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46 commits

Author SHA1 Message Date
LLLin000
c34ebbce81 feat: rebuild speed-up with parallel rebuild, threaded asset cropping, maintenance refactor, embed progress, CLI docs 2026-07-05 19:43:07 +08:00
LLLin000
4dbeb5ae50 fix: address 4 review items — remove dead INTENTS dict, drop unused --limit from paper-navigation, add -> int return types, guard subsection section_path 2026-07-05 14:46:26 +08:00
LLLin000
bc27ac2255 feat: add Layer 4 gateway command surface 2026-07-05 14:12:50 +08:00
LLLin000
63915e98a4 feat: PR B — CLI manifest/keys + keyed redo 
- list_parser: added --manifest and --keys args
- redo_parser: added positional keys args
- _run_ocr_list: manifest mode (calls compute_maintenance_manifest)
  and keys filtering
- _run_ocr_redo: keyed redo for specific papers + fallback to old path
- 11 new tests (56 total, 0 failed)
 2026-07-05 01:02:55 +08:00
Research Assistant
ebe5c07969 ocr rebuild: add --resume checkpoint, fix garbled progress bar, remove debug print 2026-06-26 17:31:52 +08:00
Research Assistant
ccafb8bae7 feat: add OCR maintenance tab with rebuild and redo controls 
- Add OCRMaintenanceRow model (ocr_maintenance.py) for clean table data
- Add paperforge ocr list --json for plugin consumption
- Add paperforge ocr rebuild command (rebuild-derived from raw OCR)
- Add maintenance tab in plugin settings with paper table
- Table: select, key, title, status, health, version, time, redo, rebuild
- Mutual exclusion: redo/rebuild per paper, filter by status
- Global rebuild-index and rebuild-memory buttons
 2026-06-19 16:22:08 +08:00
Research Assistant
b9885f369d feat: add Gemini CLI agent platform support (.gemini/skills) 2026-06-01 19:46:17 +08:00
Research Assistant
48560df7b6 fix: consolidate ocr redo logic into worker.ocr_redo_papers with validation, --dry-run, and proper frontmatter updates 2026-06-01 12:52:09 +08:00
Research Assistant
9c4d150da6 feat: add paperforge ocr redo command for re-running OCR on marked papers 2026-06-01 11:29:06 +08:00
Research Assistant
03ad9ce64f feat: stabilize paperforge query planning 2026-05-27 21:20:15 +08:00
Research Assistant
02ef2d9b52 feat(sync): auto-detect orphan papers after sync, show modal in Obsidian 
- prune.py: _enrich_orphan_preview() reads note frontmatter for metadata
- sync_service.py: always run dry-run prune, include in result
- sync.py: write sync-orphan-state.json for plugin consumption
- main.js: add checkOrphanState() + PaperForgeOrphanModal with select/toggle
- styles.css: orphan modal styles (list, tags, dimmed rows)
- cli.py: add --keys to prune command for targeted deletion
 2026-05-19 00:31:19 +08:00
Research Assistant
214453d69c feat(prune): integrate prune into sync --prune 2026-05-18 21:57:04 +08:00
Research Assistant
5a7e60864a feat(prune): standalone CLI command 2026-05-18 21:54:16 +08:00
Research Assistant
245d09e383 feat: add runtime-health CLI command 2026-05-15 01:16:16 +08:00
Research Assistant
b21c339227 feat: persist embed lifecycle and add stop command 2026-05-15 01:15:07 +08:00
Research Assistant
80db051d8c fix: add --resume CLI arg and get_collection import for embed build 2026-05-15 00:16:06 +08:00
Research Assistant
e1ff28f2e3 feat: add project-log CLI command with JSONL write + auto-render 2026-05-14 17:47:43 +08:00
Research Assistant
1284dfcd2f feat: add paper-context CLI command for reading-log safety loop 2026-05-14 17:44:20 +08:00
Research Assistant
6ccce87272 feat: upgrade reading-log to JSONL with context/tags/project fields and auto-render 2026-05-14 17:31:32 +08:00
Research Assistant
3701cc155e feat(cli): add reading-log --validate/--import/--lookup commands 2026-05-13 16:12:23 +08:00
Research Assistant
8d3e4432c3 chore: add pre-commit JS syntax hook + stage missing vector CLI files 2026-05-12 23:34:24 +08:00
Research Assistant
b12c90bca9 feat(memory): add paper_events table + reading-log write/export command 2026-05-12 20:53:33 +08:00
Research Assistant
fdeade123e feat(cli): add agent-context command for agent bootstrap 2026-05-12 19:59:12 +08:00
Research Assistant
93ca222aaa feat(memory): add FTS5 full-text search with paperforge search command 2026-05-12 18:58:25 +08:00
Research Assistant
95bf0b33c9 feat(cli): add memory build/status and paper-status commands 2026-05-12 17:52:30 +08:00
Research Assistant
0c31f89d4d feat: add deep-finalize command — signal dashboard on /pf-deep completion 
- new command paperforge deep-finalize <key>: sets deep_reading_status=done in frontmatter + refreshes index
- dashboard now only auto-refreshes on formal-library.json changes (removed per-note modify handler)
- pf-deep reference updated with Post-Processing section instructing agent to call deep-finalize at end
 2026-05-10 21:50:27 +08:00
Research Assistant
15d849f7e6 fix: remove deprecated control_dir from doctor/setup/repair; enable repair button; fix UTF-8 encoding in doctor output 2026-05-10 01:50:24 +08:00
Research Assistant
05629bce82 refactor: v2.1 contract hardening — PFResult unification, ErrorCode expansion, adapter cleanup, SyncService orchestration 
Core contract:
- ErrorCode: 8→26 with _missing_() graceful degradation for unknown codes
- PFResult: +warnings/next_actions, PFError: +suggestions
- OcrStatus: 4→9 granular states (NONE/QUEUED/BLOCKED/NO_PDF/DONE_INCOMPLETE restored 1:1)
- field_registry.yaml: +owner/deprecated/replacement/enum values/default

Adapter cleanup:
- new core/io.py (read_json/write_json), core/date_utils.py (extract_year)
- new adapters/collections.py (build_collection_lookup)
- adapters/bbt.py: cut worker dependency, _private→public+alias
- worker/_utils.py + _domain.py: re-export from core instead of duplicate defs

Command unification:
- All 6 commands (sync/status/ocr/deep/repair/dashboard) → PFResult
- cli.py --json dest unified to 'json' (was json_output on status/doctor)
- commands/sync.py → SyncService (no more int/dict/PFResult mixing)

Service hardening:
- SyncService.run() orchestrates full sync lifecycle (select→index→clean)
- cleanup loops (orphaned records, flat notes) migrated from worker
- worker/sync.py: freeze line + services→worker one-way dependency
- plugin/main.js: formal-library.json fallback deprecation warning

Verification: 181/181 tests, 0 new lint errors
 2026-05-09 22:20:07 +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
fa3187519d fix: add --version to CLI, fix plugin version detection to use python -c 2026-05-08 01:35:24 +08:00
Research Assistant
dd71bb0f79 fix: v1.4.17rc2 — OCR quote fix, 4-stage lifecycle, .env fallback, Codex support, deep-reading anchors, auto-update pip 2026-05-08 01:26:04 +08:00
Research Assistant
68e888a010 feat(48-textual-tui-removal): update CLI help and remove textual dependency 
- Update setup parser help text (remove 'Textual-based' reference)
- Remove textual>=0.47.0 from pyproject.toml dependencies
- Remove textual from scripts/validate_setup.py required dict
 2026-05-07 19:41:51 +08:00
Research Assistant
80664588ff feat(26-02): wire context command into CLI subparser, registry, and dispatch 
- Add 'context' to _COMMAND_REGISTRY for dynamic module loading
- Add context subparser with key (nargs='?'), --domain, --collection, --all
- Dispatch in main() to paperforge.commands.context.run(args)
- D-06: always outputs JSON, no --json flag needed
 2026-05-04 12:43:43 +08:00
Research Assistant
9691d68970 feat(23-02): add workspace path fields, frontmatter mirroring, and --rebuild-index CLI flag 
- Add paper_root, main_note_path, fulltext_path, deep_reading_path, ai_path
  to _build_entry() result dict (Phase 22 paper workspace layout, D-12)
- Mirror workspace path fields in formal note frontmatter for Base views (D-14)
- Add --rebuild-index flag to cli.py sync command parser
- Thread rebuild_index parameter through commands/sync.py -> run_index_refresh()
- Existing system paths (ocr_path, meta_path, note_path) preserved (D-13)
- All 14 existing tests pass
 2026-05-04 00:46:34 +08:00
Research Assistant
f617054d5a feat: paperforge status --json, plugin panel with OCR progress bar 2026-04-28 19:21:52 +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
0505fd2fda feat: add paperforge setup CLI command, one-click install script, sync __version__ to 1.4.0, detect local version from pip metadata 2026-04-27 21:34:03 +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
ca7d665896 feat(13-logging-foundation): add global --verbose flag and wire configure_logging() in cli.py 
- Import configure_logging from paperforge.logging_config
- Add --verbose/-v as root parser argument (global flag for all subcommands)
- Remove per-subcommand --verbose from deep-reading and repair subparsers
  (users now use 'paperforge -v deep-reading' style instead)
- Call configure_logging(verbose=args.verbose) in main() before command dispatch
- validate: root-level --verbose works across all subcommands
- deviation per Rule 2: subparser --verbose removed; backward compat for
  'deep-reading -v' requires root-level style 'paperforge -v deep-reading'
  (argparse does not inherit root flags to subparsers)
 2026-04-27 15:10:26 +08:00
Research Assistant
660204352f fix(cli): add missing 'update' subcommand 
- worker/update.py had run_update() but CLI never registered it
- Users can now run: paperforge update
 2026-04-25 00:08:46 +08:00
Research Assistant
498a9edfe5 feat(phase-12): extract worker modules from literature_pipeline.py 
- Create paperforge/worker/ package with sync.py, ocr.py, repair.py,
  status.py, deep_reading.py, update.py, base_views.py
- Update paperforge/commands/*.py to import from new worker modules
- Update paperforge/cli.py _import_worker_functions for new paths
- Update paperforge/config.py ld_deep_script resolution with fallback
- Update setup_wizard.py for new worker/skills paths
- Add function-level imports to break circular dependencies
 2026-04-24 22:32:25 +08:00
Research Assistant
434660c626 feat(11-01): integrate path_error with repair and status commands 
- Add --fix-paths flag to paperforge repair CLI
- Add repair_pdf_paths(): re-resolves PDF paths for items with path_error
- Add _detect_path_errors(): scans library-records for path_error fields
- Update run_repair(): detects path_error, reports summary counts by type
- Update run_status(): shows path_error count and suggests repair --fix-paths
- Update repair.py wrapper: prints path_error summary, returns proper exit code
- Update status.py: document path_error reporting in module docstring
 2026-04-24 20:08:46 +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
27d22c7014 refactor(phase-9): refactor cli.py to use shared command modules 2026-04-24 16:31:26 +08:00
Research Assistant
59457d15c7 refactor(phase-9): rename paperforge_lite package to paperforge 
- Rename directory: paperforge_lite/ → paperforge/
- Update pyproject.toml: package name, entry point, includes
- Verified: python -m paperforge --help works
 2026-04-24 16:15:13 +08:00
Renamed from paperforge_lite/cli.py (Browse further)