Skip to content

Research Memory Runtime + User-Side Stabilization#8

Merged
LLLin000 merged 132 commits into
masterfrom
feature/memory
May 14, 2026
Merged

Research Memory Runtime + User-Side Stabilization#8
LLLin000 merged 132 commits into
masterfrom
feature/memory

Conversation

@LLLin000
Copy link
Copy Markdown
Owner

@LLLin000 LLLin000 commented May 14, 2026

Summary

  • Research Memory Core: reading-log / project-log JSONL permanent storage with SQLite derived index
  • Correction log: permanent correction-log.jsonl survives DB rebuilds
  • Unified skill: single paperforge skill with 6 workflows (replaces literature-qa + logging + methodology)
  • Stabilization: OCR nopdf deadlock fix, FTS safe query fallback, bootstrap path+Python fix, vector DB preflight

Data Flow (post-merge)

reading-log.jsonl     ← single source of truth
correction-log.jsonl  ← permanent corrections
project-log.jsonl     ← work session logs
reading_log table     ← derived index (auto-synced on memory build)

Commits (16)

  • reading-log JSONL unification + correction permanent storage
  • project-log CLI + paper-context CLI
  • FTS 3-level fallback (raw → quoted token → LIKE)
  • OCR nopdf reset fix
  • bootstrap vault_config nest + python_verified
  • Vector DB: ghost code removal, deps, preflight, retrieve guard
  • Skill: router expansion, engineering workflow, safety rules
  • pyproject package-data migration to skills/paperforge/**

Research Assistant added 30 commits May 12, 2026 17:32
feat(config): add memory_db path key for Memory Layer
139d5b6
feat(memory): add db.py with connection and path resolution
772954f
feat(memory): add schema module with table definitions and tests
fb17c58
feat(memory): add builder module that populates SQLite from formal-li…
f6bc234 
…brary.json
feat(memory): add query module for paper lookup and status check
afcbd3c
feat(cli): add memory build/status and paper-status commands
3c906e8
test(memory): add integration test for memory build/status workflow
65cbf86
style(memory): apply ruff fixes (ternary, nested-if, dict-keys)
95ca8fc
feat(memory): add schema exports to __init__.py
339ffe2
bump: 1.5.5 -> 1.5.6rc1 (Memory Layer RC1)
02c1e5b
feat(frontmatter): add citation_key field and alias from BBT citationKey
6c6b8ce
fix(memory): restore row.keys() iteration (sqlite3.Row iterates value…
5673f68 
…s, not keys)
feat(memory): add FTS5 full-text search with paperforge search command
1acbeaa
fix(memory): match FTS column names to papers table (authors_json, co…
4bb750b 
…llections_json)
docs(spec): add Memory Layer Phase 2-5 design (agent-context, dashboa…
eedf02c 
…rd, refresh, retrieve)
docs(plan): add agent-context implementation plan
5f7f2cd
feat(memory): add agent context query module
2b91e09
feat(cli): add agent-context command for agent bootstrap
551abd0
test(memory): verify agent-context on test vault — 150 papers, 26 col…
3ee0320 
…lections, 4 rules
feat(memory): dashboard reads from SQLite + incremental refresh_paper()
d4df673
docs(spec): add Phase 6 — paper_events, reading/working logs, vector …
4ffcd4c 
…retrieval
feat(memory): add paper_events table + reading-log write/export command
99ab29b
feat(skills): add /pf-log-reading and /pf-log-session slash commands
babfe06
feat(skills): add literature-logging skill (reading-log + working-log)
11be2b8
docs(spec): plugin settings redesign — tabbed UI, skill manager, feat…
fffc0c3 
…ure toggles, vector DB panel
fix(spec): add DEFAULT_SETTINGS whitelist note, source: paperforge re…
2551eec 
…quirement, CLI toggle read
docs(spec): add Phase 7 vector retrieval — ChromaDB + local/API embed…
9016a87 
…ding + chunking
feat(plugin): tabbed settings UI (Installation + Features) with skill…
0d83278 
… manager and feature toggles
fix(plugin): single memory toggle + platform skill selector + vector …
3532b34 
…UX improvements
fix(plugin): remove dead cascading keys, fix skill toggle content syn…
053b303 
…c, remove unused disableMatch
Research Assistant added 28 commits May 14, 2026 01:21
spec: dashboard copy interaction + per-paper metadata enhancement
eed4817
spec: remove copy icon — clean click-to-copy with dashed underline only
6f6c1ae
fix(plugin): replace deprecated revealLeaf().setViewState with intern…
b4632e3 
…alPlugins toggle
fix(plugin): simplify file-explorer open to enable() call
9af8bbf
fix(plugin): use getLeavesOfType + revealLeaf to focus existing file-…
d6960a7 
…explorer
fix(plugin): open .base file directly instead of file-explorer + trim…
97d9715 
… domain basename
fix(plugin): fall back to global mode when Base domain has no matchin…
cfc0755 
…g papers
feat: add reading_log and project_log tables to memory schema
5493e28
feat: add permanent JSONL storage layer for reading-log and project-log
0d1ca3a
fix: align JSONL field names with spec (type/title, add verified)
2631edb
feat: upgrade reading-log to JSONL with context/tags/project fields a…
d16b6c7 
…nd auto-render
feat: add paper-context CLI command for reading-log safety loop
b1aa222
feat: add project-log CLI command with JSONL write + auto-render
06a3f2b
feat: import JSONL into DB on memory build
5a44926
feat: add METHODOLOGY_COMPACT.md for agent guidance
95bfb22
refactor: unify skills into paperforge compound skill (6 workflows)
df135bf
fix: reset nopdf OCR status to pending when paper re-enters queue
5f07a8f
refactor: unify reading-log reads to JSONL, deprecate paper_events wr…
f248f81 
…ites
fix: bootstrap vault_config nest, python fallback with verified flag
9b0bc59
feat: permanent correction-log.jsonl, fix original_id field alignment
054ca3e
feat: safe FTS search with token-quote and LIKE fallback
002173f
fix: remove ghost settings code, add vector deps, add embed preflight
2c71643
feat: retrieve empty index guard, embed status check, HF download hint
62cbb61
fix: dedupe correction import on rebuild, clean FTS row on refresh
ce86eff
fix: pf_bootstrap verified tuple return, engineering review dimensions
888bbbb
fix: import_reading_log to JSONL, correction JSONL-first, events.py w…
a76cb21 
…rapper
fix: refresh_paper FTS delete-before-upsert, import error checking
6643229
fix: update package-data from literature-qa to skills/paperforge/**
f054193
@LLLin000 LLLin000 merged commit 1eadace into master May 14, 2026
0 of 7 checks passed
@LLLin000 LLLin000 deleted the feature/memory branch May 14, 2026 15:10
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

1 participant

@LLLin000