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70 commits

Author SHA1 Message Date
Research Assistant
6cbcce84e7 docs(spec): log format validation, reading-log import/lookup, methodology skill, dashboard SQLite 2026-05-13 16:02:50 +08:00
Research Assistant
9b3e844eb8 chore: add pre-commit JS syntax hook + stage missing vector CLI files 2026-05-12 23:34:24 +08:00
Research Assistant
9016a8734e docs(spec): add Phase 7 vector retrieval — ChromaDB + local/API embedding + chunking 2026-05-12 21:43:34 +08:00
Research Assistant
2551eec014 fix(spec): add DEFAULT_SETTINGS whitelist note, source: paperforge requirement, CLI toggle read 2026-05-12 21:19:21 +08:00
Research Assistant
fffc0c3d9f docs(spec): plugin settings redesign — tabbed UI, skill manager, feature toggles, vector DB panel 2026-05-12 21:11:15 +08:00
Research Assistant
4ffcd4c1c0 docs(spec): add Phase 6 — paper_events, reading/working logs, vector retrieval 2026-05-12 20:48:09 +08:00
Research Assistant
3ee0320fb9 test(memory): verify agent-context on test vault — 150 papers, 26 collections, 4 rules 2026-05-12 20:00:16 +08:00
Research Assistant
5f7f2cd317 docs(plan): add agent-context implementation plan 2026-05-12 19:54:19 +08:00
Research Assistant
eedf02c462 docs(spec): add Memory Layer Phase 2-5 design (agent-context, dashboard, refresh, retrieve) 2026-05-12 19:44:38 +08:00
Research Assistant
02c1e5b8a0 bump: 1.5.5 -> 1.5.6rc1 (Memory Layer RC1) 2026-05-12 18:11:37 +08:00
Research Assistant
316b8bdcb2 feat: restructure literature-qa v2 — SKILL.md as central hub with decision tree, add multi-reading, simplify refs 2026-05-11 23:58:46 +08:00
Research Assistant
d570aa409b fix(literature-qa): prohibit hardcoded path construction in skill references 2026-05-11 23:17:05 +08:00
Research Assistant
fd82c28991 docs: replace git+https install URLs with pip install paperforge (PyPI) 2026-05-11 19:25:38 +08:00
Research Assistant
7bb32f2571 feat: PyPI publish support — install paperforge from PyPI with git fallback 2026-05-11 18:04:17 +08:00
Research Assistant
a6b90f8538 chore: remove CI workflows pending rewrite 2026-05-11 17:00:23 +08:00
Research Assistant
5138a70645 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
59a024abba 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
cc9a5baa98 docs: add dashboard ui refinement specs and plans 2026-05-10 20:52:21 +08:00
Research Assistant
6b52d44db9 docs: align dashboard ux contract with refined ui 2026-05-10 20:52:21 +08:00
Research Assistant
be3d0fc6f6 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
ae0da5b29a 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
085cfb5944 docs: remove control_dir from all user-facing documentation; add v1.4.17 changelog 2026-05-10 01:55:35 +08:00
Research Assistant
7148077153 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
91cf548dd6 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
b635069990 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
7b7cccf021 docs(merge-gate): update planning state, roadmap, and agent documentation for milestone completion 2026-05-07 21:52:31 +08:00
Research Assistant
5abcb7b651 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
d5818e8acd 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
548417a8c5 docs: update dashboard screenshot 2026-05-02 14:56:14 +08:00
Research Assistant
04adc36b9b docs: redesign README with banner and dashboard preview 2026-05-02 14:52:59 +08:00
Research Assistant
c12128ede9 fix: update pip installs from GitHub source instead of package index 2026-04-29 00:16:13 +08:00
Research Assistant
792f039e9f docs(plan): multi-agent platform implementation plan 2026-04-28 16:00:58 +08:00
Research Assistant
bd301fc4d5 docs(spec): add multi-agent platform design spec 2026-04-28 15:51:03 +08:00
Research Assistant
7dcf0b8f1f docs: split AI setup guide into EN and ZH versions 2026-04-28 15:01:31 +08:00
Research Assistant
4ce0f75b3e docs: bilingual AI setup guide — detect language, use matching prompts 2026-04-28 14:50:18 +08:00
Research Assistant
a26e943499 docs: bilingual AI install prompts, add cd-to-vault step 2026-04-28 14:44:44 +08:00
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