.env.example
.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
README.md
SECURITY.md
cliff.toml
pyproject.toml
uv.lock
vault.yaml
.claude/settings.json
.claude-plugin/marketplace.json
.claude-plugin/plugin.json
.claude/hooks/uv-guard.py
.github/dependabot.yml
.github/workflows/release.yml
assets/architecture.svg
assets/banner-light.svg
assets/banner.svg
assets/pipeline.svg
assets/sili_no_bg.png
assets/web_gui_screenshot.png
evals/__init__.py
evals/_shared.py
evals/conftest.py
evals/factscore.py
evals/oracle.py
evals/paired_stats.py
evals/phase0_gates.py
evals/probe_abstention_rubric.py
evals/probe_code_why.py
evals/probe_cooccur_scoring.py
evals/probe_dedup_batch.py
evals/probe_explain_rubric.py
evals/probe_explain_spans.py
evals/probe_judge_ab.py
evals/probe_judge_floor.py
evals/probe_ppr_phase0.py
evals/probe_ppr_phase2.py
evals/probe_recall_rank.py
evals/probe_regrade_sweep.py
evals/probe_single_hop_regrade.py
evals/probe_temporal_regrade.py
evals/probe_window_sweep.py
evals/test_factscore.py
evals/test_oracle.py
evals/test_phase0_gates.py
evals/test_probe_code_why.py
evals/test_probe_explain_rubric.py
evals/test_probe_explain_spans.py
evals/test_probe_ppr_phase0.py
evals/test_probe_ppr_phase2.py
evals/test_probe_recall_rank.py
evals/test_probe_window_sweep.py
evals/test_vault_energy_bench.py
evals/test_vault_energy_realdriver.py
evals/golden/__init__.py
evals/golden/__main__.py
evals/golden/baseline.json
evals/golden/probe_classify.py
evals/golden/probe_correlate.py
evals/golden/probe_dedup.py
evals/golden/probe_fusion.py
evals/golden/probe_links.py
evals/golden/runner.py
evals/locomo/__init__.py
evals/locomo/__main__.py
evals/locomo/repair_dangling.py
evals/locomo/runner.py
evals/locomo/test_hybrid_overlay.py
evals/locomo/test_locomo_adapter.py
evals/locomo/test_locomo_e2e.py
evals/locomo/test_locomo_timeline.py
evals/longmemeval/__init__.py
evals/longmemeval/__main__.py
evals/longmemeval/metrics.json
evals/longmemeval/probes.py
evals/longmemeval/runner.py
evals/longmemeval/test_longmemeval_adapter.py
evals/longmemeval/test_probes.py
evals/musique/__init__.py
evals/musique/__main__.py
evals/musique/metrics.json
evals/musique/runner.py
evals/musique/test_musique_adapter.py
examples/taxonomy.example.yaml
scripts/smoke_cli.py
silica/.env.example
silica/__init__.py
silica/_version.py
silica/cli.py
silica/config.py
silica/prompts.py
silica/update.py
silica/agent/__init__.py
silica/agent/bounds.py
silica/agent/bus.py
silica/agent/commit.py
silica/agent/compaction.py
silica/agent/concurrency.py
silica/agent/constraints.py
silica/agent/events.py
silica/agent/llm.py
silica/agent/loop.py
silica/agent/providers.py
silica/agent/recall_watch.py
silica/agent/subagent.py
silica/capabilities/__init__.py
silica/capabilities/_base.py
silica/capabilities/codewiki.py
silica/capabilities/dedup.py
silica/capabilities/enrich.py
silica/capabilities/expand.py
silica/capabilities/orphan.py
silica/capabilities/profile.py
silica/capabilities/profiles_builtin.py
silica/capabilities/refine.py
silica/capabilities/runtime.py
silica/capabilities/prompts/_anti_slop.txt
silica/capabilities/prompts/dedup_prompt.txt
silica/capabilities/prompts/distiller_prompt.txt
silica/capabilities/prompts/expand_prompt.txt
silica/capabilities/prompts/orphan_prompt.txt
silica/capabilities/prompts/refiner_prompt.txt
silica/capabilities/prompts/profiles/default/examples.md
silica/capabilities/prompts/profiles/default/quality.md
silica/capabilities/prompts/profiles/default/rubric.md
silica/capabilities/prompts/profiles/extractive/examples.md
silica/capabilities/prompts/profiles/extractive/quality.md
silica/capabilities/prompts/profiles/extractive/rubric.md
silica/capabilities/prompts/profiles/transcript/examples.md
silica/capabilities/prompts/profiles/transcript/quality.md
silica/capabilities/prompts/profiles/transcript/rubric.md
silica/domains/codebase.yaml
silica/driver/__init__.py
silica/driver/base.py
silica/driver/fs_backend.py
silica/driver/ws_backend.py
silica/kernel/__init__.py
silica/kernel/analyst_plan.py
silica/kernel/contested_register.py
silica/kernel/context_builder.py
silica/kernel/graph_diff.py
silica/kernel/partition.py
silica/kernel/plans.py
silica/kernel/prep_delegation.py
silica/kernel/progress.py
silica/kernel/vault_manifest.py
silica/kernel/workqueue.py
silica/kernel/code/__init__.py
silica/kernel/code/codedocs.py
silica/kernel/code/codegraph.py
silica/kernel/code/codepack.py
silica/kernel/code/codetree.py
silica/kernel/code/codewiki.py
silica/kernel/code/gitstate.py
silica/kernel/code/ipynb.py
silica/kernel/code/codeast/__init__.py
silica/kernel/code/codeast/base.py
silica/kernel/code/codeast/c.py
silica/kernel/code/codeast/java.py
silica/kernel/code/codeast/python.py
silica/kernel/code/codeast/ts.py
silica/kernel/link/__init__.py
silica/kernel/link/ast.py
silica/kernel/link/autolink.py
silica/kernel/link/correlate.py
silica/kernel/link/linter.py
silica/kernel/link/ofm.py
silica/kernel/link/rename.py
silica/kernel/link/health/__init__.py
silica/kernel/link/health/lint.py
silica/kernel/organize/__init__.py
silica/kernel/organize/classify.py
silica/kernel/organize/taxonomy.py
silica/kernel/recall/__init__.py
silica/kernel/recall/assembly.py
silica/kernel/recall/cooccurrence.py
silica/kernel/recall/curator.py
silica/kernel/recall/deferred.py
silica/kernel/recall/embed.py
silica/kernel/recall/episodic.py
silica/kernel/recall/graph_export.py
silica/kernel/recall/lexical.py
silica/kernel/recall/memory_lane.py
silica/kernel/recall/mindmap.py
silica/kernel/recall/paths.py
silica/kernel/recall/perception.py
silica/kernel/recall/recall_weights.py
silica/kernel/recall/relatedness.py
silica/kernel/recall/rerank.py
silica/kernel/recall/run_log.py
silica/kernel/recall/run_substrate.py
silica/kernel/recall/vault_map.py
silica/kernel/report/__init__.py
silica/kernel/report/minhash_dedup.py
silica/kernel/report/quiz.py
silica/kernel/report/vault_energy.py
silica/kernel/report/graph_report/__init__.py
silica/kernel/report/graph_report/code_signals.py
silica/kernel/report/graph_report/compute.py
silica/kernel/report/graph_report/cooccur_delta.py
silica/kernel/report/graph_report/embed_signals.py
silica/kernel/report/graph_report/models.py
silica/kernel/report/graph_report/render.py
silica/kernel/text/__init__.py
silica/kernel/text/cohesion.py
silica/kernel/text/keyphrase.py
silica/kernel/text/language.py
silica/kernel/text/media.py
silica/kernel/text/overlay.py
silica/kernel/text/payload.py
silica/kernel/text/recon.py
silica/kernel/text/sanitize.py
silica/kernel/text/text.py
silica/kernel/text/title.py
silica/kernel/write/__init__.py
silica/kernel/write/atomic_write.py
silica/kernel/write/bulk.py
silica/kernel/write/checkpoints.py
silica/kernel/write/contested.py
silica/kernel/write/frontmatter.py
silica/kernel/write/ledger.py
silica/kernel/write/merge.py
silica/kernel/write/moc.py
silica/kernel/write/ops.py
silica/kernel/write/ops_io.py
silica/kernel/write/provenance.py
silica/kernel/write/templates.py
silica/kernel/write/timeline.py
silica/kernel/write/undo_journal.py
silica/kernel/write/validate.py
silica/onboarding/__init__.py
silica/onboarding/adopt.py
silica/onboarding/checks.py
silica/onboarding/serve.py
silica/onboarding/setup_client.py
silica/onboarding/wizard.py
silica/overlays/italian.yaml
silica/recipes/injector.yaml
silica/recipes/organizer.yaml
silica/router/__init__.py
silica/router/base_fsm.py
silica/router/coordinator.py
silica/router/orchestrator.py
silica/router/organize_fsm.py
silica/router/overlay.py
silica/router/prefetch.py
silica/router/recipe_parser.py
silica/router/warning_ledger.py
silica/router/states/__init__.py
silica/router/states/collision.py
silica/router/states/distill.py
silica/router/states/finalize.py
silica/router/states/linking.py
silica/router/states/setup.py
silica/router/states/write.py
silica/sources/__init__.py
silica/sources/base.py
silica/sources/code.py
silica/sources/convert.py
silica/sources/notebook.py
silica/sources/prose.py
silica/sources/registry.py
silica/sources/web_fetch.py
silica/sources/web_research.py
silica/tools/__init__.py
silica/tools/atomic.py
silica/tools/codedocs_tool.py
silica/tools/composed.py
silica/tools/curate.py
silica/tools/delegate_tool.py
silica/tools/graph.py
silica/tools/notes.py
silica/tools/pipeline.py
silica/tools/runners.py
silica/tools/wrapped.py
silica/ui/__init__.py
silica/ui/banner.py
silica/ui/commands.py
silica/ui/connect.py
silica/ui/console.py
silica/ui/home.py
silica/ui/logging.py
silica/ui/mcp.py
silica/ui/prompt.py
silica/ui/renderer.py
silica/ui/style.py
silica/ui/theme.py
silica/ui/web/__init__.py
silica/ui/web/callback.py
silica/ui/web/graph_view.py
silica/ui/web/server.py
silica/ui/web/static/3d-force-graph.min.js
silica/ui/web/static/app.css
silica/ui/web/static/app.js
silica/ui/web/static/index.html
silica/ui/web/static/lexend-latin.woff2
silica/ui/web/static/martian-mono-latin.woff2
silica/ui/web/static/mermaid.min.js
silica_agent.egg-info/PKG-INFO
silica_agent.egg-info/SOURCES.txt
silica_agent.egg-info/dependency_links.txt
silica_agent.egg-info/entry_points.txt
silica_agent.egg-info/requires.txt
silica_agent.egg-info/scm_file_list.json
silica_agent.egg-info/scm_version.json
silica_agent.egg-info/top_level.txt
skills/silica/SKILL.md
tests/__init__.py
tests/conftest.py
tests/llm_mocks.py
tests/test_agent_constraints.py
tests/test_agent_guards_and_provider.py
tests/test_agent_history_repair.py
tests/test_analyst_plan.py
tests/test_anneal.py
tests/test_anti_slop.py
tests/test_assembly.py
tests/test_assembly_perception.py
tests/test_atomic_write.py
tests/test_atomic_write_bytes.py
tests/test_autolink.py
tests/test_autolink_facade.py
tests/test_autolink_note_title_index.py
tests/test_bounds.py
tests/test_bulk.py
tests/test_bulk_verify.py
tests/test_bus.py
tests/test_cancel_token.py
tests/test_cancel_tool_seam.py
tests/test_capability_seam.py
tests/test_checkpoints.py
tests/test_claim_stamp.py
tests/test_clean_tag.py
tests/test_cli_clear.py
tests/test_cli_flags.py
tests/test_cli_subcommands.py
tests/test_cluster_cache.py
tests/test_codeast.py
tests/test_codedocs.py
tests/test_codegraph.py
tests/test_codepack.py
tests/test_codetree.py
tests/test_codewiki.py
tests/test_codewiki_capability.py
tests/test_coherence_seams.py
tests/test_cohesion.py
tests/test_collision_intra_chunk.py
tests/test_commit.py
tests/test_compaction.py
tests/test_compaction_wiring.py
tests/test_confidence_tier.py
tests/test_config_domain.py
tests/test_config_failfast.py
tests/test_config_git.py
tests/test_config_ws.py
tests/test_connect.py
tests/test_contested.py
tests/test_context_builder.py
tests/test_convert.py
tests/test_cooccur_key.py
tests/test_cooccurrence.py
tests/test_cooccurrence_community_labels.py
tests/test_cooccurrence_refresh_tool.py
tests/test_coordinator.py
tests/test_correlate.py
tests/test_curate_apply.py
tests/test_curate_stale_guard.py
tests/test_curator.py
tests/test_dedup_batch.py
tests/test_dedup_gate.py
tests/test_dedup_near_title_score.py
tests/test_dedup_refine_commands.py
tests/test_deferred.py
tests/test_deferred_flush.py
tests/test_diagram.py
tests/test_distill_cascade.py
tests/test_distill_prefetch.py
tests/test_distill_profiles.py
tests/test_distiller_resilience.py
tests/test_distiller_schema.py
tests/test_document_rbac.py
tests/test_document_tool.py
tests/test_embed.py
tests/test_embed_binary.py
tests/test_embed_phantom_cleanup.py
tests/test_embed_search_topk.py
tests/test_embed_title_search.py
tests/test_episodic.py
tests/test_expand_capability.py
tests/test_extractive_grounding.py
tests/test_files_cap.py
tests/test_files_inbox.py
tests/test_finalize_provenance.py
tests/test_finalize_status.py
tests/test_flag_note.py
tests/test_freshness_hook.py
tests/test_fs_backend_create.py
tests/test_fs_backend_graph.py
tests/test_fs_body_cache.py
tests/test_fs_create_index.py
tests/test_fs_move_rewrite.py
tests/test_fsm.py
tests/test_fsm_domain_wiring.py
tests/test_fsm_op_stream.py
tests/test_gate_leniency.py
tests/test_git_autocommit.py
tests/test_gitstate.py
tests/test_gitstate_codegraph.py
tests/test_golden_probes.py
tests/test_graph_community_labels.py
tests/test_graph_delta.py
tests/test_graph_diff.py
tests/test_graph_render_html.py
tests/test_graph_report.py
tests/test_graph_report_convention.py
tests/test_graph_tools.py
tests/test_graph_view_export.py
tests/test_graph_view_tree.py
tests/test_grounding_invariant.py
tests/test_gui_web.py
tests/test_hub_desc.py
tests/test_impact.py
tests/test_import_boundaries.py
tests/test_injector_atomic_parity.py
tests/test_interrupt_no_writes.py
tests/test_ipynb.py
tests/test_keyphrase.py
tests/test_knn_edges.py
tests/test_lang_detect.py
tests/test_language.py
tests/test_ledger_integrity.py
tests/test_lexical.py
tests/test_lexical_fusion.py
tests/test_lexical_refresh_tool.py
tests/test_lexical_write_hook.py
tests/test_linter_documents.py
tests/test_linter_expires_at.py
tests/test_llm_bounded_call.py
tests/test_llm_streaming.py
tests/test_llm_structured_output.py
tests/test_llm_temperature.py
tests/test_load_recipe_domain.py
tests/test_logging.py
tests/test_loop_cancel.py
tests/test_map_layout.py
tests/test_map_serialize.py
tests/test_max_tokens_clamp.py
tests/test_mcp_surface.py
tests/test_media.py
tests/test_memory_lane.py
tests/test_mention_index.py
tests/test_merge_wiring.py
tests/test_message_provenance.py
tests/test_mineru_error.py
tests/test_minhash_dedup.py
tests/test_model_limits.py
tests/test_multi_file_injector.py
tests/test_note_edges.py
tests/test_notebook_adapter.py
tests/test_notes_documents.py
tests/test_novelty_gate.py
tests/test_nucleate_dispatch.py
tests/test_nucleate_log.py
tests/test_onboarding_checks.py
tests/test_onboarding_wizard.py
tests/test_ops_io.py
tests/test_organize_fsm.py
tests/test_orphan_candidates_facade.py
tests/test_overlay.py
tests/test_overwrite_base_content.py
tests/test_partition.py
tests/test_payload_gate.py
tests/test_perception.py
tests/test_plans_loop.py
tests/test_profiles_registry.py
tests/test_progress_ledger.py
tests/test_prompt_cache_stability.py
tests/test_provenance.py
tests/test_provenance_dedup.py
tests/test_providers.py
tests/test_quarantine.py
tests/test_quiz_loop.py
tests/test_reading_path.py
tests/test_readme_sync.py
tests/test_recall_partial.py
tests/test_recall_weights.py
tests/test_recipe_overlay.py
tests/test_recon.py
tests/test_regression_validation.py
tests/test_relate.py
tests/test_related_tool.py
tests/test_relatedness.py
tests/test_relatedness_boundary.py
tests/test_reliability_tier.py
tests/test_rename_kernel.py
tests/test_reply_language.py
tests/test_repo_mode.py
tests/test_repo_root.py
tests/test_report_analytics.py
tests/test_report_code_signals.py
tests/test_rerank.py
tests/test_retry_transient.py
tests/test_reuse_probe.py
tests/test_revert_command.py
tests/test_review_queue.py
tests/test_run.py
tests/test_run_log.py
tests/test_run_substrate_facade.py
tests/test_run_worker.py
tests/test_sanitize.py
tests/test_schematize.py
tests/test_search_context_cap.py
tests/test_search_name_cap.py
tests/test_search_stale_flags.py
tests/test_semantic_related_stale_flags.py
tests/test_serve.py
tests/test_setup_client.py
tests/test_shared_memory_leases.py
tests/test_silica_delegate.py
tests/test_silicaignore.py
tests/test_smoke.py
tests/test_snippet_gate.py
tests/test_source_adapters.py
tests/test_source_leaves.py
tests/test_span_grounding.py
tests/test_stale_command.py
tests/test_stale_read_gate.py
tests/test_stale_snapshot.py
tests/test_status_command.py
tests/test_steer_feedback.py
tests/test_store_seam.py
tests/test_structural_gaps.py
tests/test_subagent.py
tests/test_superseded.py
tests/test_target_dir_resolution.py
tests/test_taxonomy.py
tests/test_templates.py
tests/test_text_seam.py
tests/test_three_way_merge.py
tests/test_timeline.py
tests/test_title_identity.py
tests/test_title_index_cache.py
tests/test_token_meter.py
tests/test_tool_budget.py
tests/test_tool_call_fanout.py
tests/test_tool_collapse_field.py
tests/test_tool_progress.py
tests/test_tool_sensitive.py
tests/test_trie_incremental.py
tests/test_ui_commands.py
tests/test_undo_journal.py
tests/test_update.py
tests/test_validate_body_field_coercion.py
tests/test_validate_links.py
tests/test_validate_title_gate_scope.py
tests/test_vault_codebase_switch.py
tests/test_vault_command.py
tests/test_vault_config_paths.py
tests/test_vault_conventions.py
tests/test_vault_display.py
tests/test_vault_energy.py
tests/test_vault_factory.py
tests/test_vault_manifest.py
tests/test_vault_map.py
tests/test_vault_pin_source.py
tests/test_vault_root_silica.py
tests/test_warning_ledger.py
tests/test_web_escalation.py
tests/test_web_fetch.py
tests/test_web_research.py
tests/test_wikilink.py
tests/test_worker_concurrency.py
tests/test_worker_config.py
tests/test_worker_profile.py
tests/test_workqueue.py
tests/test_workqueue_sentinel.py
tests/test_write_boundary_regression.py
tests/test_write_dir.py
tests/test_write_note_tool.py
tests/test_ws_backend.py
tests/fixtures/__init__.py
tests/fixtures/vault_factory.py
tests/golden/__init__.py
tests/golden/autolink_cases.json
tests/golden/collision_threshold_cases.json
tests/golden/keyphrase_cases.json
tests/golden/test_driver_parity.py
tests/golden/test_eval_autolink.py
tests/golden/test_eval_correlate.py
tests/golden/test_eval_fusion.py
tests/golden/test_eval_keyphrase.py
tests/golden/test_golden_regression.py
web/README.md
web/animation.html
web/index.html
web/silica-favicon.svg
web/silica-logo.svg
web/style.css
web/vercel.json
web/fonts/martian-mono-latin.woff2