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58 commits

Author SHA1 Message Date
Research Assistant
3a25c02836 docs: replace git+https install URLs with pip install paperforge (PyPI) 2026-05-11 19:25:38 +08:00
Research Assistant
2e0657479a feat: PyPI publish support — install paperforge from PyPI with git fallback 2026-05-11 18:04:17 +08:00
Research Assistant
566697fc31 chore: remove CI workflows pending rewrite 2026-05-11 17:00:23 +08:00
Research Assistant
30f9613482 merge: integrate dashboard-refine (deep-finalize + slug-freeze) into skill-refine 
Resolved conflicts:
- styles.css: take dashboard-refine (more refined CSS)
- SKILL.md, deep-reading.md, paper-resolution.md: take skill-refine (modular skill redesign)
 2026-05-10 23:28:13 +08:00
Research Assistant
9b88c441b0 refactor(skills): modular literature-qa skill with router-first architecture 
- Replace 6 scattered pf-*.md files with single SKILL.md router + 4 reference files
- Add paper_resolver.py: deterministic key/DOI/field search (4 subcommands)
- Remove pf-sync/ocr/status (CLI-only commands, no skill wrapper needed)
- Move chart-reading/ into references/ for flat structure
- Make ld_deep.py --vault optional (auto-detect from cwd)
- Add 26 unit tests for paper_resolver
- All paths dynamically resolved from paperforge.json, zero hardcoding
 2026-05-10 20:56:28 +08:00
Research Assistant
61822c8a94 docs: add dashboard ui refinement specs and plans 2026-05-10 20:52:21 +08:00
Research Assistant
d8a0d4d83e docs: align dashboard ux contract with refined ui 2026-05-10 20:52:21 +08:00
Research Assistant
d00977ccbb docs: update UX contract for redesigned dashboard with 3-mode views 
- Replace W4-S3 (old lifecycle stepper) with new paper mode specs: status strip, overview card, discussion card, workflow toggles, files row, technical details
- Add W4-S4: workspace path detection keeps paper mode for fulltext.md
- Add W4-S5: global mode as system homepage
- Add W4-S6: workflow toggle checkboxes sync to Base via processFrontMatter (no extra sync needed)
 2026-05-10 14:07:53 +08:00
Research Assistant
36a8ba8400 refactor(dashboard): Phase 1 cleanup - remove Copy Context, deep-reading dead code, static Quick Actions grid 
- Delete Copy Context and Copy Collection Context from ACTIONS array
- Remove all _renderDeep* dead methods (StatusCard, Pass1Card, QACard)
- Remove _getPassCompletion and _extractPass1Content helpers
- Remove deep-reading mode case from _renderModeHeader
- Remove Copy Context handlers from _runAction
- Remove copy-context command palette registrations
- Delete static Quick Actions section from _buildPanel
- Delete _renderActions method
- Replace ready-state Copy Context fallback in _renderNextStepCard
- Add implementation plan at docs/superpowers/plans/
 2026-05-10 13:44:50 +08:00
Research Assistant
0c888ced0d docs: remove control_dir from all user-facing documentation; add v1.4.17 changelog 2026-05-10 01:55:35 +08:00
Research Assistant
bbd39a90d3 v1.4.17rc4 
Milestone v2.1: Contract-Driven Architecture & Engineering Hardening

- Stop the Bleeding: version sync checker, PyYAML hardening, install docs unification
- Contract Layer: PFResult/PFError dataclasses, ErrorCode enum, --json wrapping
- Service Extraction: sync.py decomposed into 3 adapters + SyncService
- State Machine: PdfStatus/OcrStatus/Lifecycle enums, transitions, field registry
- Setup Modularization: setup_wizard.py decomposed into 6 classes

173 tests passing, 0 regressions.
 2026-05-09 17:05:07 +08:00
Research Assistant
341941ab09 feat(54-001): add UX contract and user journey tests 
- docs/ux-contract.md: verifiable step sequences for install, sync, OCR, dashboard
- tests/journey/conftest.py: journey_fresh_vault, journey_established_vault, journey_cli_invoker fixtures with isolation guards
- tests/journey/test_onboarding.py: JNY-02 new user onboarding (sync -> OCR -> analyze -> deep-read)
- tests/journey/test_daily_workflow.py: JNY-03 existing user adds paper workflow
 2026-05-09 00:52:55 +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
8447867f88 docs(48-textual-tui-removal): update docs for headless-only setup 
- 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
 2026-05-07 19:42:45 +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
da5b8f0c07 docs: update dashboard screenshot 2026-05-02 14:56:14 +08:00
Research Assistant
681f7a4ce4 docs: redesign README with banner and dashboard preview 2026-05-02 14:52:59 +08:00
Research Assistant
6b567d004f fix: update pip installs from GitHub source instead of package index 2026-04-29 00:16:13 +08:00
Research Assistant
4b7648efb0 docs(plan): multi-agent platform implementation plan 2026-04-28 16:00:58 +08:00
Research Assistant
fb934b7d40 docs(spec): add multi-agent platform design spec 2026-04-28 15:51:03 +08:00
Research Assistant
e5573a9c8c docs: split AI setup guide into EN and ZH versions 2026-04-28 15:01:31 +08:00
Research Assistant
506b6ef6d7 docs: bilingual AI setup guide — detect language, use matching prompts 2026-04-28 14:50:18 +08:00
Research Assistant
3ff375675a docs: bilingual AI install prompts, add cd-to-vault step 2026-04-28 14:44:44 +08:00
Research Assistant
91434f93df docs: Zotero data dir — auto-detect first, always let user override 2026-04-28 14:33:35 +08:00
Research Assistant
53ab3f1d07 docs: rewrite AI setup guide — ask ALL params, explain dirs, promote BBT JSON export 2026-04-28 14:33:35 +08:00
Research Assistant
859fa5ff97 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