LICENSE
README.md
pyproject.toml
paperforge/__init__.py
paperforge/__main__.py
paperforge/accept_proposal.py
paperforge/cli.py
paperforge/config.py
paperforge/credentials.py
paperforge/figure_reconciliation.py
paperforge/fulltext_reconciliation.py
paperforge/lineage.py
paperforge/logging_config.py
paperforge/ocr_diagnostics.py
paperforge/pdf_resolver.py
paperforge/promote_r.py
paperforge/query_planning.py
paperforge/reader_gate.py
paperforge/reconcile.py
paperforge/render_audit.py
paperforge/runtime_pointer.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/actions/chain.py
paperforge/actions/preflight_projection.py
paperforge/actions/registry.py
paperforge/actions/runner.py
paperforge/actions/types.py
paperforge/adapters/__init__.py
paperforge/adapters/bbt.py
paperforge/adapters/collections.py
paperforge/adapters/obsidian_frontmatter.py
paperforge/adapters/zotero_paths.py
paperforge/architecture_audit/__init__.py
paperforge/architecture_audit/canonical.py
paperforge/architecture_audit/fixtures.py
paperforge/architecture_audit/layers.py
paperforge/architecture_audit/reconcile.py
paperforge/architecture_audit/collectors/__init__.py
paperforge/architecture_audit/collectors/authority.py
paperforge/architecture_audit/collectors/common.py
paperforge/architecture_audit/collectors/orchestrator.py
paperforge/architecture_audit/collectors/python_ast.py
paperforge/architecture_audit/fixtures/golden_126_ocr_rebuild.json
paperforge/architecture_audit/fixtures/golden_127_sync_embed.json
paperforge/architecture_audit/fixtures/golden_129_display_restore.json
paperforge/architecture_audit/fixtures/synthetic_implicit_remote_followup.json
paperforge/architecture_audit/fixtures/synthetic_intentional_exception.json
paperforge/architecture_audit/fixtures/synthetic_partial_coverage.json
paperforge/architecture_audit/fixtures/synthetic_planned_gap.json
paperforge/architecture_audit/fixtures/synthetic_publication_bypass.json
paperforge/architecture_audit/fixtures/synthetic_query_side_effect.json
paperforge/architecture_audit/fixtures/synthetic_ui_canonical_write.json
paperforge/architecture_audit/fixtures/synthetic_unmatched_signal.json
paperforge/architecture_audit/report/__init__.py
paperforge/architecture_audit/report/gate.py
paperforge/architecture_audit/report/render_html.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/action.py
paperforge/commands/agent_context.py
paperforge/commands/auth.py
paperforge/commands/config.py
paperforge/commands/content_discovery.py
paperforge/commands/context.py
paperforge/commands/dashboard.py
paperforge/commands/deep.py
paperforge/commands/embed.py
paperforge/commands/finalize.py
paperforge/commands/memory.py
paperforge/commands/note.py
paperforge/commands/ocr.py
paperforge/commands/paper_context.py
paperforge/commands/paper_lookup.py
paperforge/commands/paper_navigation.py
paperforge/commands/paper_status.py
paperforge/commands/probe.py
paperforge/commands/project_log.py
paperforge/commands/prune.py
paperforge/commands/query_plan.py
paperforge/commands/read.py
paperforge/commands/reading_log.py
paperforge/commands/reconcile.py
paperforge/commands/render.py
paperforge/commands/repair.py
paperforge/commands/retrieve.py
paperforge/commands/runtime_health.py
paperforge/commands/scoped_fetch.py
paperforge/commands/search.py
paperforge/commands/status.py
paperforge/commands/sync.py
paperforge/commands/trash.py
paperforge/commands/versions.py
paperforge/core/__init__.py
paperforge/core/cancellation.py
paperforge/core/date_utils.py
paperforge/core/errors.py
paperforge/core/io.py
paperforge/core/keys.py
paperforge/core/ndjson.py
paperforge/core/next_actions.py
paperforge/core/result.py
paperforge/core/settlement.py
paperforge/core/state.py
paperforge/core/timing.py
paperforge/data/__init__.py
paperforge/data/nlm_journal_abbreviations.json
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/build_target.py
paperforge/embedding/builder.py
paperforge/embedding/dim_detect.py
paperforge/embedding/preflight.py
paperforge/embedding/query_rewrite.py
paperforge/embedding/search.py
paperforge/embedding/status.py
paperforge/embedding/substrate.py
paperforge/embedding/backends/__init__.py
paperforge/embedding/backends/base.py
paperforge/embedding/backends/chroma_backend.py
paperforge/embedding/backends/lance_backend.py
paperforge/embedding/providers/__init__.py
paperforge/embedding/providers/base.py
paperforge/embedding/providers/openai_compatible.py
paperforge/embedding/providers/requests_fallback.py
paperforge/materialization/__init__.py
paperforge/materialization/ocr.py
paperforge/materialization/retrieval.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/paper_state.py
paperforge/memory/permanent.py
paperforge/memory/query.py
paperforge/memory/refresh.py
paperforge/memory/runtime_health.py
paperforge/memory/schema.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/plugin/test/fixtures/build_e2e_vault.py
paperforge/plugin/test/fixtures/e2e_keyring.py
paperforge/policies/ocr_readiness_v1.yaml
paperforge/providers/paddleocr.py
paperforge/retrieval/__init__.py
paperforge/retrieval/gateway.py
paperforge/retrieval/manifest.py
paperforge/retrieval/structure_tree.py
paperforge/retrieval/units.py
paperforge/schema/__init__.py
paperforge/services/__init__.py
paperforge/services/embedding.py
paperforge/services/local_read.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/architecture-review/scripts/review_harness.py
paperforge/skills/architecture-review/scripts/skill_benchmark.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/fs_probe.py
paperforge/worker/ocr.py
paperforge/worker/ocr_artifacts.py
paperforge/worker/ocr_attach.py
paperforge/worker/ocr_banding.py
paperforge/worker/ocr_bio.py
paperforge/worker/ocr_blocks.py
paperforge/worker/ocr_decisions.py
paperforge/worker/ocr_document.py
paperforge/worker/ocr_emit.py
paperforge/worker/ocr_errors.py
paperforge/worker/ocr_evidence.py
paperforge/worker/ocr_families.py
paperforge/worker/ocr_figure_domain.py
paperforge/worker/ocr_figure_reader.py
paperforge/worker/ocr_figure_vnext_accounting_pass.py
paperforge/worker/ocr_figure_vnext_bundle_pass.py
paperforge/worker/ocr_figure_vnext_classic_seq_pass.py
paperforge/worker/ocr_figure_vnext_composite_pass.py
paperforge/worker/ocr_figure_vnext_corpus.py
paperforge/worker/ocr_figure_vnext_group_seq_pass.py
paperforge/worker/ocr_figure_vnext_locator_pass.py
paperforge/worker/ocr_figure_vnext_passes.py
paperforge/worker/ocr_figure_vnext_sidecar_pass.py
paperforge/worker/ocr_figure_vnext_state.py
paperforge/worker/ocr_figure_vnext_types.py
paperforge/worker/ocr_figures.py
paperforge/worker/ocr_fulltext_state.py
paperforge/worker/ocr_hash.py
paperforge/worker/ocr_health.py
paperforge/worker/ocr_index.py
paperforge/worker/ocr_layout.py
paperforge/worker/ocr_maintenance.py
paperforge/worker/ocr_math.py
paperforge/worker/ocr_metadata.py
paperforge/worker/ocr_object_writeback.py
paperforge/worker/ocr_objects.py
paperforge/worker/ocr_orchestrator.py
paperforge/worker/ocr_pairing_framework.py
paperforge/worker/ocr_pairing_state.py
paperforge/worker/ocr_pairing_types.py
paperforge/worker/ocr_pdf_spans.py
paperforge/worker/ocr_post_match_normalize.py
paperforge/worker/ocr_pre_match_normalize.py
paperforge/worker/ocr_profiles.py
paperforge/worker/ocr_quality.py
paperforge/worker/ocr_quality_feedback.py
paperforge/worker/ocr_rebuild.py
paperforge/worker/ocr_reference_signals.py
paperforge/worker/ocr_render.py
paperforge/worker/ocr_roles.py
paperforge/worker/ocr_scores.py
paperforge/worker/ocr_signatures.py
paperforge/worker/ocr_structural_gate.py
paperforge/worker/ocr_table_domain.py
paperforge/worker/ocr_table_passes.py
paperforge/worker/ocr_tables.py
paperforge/worker/ocr_tail_settlement.py
paperforge/worker/ocr_versions.py
paperforge/worker/paper_meta.py
paperforge/worker/paper_resolver.py
paperforge/worker/prune.py
paperforge/worker/repair.py
paperforge/worker/runtime_repair.py
paperforge/worker/status.py
paperforge/worker/status_probe.py
paperforge/worker/sync.py
paperforge/worker/trash.py
paperforge/worker/update.py
paperforge/worker/vector_db.py
tests/test_accept_proposal.py
tests/test_action_registry.py
tests/test_appendix_figure_numbering.py
tests/test_architecture_audit_canonical.py
tests/test_architecture_audit_collectors.py
tests/test_architecture_audit_fixtures.py
tests/test_architecture_audit_reconcile.py
tests/test_architecture_audit_report.py
tests/test_architecture_audit_schemas.py
tests/test_architecture_boundaries.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_build_incremental_ocr.py
tests/test_chain.py
tests/test_chroma_migration.py
tests/test_ci_coverage_contract.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_core_keys.py
tests/test_credentials.py
tests/test_deep_search.py
tests/test_discussion.py
tests/test_doctor.py
tests/test_e2e_cli.py
tests/test_e2e_embed_retrieve.py
tests/test_e2e_ocr_pipeline.py
tests/test_e2e_pipeline.py
tests/test_embed_eligibility.py
tests/test_embed_integration.py
tests/test_embed_scoped.py
tests/test_figure_reconciliation.py
tests/test_finalize_command.py
tests/test_fulltext_reconciliation.py
tests/test_layer4_gateway_commands.py
tests/test_layer4_lance_backend.py
tests/test_layer4_paper_lookup.py
tests/test_layer4_structure_tree.py
tests/test_layer4_units_and_fts.py
tests/test_layer4_vector_backend.py
tests/test_legacy_ocr_backfill.py
tests/test_legacy_worker_compat.py
tests/test_lineage.py
tests/test_literature_hub_regressions.py
tests/test_local_read.py
tests/test_materialization_ssot.py
tests/test_memory_build_scoped.py
tests/test_memory_restore.py
tests/test_migration.py
tests/test_next_actions.py
tests/test_no_raw_delete.py
tests/test_note_set_flag.py
tests/test_ocr.py
tests/test_ocr_artifact_paths_config.py
tests/test_ocr_artifacts.py
tests/test_ocr_attachments.py
tests/test_ocr_backfill_real_payloads.py
tests/test_ocr_bio.py
tests/test_ocr_blocks.py
tests/test_ocr_classify.py
tests/test_ocr_control_plane.py
tests/test_ocr_decisions.py
tests/test_ocr_doctor.py
tests/test_ocr_document.py
tests/test_ocr_emission_regressions.py
tests/test_ocr_entrypoints.py
tests/test_ocr_errors.py
tests/test_ocr_evidence.py
tests/test_ocr_families.py
tests/test_ocr_figure_ghost_suppression.py
tests/test_ocr_figure_reader.py
tests/test_ocr_figure_vnext_accounting_pass.py
tests/test_ocr_figure_vnext_bundle_pass.py
tests/test_ocr_figure_vnext_classic_seq_pass.py
tests/test_ocr_figure_vnext_compare.py
tests/test_ocr_figure_vnext_composite_pass.py
tests/test_ocr_figure_vnext_corpus.py
tests/test_ocr_figure_vnext_group_seq_pass.py
tests/test_ocr_figure_vnext_locator_pass.py
tests/test_ocr_figure_vnext_passes.py
tests/test_ocr_figure_vnext_real_papers.py
tests/test_ocr_figure_vnext_reservations.py
tests/test_ocr_figure_vnext_sidecar_pass.py
tests/test_ocr_figure_vnext_state.py
tests/test_ocr_figure_vnext_types.py
tests/test_ocr_figures.py
tests/test_ocr_fulltext_state.py
tests/test_ocr_hash_contract.py
tests/test_ocr_health.py
tests/test_ocr_high_risk_rule_audit.py
tests/test_ocr_index.py
tests/test_ocr_initial_fulltext_writeback.py
tests/test_ocr_integration_fixtures.py
tests/test_ocr_layout_first_regressions.py
tests/test_ocr_layout_zones.py
tests/test_ocr_maintenance.py
tests/test_ocr_metadata.py
tests/test_ocr_object_writeback.py
tests/test_ocr_objects.py
tests/test_ocr_pairing_framework.py
tests/test_ocr_pdf_spans.py
tests/test_ocr_pdf_text_fallback.py
tests/test_ocr_phase41_cleanup.py
tests/test_ocr_pipeline_v3.py
tests/test_ocr_preflight.py
tests/test_ocr_profiles.py
tests/test_ocr_quality.py
tests/test_ocr_quality_feedback.py
tests/test_ocr_reading_order_fixtures.py
tests/test_ocr_real_paper_audit_contracts.py
tests/test_ocr_real_paper_contract.py
tests/test_ocr_real_paper_reader_audit.py
tests/test_ocr_real_paper_regressions.py
tests/test_ocr_rebuild.py
tests/test_ocr_redo.py
tests/test_ocr_render.py
tests/test_ocr_render_stabilization.py
tests/test_ocr_render_v2.py
tests/test_ocr_rendering.py
tests/test_ocr_roles.py
tests/test_ocr_route_audit.py
tests/test_ocr_runtime_preflight.py
tests/test_ocr_scores.py
tests/test_ocr_signatures.py
tests/test_ocr_spec_contracts.py
tests/test_ocr_state_machine.py
tests/test_ocr_structural_gate.py
tests/test_ocr_synthetic_fixtures.py
tests/test_ocr_table_pairing_framework.py
tests/test_ocr_tables.py
tests/test_ocr_tail_settlement.py
tests/test_ocr_trace_vs_expectations.py
tests/test_ocr_v2_contract_audit.py
tests/test_ocr_v2_structural_regressions.py
tests/test_ocr_versions.py
tests/test_openai_compatible.py
tests/test_paper_context_evidence.py
tests/test_paper_lookup_from_path.py
tests/test_pdf_resolver.py
tests/test_pf_bootstrap_capabilities.py
tests/test_phase2a_backup.py
tests/test_pr9a_resume_rebuild.py
tests/test_pr9b_embed_parallel.py
tests/test_pr9c_streaming_embed.py
tests/test_prepare_rollback.py
tests/test_probe.py
tests/test_promote_r.py
tests/test_query_command_diagnostics.py
tests/test_query_plan.py
tests/test_read_model_cutover.py
tests/test_reconcile.py
tests/test_redo_orphan_recovery.py
tests/test_render_audit.py
tests/test_render_wire.py
tests/test_repair.py
tests/test_restore_drift.py
tests/test_retrieval_integrity.py
tests/test_retrieve_evidence.py
tests/test_runtime_pointer.py
tests/test_runtime_repair.py
tests/test_search_command_diagnostics.py
tests/test_second_pass_cross_validation.py
tests/test_selection_sync_pdf.py
tests/test_settlement.py
tests/test_setup_layout.py
tests/test_setup_plan_v2.py
tests/test_setup_wizard.py
tests/test_shadow_rebuild.py
tests/test_skill_architecture_review.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_sync_next_actions.py
tests/test_sync_service_ocr_versions.py
tests/test_sync_timing.py
tests/test_t7_journey.py
tests/test_timing.py
tests/test_update_lifecycle.py
tests/test_utils_journal.py
tests/test_utils_json.py
tests/test_utils_slugify.py
tests/test_utils_yaml.py
tests/test_vector_schema.py
tests/test_versions_command.py