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Author SHA1 Message Date
Research Assistant
8b2e5357f2 ci: explicit PYPI_TOKEN secret in publish workflow 2026-05-11 18:07:08 +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
0376fdb512 feat(plugin): enhanced diagnostic — git/PATH/vault path on install failure 2026-05-11 17:51:14 +08:00
Research Assistant
c81f892625 fix(base): use !zotero_key.isEmpty() filter syntax 2026-05-11 17:47:05 +08:00
Research Assistant
3c3f62182a docs: update v1.5.1 changelog with all hotfixes 2026-05-11 17:44:56 +08:00
Research Assistant
12fa24034d fix: prepend v to git tag ref in all pip install URLs 2026-05-11 17:41:59 +08:00
Research Assistant
e7707cc26e debug: log pip stderr on Sync Runtime failure 2026-05-11 17:38:38 +08:00
Research Assistant
7906c1b114 fix(plugin): pass enriched env through runSubprocess for Sync Runtime button 2026-05-11 17:32:19 +08:00
Research Assistant
0867f844ce feat(plugin): cross-platform git detection (win/mac/linux) for pip install PATH 2026-05-11 17:28:34 +08:00
Research Assistant
0bf629bb33 feat(plugin): resolve git via ComSpec and inject into PATH for pip install spawns 2026-05-11 17:26:35 +08:00
Research Assistant
7b5f5aebe0 fix(base): filter by zotero_key != "" instead of filename exclusion 2026-05-11 17:11:51 +08:00
Research Assistant
b599b59cb9 fix(base): exclude fulltext.md from Base views to prevent workspace clutter 2026-05-11 17:10:34 +08:00
Research Assistant
b90fa546f9 feat(update): add zip fallback when pip/git update fails (e.g. missing git) 2026-05-11 17:04:30 +08:00
Research Assistant
566697fc31 chore: remove CI workflows pending rewrite 2026-05-11 17:00:23 +08:00
Research Assistant
8488437c0b chore: bump version to v1.5.1 2026-05-11 16:50:07 +08:00
Research Assistant
813980b7d3 hotfix: fix Base filter syntax error, = to == 2026-05-11 16:43:58 +08:00
Research Assistant
e6770b9ec9 hotfix: remove py launcher from auto-detection to prevent spawn ENOENT on Windows 2026-05-11 16:40:22 +08:00
Research Assistant
3b98c51622 docs: update README version refs to v1.5.0, add Dashboard three-mode / pf-end sections 2026-05-11 12:55:31 +08:00
Research Assistant
a473710f68 docs: add v1.5.0 changelog entries 2026-05-11 00:56:39 +08:00
Research Assistant
02d8ba1448 fix: deep_reading_status read from frontmatter, key extraction walkup, remove body status fields 
- _build_entry: read deep_reading_status from frontmatter first, body detection fallback

- _extractZoteroKeyFromPath: walk up directory tree for 8-char key (handles ai/discussion.md etc.)

- frontmatter_note: remove duplicate PDF/OCR/deep_reading status from body (frontmatter is source of truth)
 2026-05-11 00:52:07 +08:00
Research Assistant
dfdbc09f6d ci: add contents:write permission to release workflow 2026-05-11 00:23:48 +08:00
Research Assistant
20acbbfc23 chore: bump version to v1.5.0 2026-05-11 00:21:35 +08:00
Research Assistant
41b8b7d5eb test: update headless_setup tests for refactored literature-qa skill directory 
Refactored deploy_skills service creates a single literature-qa skill dir

instead of individual pf-deep/pf-paper/etc. Update all 4 agent

platform tests to check for literature-qa instead of old names.
 2026-05-11 00:18:24 +08:00
Research Assistant
e25a6b193e fix(dashboard): use same wikilink parser as Open PDF button for PDF detection 2026-05-11 00:17:21 +08:00
Research Assistant
ba6fffa1f7 feat(dashboard): PDF files now trigger per-paper mode via index pdf_path match 2026-05-11 00:15:42 +08:00
Research Assistant
66ab2fad2e fix(setup,test): replace orphaned imported_skills variable and update bootstrap test 
headless_setup Phase 7 used imported_skills which was removed during

skill_deploy refactor. Use skill_result['skill_deployed'] instead.

Also update bootstrap test that asserted old command_files string.
 2026-05-11 00:11:00 +08:00
Research Assistant
aa86e9bb75 Merge branch 'fix/setup-v2' 2026-05-11 00:06:20 +08:00
Research Assistant
8d8c1cd068 test: update AGENT_CONFIGS tests for refactored AGENT_SKILL_DIRS flat dict 
Setup wizard no longer defines AGENT_CONFIGS; the refactored

skill_deploy.py exports AGENT_SKILL_DIRS instead. Update

test imports and assertions accordingly.
 2026-05-11 00:05:59 +08:00
Research Assistant
8d084860b0 fix(setup): align setup_wizard and skill_deploy API with refactored master 
Use AGENT_SKILL_DIRS (flat dict) instead of AGENT_CONFIGS (nested),

matching the skill_deploy.py refactor already on master.
 2026-05-11 00:03:03 +08:00
Research Assistant
20f9ea396e fix(setup): use AGENT_CONFIGS import to match master skill_deploy.py API 
fix/setup branched from master where skill_deploy still exports

AGENT_CONFIGS (not AGENT_SKILL_DIRS which was renamed later).
 2026-05-10 23:54:33 +08:00
Research Assistant
1001674a72 fix(dashboard): workspace path detection now triggers paper mode for any file in workspace dir 
- Remove _findEntry() precondition — works even if index not yet loaded
- Add case-insensitive flag to key regex (/i)
 2026-05-10 23:40:35 +08:00
Lin Zhaoxuan
0c7082dcec Merge pull request #7 from LLLin000/feature/skill-refine 
feat: unified release — skill redesign + deep-finalize + sync safety + dashboard v2
 2026-05-10 23:32:23 +08:00
Lin Zhaoxuan
c4adf201be Merge pull request #6 from LLLin000/fix/setup 
fix(setup,plugin): rewrite BBT detection for Zotero 7 .xpi compatibility
 2026-05-10 23:31:44 +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
c0cc05ab32 refactor(skills): simplify skill deployment — single copytree for all platforms 
- Remove format dispatch (flat_command/skill_directory/rules_file) — all platforms unified
- skill_deploy.py: 257→81 lines, only AGENT_SKILL_DIRS + copytree + AGENTS.md
- AgentInstaller switches to vault-local paths, removes deploy_commands step
- Remove _deploy_skills dead code in update.py
 2026-05-10 23:22:42 +08:00
Research Assistant
7fedced9f6 fix(setup,plugin): rewrite BBT detection for Zotero 7 .xpi compatibility 
Setup wizard (Python):

- Replace broken manual_path direct-candidate scan with unified platform-path-first approach

- Use _looks_like_bbt() — normalize to alnum+lower, match 'betterbibtex'

- Accept both .xpi files (Zotero 7) and directories (Zotero 6)

- Correct Linux profile path (.zotero/zotero/<random>, not .zotero/zotero/Profiles)

Plugin (JS):

- Remove isDirectory() restriction in scanBbtUnderProfiles/scanBbtDirectChildren

- Accept .xpi file entries for Zotero 7 compatibility

- Also remove all control_dir references (CLI argument removed in v1.4.17)
 2026-05-10 23:18:14 +08:00
Research Assistant
d50c2ff4c0 fix(plugin): remove all control_dir references — CLI argument was removed in v1.4.17 
- Remove --control-dir from setup args (CLI no longer accepts it)

- Remove control_dir from DEFAULTS, config parser, valid path keys

- Remove control_dir from settings assignment and JSDoc

- Remove dir_index display and validate_index check
 2026-05-10 23:05:22 +08:00
Research Assistant
a5dd71bb13 fix(sync): freeze workspace slug + frontmatter-only update to prevent deep-reading data loss 
- Slug freeze: reuse existing workspace dir when title slug changes in Zotero
- Frontmatter-only: for existing notes, replace only YAML block, never touch body
- extract_preserved_deep_reading: match both ##精读 and ##🔍精读 + skip placeholder-only sections
 2026-05-10 22:31:16 +08:00
Research Assistant
f8c05959ed style: align collection workflow overview with global library snapshot 
- Match outer frame padding/background/shadow to library-snapshot

- Match inner stage card padding/background/layout to snapshot-pill

- Use align-items: stretch on funnel (pill parity), arrow stays centered

- Reduce collection-header bottom gap for tighter domain-to-card spacing

- Synchronize stage-label font-size (12px -> 11px)
 2026-05-10 22:22:31 +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
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
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
50d47d41d0 test: update bootstrap test to match fixed agents_src code 2026-05-10 21:05:16 +08:00
Research Assistant
7abb90b91b test: update bootstrap test to match fixed agents_src code 2026-05-10 21:05:05 +08:00
Research Assistant
007e36e45c fix(setup): resolve NameError for undefined agents_src in Phase 7 verification 2026-05-10 20:59:57 +08:00
Research Assistant
78a8ed312e fix(skills): narrow description triggers to avoid false matches 2026-05-10 20:56:28 +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
5c6ccaad34 feat: dashboard ui refine — arrow icons, maillard colors, responsive grid, setup bugfix 
Dashboard UI:

- Replace text expand/collapse with SVG arrow + clickable gradient container

- Map agent_platform key to display name (OpenCode, not opencode)

- Maillard/Morandi palette for OCR progress bars (pending brown, done deep green)

- Shorten 'Needs Attention' to 'Attention' to prevent label wrap

- Responsive workflow overview: CSS Grid + container queries (narrow: 2x2, wide: 4x1 with max-width 160px stop)

Setup Wizard:

- Fix Phase 7 verification crash (undefined agents_src/agents_dst variables)

Skill restructure:

- Move chart-reading references under references/ directory

- Remove old pf-*.md script files (deployed via skill_deploy service)

- Add new reference files (deep-reading, paper-qa, paper-resolution, save-session)
 2026-05-10 20:56:27 +08:00
Research Assistant
c6c5723296 style: tighten collection header spacing, fix u00B7 encoding, add stage max-width 
- Fix CSS unicode escape: \\u00B7 -> literal middle dot character

- Remove 'papers' count line in collection header

- Tighten collection-header padding from 64px to 14px top only

- Reset collection-title margin to 0

- Add max-width: 160px + justify-self: center to workflow stages

- workflow-stage-label font-size: 11px -> 12px
 2026-05-10 20:52:22 +08:00