolve_vault_for_validate checks PAPERFORGE_VAULT before VAULT_PATH
before cwd (matching the shared resolver's precedence)
- Preserves all existing validation checks
2026-04-23 12:03:08 +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
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
7191ae9e62
feat(setup): add safety harness - never overwrite user files
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- Add safe_copy() function: checks if file exists, skips if true
- Auto-backup existing files before any modification
- Safety notice at install start
- Protects Zotero DB, existing notes, and configs
2026-04-21 23:44:45 +08:00
Research Assistant
68f65ea69a
feat: add agent commands deployment
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- Add command/ directory with core lp commands:
lp-selection-sync, lp-index-refresh, lp-ocr, lp-status
ld-deep, ld-paper
- Update setup.py to deploy commands to .opencode/command/
2026-04-21 23:40:07 +08:00
Research Assistant
ab5faefd9f
refactor(welcome): remove features list, simplify to OpenCode-only
2026-04-21 23:33:12 +08:00
Research Assistant
e5173b0e6f
cleanup: remove obsolete 文献阅读.md template
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- 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
2ed577246d
refactor: move chart-reading into literature-qa skill
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- Chart guides are references for literature-qa, not standalone skill
- Move skills/chart-reading/ -> skills/literature-qa/chart-reading/
- Update setup.py deploy path
- Update prompt_deep_subagent.md references
- Update 科研读图指南.md links
2026-04-21 23:00:50 +08:00
Research Assistant
aa084e7d94
feat: simplify to core 4-worker pipeline
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- Remove candidate/search/harvest/writeback workers (7 deleted)
- Keep only: selection_sync, index_refresh, ocr, deep_reading
- Simplify setup.py: remove agent selection, remove non-core dirs
- Update AGENTS.md generation for lite architecture
- Reduce pipeline.py from ~4000 to ~3500 lines
2026-04-21 22:44:09 +08:00
Research Assistant
d916b13b50
refactor: restructure repo to generic names
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- 99_System/ -> pipeline/ + templates/
- .opencode/skills/ -> skills/
- Chart guides moved to skills/chart-reading/
- Update setup.py deploy paths accordingly
2026-04-21 22:17:45 +08:00
Research Assistant
3447f0279d
feat: add literature templates and update deployment
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- Add 文献阅读.md template for literature notes
- Add 科研读图指南.md main chart reading guide
- Update deploy_workflow_scripts to include template files
2026-04-21 22:11:48 +08:00
PaperForge Assistant
9cadab68ad
fix(setup): resolve all audit findings
2026-04-21 22:10:40 +08:00
Research Assistant
cb519dcf02
fix: remove all remaining Unicode characters from welcome.py
2026-04-21 21:37:49 +08:00
Research Assistant
03ee3afdda
style: use Overseer's horizontal-line banner with raw strings
2026-04-21 21:33:38 +08:00
Research Assistant
76c7bc0ea7
fix: replace all Unicode with ASCII-safe chars for Windows terminals
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- welcome.py: Box-drawing chars → +-=| borders
- welcome.py: Block chars → # for progress bar
- welcome.py: Emoji → [B][+][D][L][A] icons
- welcome.py: Checkmark → [OK]
- setup.py: Integrate welcome.show_welcome() at startup
2026-04-21 21:30:00 +08:00
Research Assistant
03028782d3
chore: rename repo from Research-workflow to PaperForge
2026-04-21 21:27:56 +08:00
Research Assistant
e8a37245f3
fix: replace logo with correct PAPERFORGE ASCII art
2026-04-21 21:24:58 +08:00
Research Assistant
0d900db007
feat: update logo to PAPERFORGE text
2026-04-21 21:15:52 +08:00
Research Assistant
fe4b058bb2
feat: add PaperForge welcome screen with ASCII logo
2026-04-21 21:14:25 +08:00
Research Assistant
1bd890c426
feat: multi-agent support with configurable paths
2026-04-21 21:12:12 +08:00
Research Assistant
6fb35f3965
Add workflow script deployment to setup.py
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- Add deploy_workflow_scripts() to copy core files from repo to vault
- Deploy literature_pipeline.py, ld_deep.py, prompt_deep_subagent.md
- Deploy 14 chart reading guides
- Privacy: .env in .gitignore, API keys never committed
2026-04-21 20:59:14 +08:00
Research Assistant
35b18c6b97
Initial commit: Literature workflow for medical research
2026-04-21 20:50:17 +08:00
