LICENSE
README.md
pyproject.toml
paperforge/__init__.py
paperforge/__main__.py
paperforge/cli.py
paperforge/config.py
paperforge/logging_config.py
paperforge/ocr_diagnostics.py
paperforge/pdf_resolver.py
paperforge/query_planning.py
paperforge/setup_wizard.py
paperforge.egg-info/PKG-INFO
paperforge.egg-info/SOURCES.txt
paperforge.egg-info/dependency_links.txt
paperforge.egg-info/entry_points.txt
paperforge.egg-info/requires.txt
paperforge.egg-info/top_level.txt
paperforge/adapters/__init__.py
paperforge/adapters/bbt.py
paperforge/adapters/collections.py
paperforge/adapters/obsidian_frontmatter.py
paperforge/adapters/zotero_paths.py
paperforge/command_files/pf-deep.md
paperforge/command_files/pf-end.md
paperforge/command_files/pf-log-reading.md
paperforge/command_files/pf-log-session.md
paperforge/command_files/pf-ocr.md
paperforge/command_files/pf-paper.md
paperforge/command_files/pf-status.md
paperforge/command_files/pf-sync.md
paperforge/commands/__init__.py
paperforge/commands/agent_context.py
paperforge/commands/context.py
paperforge/commands/dashboard.py
paperforge/commands/deep.py
paperforge/commands/embed.py
paperforge/commands/memory.py
paperforge/commands/ocr.py
paperforge/commands/paper_context.py
paperforge/commands/paper_status.py
paperforge/commands/project_log.py
paperforge/commands/prune.py
paperforge/commands/query_plan.py
paperforge/commands/reading_log.py
paperforge/commands/repair.py
paperforge/commands/retrieve.py
paperforge/commands/runtime_health.py
paperforge/commands/search.py
paperforge/commands/status.py
paperforge/commands/sync.py
paperforge/core/__init__.py
paperforge/core/date_utils.py
paperforge/core/errors.py
paperforge/core/io.py
paperforge/core/result.py
paperforge/core/state.py
paperforge/doctor/__init__.py
paperforge/doctor/field_validator.py
paperforge/embedding/__init__.py
paperforge/embedding/_chroma.py
paperforge/embedding/_config.py
paperforge/embedding/build_state.py
paperforge/embedding/builder.py
paperforge/embedding/preflight.py
paperforge/embedding/search.py
paperforge/embedding/status.py
paperforge/embedding/providers/__init__.py
paperforge/embedding/providers/base.py
paperforge/embedding/providers/openai_compatible.py
paperforge/memory/__init__.py
paperforge/memory/_columns.py
paperforge/memory/builder.py
paperforge/memory/chunker.py
paperforge/memory/context.py
paperforge/memory/db.py
paperforge/memory/events.py
paperforge/memory/fts.py
paperforge/memory/permanent.py
paperforge/memory/query.py
paperforge/memory/refresh.py
paperforge/memory/runtime_health.py
paperforge/memory/schema.py
paperforge/memory/state_snapshot.py
paperforge/memory/vector_db.py
paperforge/plugin/main.js
paperforge/plugin/manifest.json
paperforge/plugin/package-lock.json
paperforge/plugin/package.json
paperforge/plugin/styles.css
paperforge/plugin/tsconfig.json
paperforge/plugin/versions.json
paperforge/schema/__init__.py
paperforge/services/__init__.py
paperforge/services/skill_deploy.py
paperforge/services/sync_service.py
paperforge/setup/__init__.py
paperforge/setup/agent.py
paperforge/setup/checker.py
paperforge/setup/config_writer.py
paperforge/setup/plan.py
paperforge/setup/runtime.py
paperforge/setup/vault.py
paperforge/skills/__init__.py
paperforge/skills/paperforge/SKILL.md
paperforge/skills/paperforge/atoms/clarify-user-intent.md
paperforge/skills/paperforge/atoms/extract-methodology-card.md
paperforge/skills/paperforge/atoms/method-card-template.md
paperforge/skills/paperforge/atoms/retrieval-routing.md
paperforge/skills/paperforge/atoms/write-project-log.md
paperforge/skills/paperforge/atoms/write-project-reading-log.md
paperforge/skills/paperforge/atoms/write-reading-log-jsonl.md
paperforge/skills/paperforge/atoms/chart-reading/GSEA富集图.md
paperforge/skills/paperforge/atoms/chart-reading/INDEX.md
paperforge/skills/paperforge/atoms/chart-reading/ROC与PR曲线.md
paperforge/skills/paperforge/atoms/chart-reading/Western Blot条带图.md
paperforge/skills/paperforge/atoms/chart-reading/免疫荧光定量图.md
paperforge/skills/paperforge/atoms/chart-reading/折线图与时间序列.md
paperforge/skills/paperforge/atoms/chart-reading/散点图与气泡图.md
paperforge/skills/paperforge/atoms/chart-reading/显微照片与SEM图.md
paperforge/skills/paperforge/atoms/chart-reading/条形图与误差棒.md
paperforge/skills/paperforge/atoms/chart-reading/桑基图与弦图.md
paperforge/skills/paperforge/atoms/chart-reading/森林图与Meta分析.md
paperforge/skills/paperforge/atoms/chart-reading/火山图与曼哈顿图.md
paperforge/skills/paperforge/atoms/chart-reading/热图与聚类图.md
paperforge/skills/paperforge/atoms/chart-reading/生存曲线.md
paperforge/skills/paperforge/atoms/chart-reading/箱式图与小提琴图.md
paperforge/skills/paperforge/atoms/chart-reading/组织学半定量图.md
paperforge/skills/paperforge/atoms/chart-reading/网络图与通路图.md
paperforge/skills/paperforge/atoms/chart-reading/蛋白质结构图.md
paperforge/skills/paperforge/atoms/chart-reading/降维图(PCA-tSNE-UMAP).md
paperforge/skills/paperforge/atoms/chart-reading/雷达图与漏斗图.md
paperforge/skills/paperforge/molecules/capture-project-knowledge.md
paperforge/skills/paperforge/molecules/deep-analyze-paper.md
paperforge/skills/paperforge/molecules/discover-papers.md
paperforge/skills/paperforge/molecules/find-supporting-evidence.md
paperforge/skills/paperforge/molecules/read-known-paper.md
paperforge/skills/paperforge/scripts/pf_bootstrap.py
paperforge/skills/paperforge/scripts/pf_deep.py
paperforge/skills/paperforge/workflows/project-engineering.md
paperforge/worker/__init__.py
paperforge/worker/_domain.py
paperforge/worker/_progress.py
paperforge/worker/_retry.py
paperforge/worker/_utils.py
paperforge/worker/asset_index.py
paperforge/worker/asset_state.py
paperforge/worker/base_views.py
paperforge/worker/deep_reading.py
paperforge/worker/discussion.py
paperforge/worker/ocr.py
paperforge/worker/ocr_attach.py
paperforge/worker/ocr_body_spine.py
paperforge/worker/ocr_emit.py
paperforge/worker/ocr_layout.py
paperforge/worker/ocr_orchestrator.py
paperforge/worker/ocr_roles.py
paperforge/worker/paper_meta.py
paperforge/worker/paper_resolver.py
paperforge/worker/prune.py
paperforge/worker/repair.py
paperforge/worker/status.py
paperforge/worker/sync.py
paperforge/worker/update.py
paperforge/worker/vector_db.py
tests/test_asset_index.py
tests/test_asset_index_integration.py
tests/test_asset_state.py
tests/test_base_preservation.py
tests/test_base_views.py
tests/test_cli_paths.py
tests/test_cli_worker_dispatch.py
tests/test_command_docs.py
tests/test_config.py
tests/test_context.py
tests/test_discussion.py
tests/test_doctor.py
tests/test_e2e_cli.py
tests/test_e2e_pipeline.py
tests/test_legacy_worker_compat.py
tests/test_literature_hub_regressions.py
tests/test_migration.py
tests/test_ocr.py
tests/test_ocr_attachments.py
tests/test_ocr_body_spine.py
tests/test_ocr_classify.py
tests/test_ocr_doctor.py
tests/test_ocr_emission_regressions.py
tests/test_ocr_integration_fixtures.py
tests/test_ocr_layout_zones.py
tests/test_ocr_preflight.py
tests/test_ocr_reading_order_fixtures.py
tests/test_ocr_redo.py
tests/test_ocr_rendering.py
tests/test_ocr_roles.py
tests/test_ocr_state_machine.py
tests/test_pdf_resolver.py
tests/test_pf_bootstrap_capabilities.py
tests/test_plugin_install_bootstrap.py
tests/test_prepare_rollback.py
tests/test_query_command_diagnostics.py
tests/test_query_plan.py
tests/test_repair.py
tests/test_selection_sync_pdf.py
tests/test_setup_wizard.py
tests/test_skill_graph_contracts.py
tests/test_skill_graph_layout.py
tests/test_smoke.py
tests/test_status.py
tests/test_sync.py
tests/test_utils_journal.py
tests/test_utils_json.py
tests/test_utils_slugify.py
tests/test_utils_yaml.py