PyPI - coding-os - Versions diffs - 0.3.2__py3-none-any.whl - Mend

coding-os 0.3.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1304) hide show

adapters/claude/README.md +6 -0
adapters/claude/_install_helpers/extract_stacks.py +43 -0
adapters/claude/_install_helpers/update_mcp_json.py +75 -0
adapters/claude/adapter.yaml +164 -0
adapters/claude/hooks/README.md +40 -0
adapters/claude/hooks/agent_memory_sync.py +131 -0
adapters/claude/hooks/ensure-agent-memory-link.sh +36 -0
adapters/claude/hooks/sync-agent-memory.sh +21 -0
adapters/claude/install.sh +86 -0
adapters/claude/sdk_dispatcher.py +871 -0
adapters/claude/settings.local.template.json +31 -0
adapters/claude/settings.template.json +808 -0
adapters/claude/update_mcp_json.py +85 -0
adapters/codex/adapter.yaml +254 -0
adapters/codex/chat_provider.py +230 -0
adapters/codex/commands/formula-f1.md +129 -0
adapters/codex/commands/formula-f10.md +100 -0
adapters/codex/commands/formula-f11.md +123 -0
adapters/codex/commands/formula-f2.md +139 -0
adapters/codex/commands/formula-f3.md +127 -0
adapters/codex/commands/formula-f4.md +101 -0
adapters/codex/commands/formula-f5.md +135 -0
adapters/codex/commands/formula-f6.md +147 -0
adapters/codex/commands/formula-f7.md +111 -0
adapters/codex/commands/formula-f8.md +133 -0
adapters/codex/commands/formula-f9.md +112 -0
adapters/codex/enable_codex_hooks.py +94 -0
adapters/codex/ensure_codex_mcp.py +124 -0
adapters/codex/hooks/codex-merge-hook-output.py +72 -0
adapters/codex/hooks/codex-normalize-edit.py +96 -0
adapters/codex/hooks/codex-postedit-dispatch.sh +75 -0
adapters/codex/hooks/codex-posttool-dispatch.sh +70 -0
adapters/codex/hooks/codex-preedit-dispatch.sh +83 -0
adapters/codex/hooks/codex-pretool-dispatch.sh +82 -0
adapters/codex/hooks/codex-sessionend-dispatch.sh +20 -0
adapters/codex/hooks/codex-sessionstart-dispatch.sh +68 -0
adapters/codex/hooks/codex-stop-dispatch.sh +73 -0
adapters/codex/hooks/codex-userpromptsubmit-dispatch.sh +74 -0
adapters/codex/hooks.template.json +208 -0
adapters/codex/install.sh +83 -0
adapters/codex/sdk_dispatcher.py +449 -0
board_os/__init__.py +39 -0
board_os/_agent_runtime.py +256 -0
board_os/config.py +421 -0
board_os/git_coherence.py +107 -0
board_os/hub_adapter_manifest.py +140 -0
board_os/mcp_tools.py +3228 -0
board_os/migration.py +166 -0
board_os/parser.py +317 -0
board_os/presence.py +156 -0
board_os/sync.py +320 -0
board_os/transition_gates.py +224 -0
board_os/transition_gates_cli.py +272 -0
board_os/transition_gates_validator.py +551 -0
board_os/verify_suites.py +126 -0
board_os/verify_suites_cli.py +328 -0
board_os/workflow.py +967 -0
cli/__init__.py +0 -0
cli/_data_types.py +248 -0
cli/_init_helpers.py +587 -0
cli/_resources.py +100 -0
cli/adapter_registry.py +239 -0
cli/add_stack.py +315 -0
cli/aggregator.py +438 -0
cli/board_commands.py +1218 -0
cli/brain_commands.py +255 -0
cli/cognition.py +345 -0
cli/config_composer.py +349 -0
cli/core_version.py +41 -0
cli/cron_commands.py +278 -0
cli/db_reset.py +298 -0
cli/doc_commands.py +111 -0
cli/doctor.py +2953 -0
cli/doctor_board.py +365 -0
cli/doctor_extras.py +1121 -0
cli/doctor_graph.py +608 -0
cli/doctor_tokens.py +254 -0
cli/graph_commands.py +1265 -0
cli/hook_renderer.py +393 -0
cli/hub_commands.py +580 -0
cli/list_adapters.py +79 -0
cli/list_stacks.py +105 -0
cli/logs_commands.py +89 -0
cli/main.py +3070 -0
cli/materialize_file.py +65 -0
cli/mcp_start.py +153 -0
cli/module_commands.py +513 -0
cli/pr_commands.py +2024 -0
cli/preset_commands.py +126 -0
cli/preset_registry.py +171 -0
cli/project_overrides.py +119 -0
cli/registry.py +365 -0
cli/remove_stack.py +492 -0
cli/renderer.py +620 -0
cli/setup.py +464 -0
cli/skill_commands.py +689 -0
cli/skill_registry.py +235 -0
cli/skills_list.py +332 -0
cli/stack_lint.py +351 -0
cli/stack_registry.py +688 -0
cli/subsystems.py +335 -0
cli/sync_all.py +310 -0
cli/tail_command.py +410 -0
cli/update.py +608 -0
cli/verify_since_edit.py +439 -0
coding_os-0.3.2.dist-info/METADATA +508 -0
coding_os-0.3.2.dist-info/RECORD +1304 -0
coding_os-0.3.2.dist-info/WHEEL +5 -0
coding_os-0.3.2.dist-info/entry_points.txt +5 -0
coding_os-0.3.2.dist-info/licenses/LICENSE +201 -0
coding_os-0.3.2.dist-info/top_level.txt +10 -0
core/__init__.py +0 -0
core/board_os/__init__.py +39 -0
core/board_os/_agent_runtime.py +256 -0
core/board_os/config.py +421 -0
core/board_os/git_coherence.py +107 -0
core/board_os/hub_adapter_manifest.py +140 -0
core/board_os/mcp_tools.py +3228 -0
core/board_os/migration.py +166 -0
core/board_os/parser.py +317 -0
core/board_os/presence.py +156 -0
core/board_os/sync.py +320 -0
core/board_os/transition-gates.yaml +176 -0
core/board_os/transition_gates.py +224 -0
core/board_os/transition_gates_cli.py +272 -0
core/board_os/transition_gates_validator.py +551 -0
core/board_os/verify-suites.yaml +113 -0
core/board_os/verify_suites.py +126 -0
core/board_os/verify_suites_cli.py +328 -0
core/board_os/workflow.py +967 -0
core/commands/board.md +27 -0
core/commands/classify.md +23 -0
core/commands/compose.md +23 -0
core/commands/daily.md +31 -0
core/commands/diagnose.md +7 -0
core/commands/memory-search.md +23 -0
core/commands/new-project.md +33 -0
core/commands/retro.md +38 -0
core/commands/review.md +14 -0
core/commands/task.md +17 -0
core/commands/verify.md +34 -0
core/docs/thinking_os-final-edition.md +1449 -0
core/doctor-config.yaml +74 -0
core/graph_os/__init__.py +29 -0
core/graph_os/backend.py +233 -0
core/graph_os/backends/__init__.py +13 -0
core/graph_os/backends/sqlite_backend.py +1053 -0
core/graph_os/bench/__init__.py +17 -0
core/graph_os/bench/fixtures.py +56 -0
core/graph_os/bench/harness.py +95 -0
core/graph_os/bench/persian_precision.py +142 -0
core/graph_os/bench/scale_500k.py +120 -0
core/graph_os/bench/token_cost.py +170 -0
core/graph_os/bench/viewer_fps.py +110 -0
core/graph_os/communities.py +410 -0
core/graph_os/enterprise.py +218 -0
core/graph_os/entry_points.py +226 -0
core/graph_os/extractors/__init__.py +25 -0
core/graph_os/extractors/code_generic.py +914 -0
core/graph_os/extractors/code_go.py +1422 -0
core/graph_os/extractors/code_json.py +340 -0
core/graph_os/extractors/code_php.py +979 -0
core/graph_os/extractors/code_python.py +1454 -0
core/graph_os/extractors/code_shell.py +538 -0
core/graph_os/extractors/code_toml.py +302 -0
core/graph_os/extractors/code_ts.py +1665 -0
core/graph_os/extractors/code_yaml.py +394 -0
core/graph_os/extractors/contracts.py +1592 -0
core/graph_os/extractors/md_links.py +890 -0
core/graph_os/extractors/task_deps.py +345 -0
core/graph_os/groups/__init__.py +22 -0
core/graph_os/groups/cross_repo.py +156 -0
core/graph_os/groups/manifest.py +141 -0
core/graph_os/ingest/__init__.py +19 -0
core/graph_os/ingest/base.py +306 -0
core/graph_os/ingest/github.py +112 -0
core/graph_os/ingest/zip.py +95 -0
core/graph_os/toolchain.py +393 -0
core/graph_os/tools/__init__.py +9 -0
core/graph_os/tools/graph.py +5573 -0
core/graph_os/tools/reindex_dispatch.py +730 -0
core/graph_os/tree_sitter_overlay.py +235 -0
core/graph_os/types.py +252 -0
core/graph_os/vec_index.py +277 -0
core/graph_os/viewer/__init__.py +12 -0
core/graph_os/viewer/exporter.py +93 -0
core/graph_os/viewer/template.py +189 -0
core/hooks/_helpers/_paths.py +40 -0
core/hooks/_helpers/advance_role.py +72 -0
core/hooks/_helpers/auto_compose.py +228 -0
core/hooks/_helpers/auto_validate_lessons.py +55 -0
core/hooks/_helpers/branch_guard_check.py +796 -0
core/hooks/_helpers/check_commit_message.py +108 -0
core/hooks/_helpers/check_dangerous_rm.py +80 -0
core/hooks/_helpers/check_git_bypass.py +154 -0
core/hooks/_helpers/check_git_destructive.py +77 -0
core/hooks/_helpers/check_settings_write.py +97 -0
core/hooks/_helpers/consume_override.py +51 -0
core/hooks/_helpers/context_budget.py +77 -0
core/hooks/_helpers/cos_say_json.py +103 -0
core/hooks/_helpers/destructive_edit_check.py +163 -0
core/hooks/_helpers/detect_status_transition.py +82 -0
core/hooks/_helpers/digest_regen.py +56 -0
core/hooks/_helpers/doc_sync_check.py +498 -0
core/hooks/_helpers/drain_embedding_outbox.py +52 -0
core/hooks/_helpers/extract_additional_context.py +51 -0
core/hooks/_helpers/extract_commit_msg_arg.py +74 -0
core/hooks/_helpers/git_command_parse.py +424 -0
core/hooks/_helpers/git_settings_fields.py +47 -0
core/hooks/_helpers/graph_context_match.py +37 -0
core/hooks/_helpers/graph_marker_check.py +70 -0
core/hooks/_helpers/jit_recall.py +56 -0
core/hooks/_helpers/json_field.py +41 -0
core/hooks/_helpers/narrative_signal.py +59 -0
core/hooks/_helpers/observation_count.py +31 -0
core/hooks/_helpers/pre_commit_batch.py +177 -0
core/hooks/_helpers/pre_commit_fake_input.py +42 -0
core/hooks/_helpers/presence_gc.py +102 -0
core/hooks/_helpers/presence_write.py +167 -0
core/hooks/_helpers/recover_indirect.py +35 -0
core/hooks/_helpers/routing_evolution.py +104 -0
core/hooks/_helpers/session_recap.py +72 -0
core/hooks/_helpers/skill_primer.py +229 -0
core/hooks/_helpers/task_sync.py +59 -0
core/hooks/_helpers/tool_failure_capture.py +147 -0
core/hooks/_helpers/trajectory_autosnap.py +278 -0
core/hooks/_helpers/trajectory_startup.py +62 -0
core/hooks/_helpers/turn_summary.py +82 -0
core/hooks/_helpers/validate_task_frontmatter.py +98 -0
core/hooks/_helpers/wip_limit_check.py +103 -0
core/hooks/_helpers/wip_lines.py +53 -0
core/hooks/_helpers/work_log_append.py +89 -0
core/hooks/_helpers/wrap_dispatch_output.py +82 -0
core/hooks/advance-role.sh +48 -0
core/hooks/agent-presence.sh +179 -0
core/hooks/auto-brain-decay.sh +184 -0
core/hooks/auto-compose-roles.sh +83 -0
core/hooks/auto-graph-reconcile-shell.sh +119 -0
core/hooks/auto-regen-doc-index.sh +120 -0
core/hooks/auto-reindex-docs.sh +130 -0
core/hooks/auto-task-sync.sh +56 -0
core/hooks/auto-trace-rotate.sh +88 -0
core/hooks/block-bad-patterns.sh +212 -0
core/hooks/block-dangerous-commands.sh +182 -0
core/hooks/block-hardcoded-literals.sh +90 -0
core/hooks/block-migration-conflict.sh +114 -0
core/hooks/block-protected-files.sh +129 -0
core/hooks/block-secrets.sh +185 -0
core/hooks/block-shared-tree-edit.sh +75 -0
core/hooks/block-uv-heredoc.sh +78 -0
core/hooks/branch-guard.sh +122 -0
core/hooks/capture-observation.sh +76 -0
core/hooks/capture-tool-failure.sh +24 -0
core/hooks/capture-work-log.sh +89 -0
core/hooks/check-agents-md-refs.sh +75 -0
core/hooks/check-agents-md-size.sh +49 -0
core/hooks/check-capture-worked.sh +148 -0
core/hooks/check-doc-size.sh +61 -0
core/hooks/check-mcp-extras.sh +92 -0
core/hooks/check-state.sh +87 -0
core/hooks/classify-task-mode.sh +103 -0
core/hooks/cos-env.sh +1301 -0
core/hooks/drain-embedding-outbox.sh +24 -0
core/hooks/enforce-anti-ambiguity.sh +74 -0
core/hooks/enforce-commit-message.sh +73 -0
core/hooks/enforce-doc-anchor.sh +224 -0
core/hooks/enforce-doc-sync.sh +206 -0
core/hooks/enforce-graph-context.sh +89 -0
core/hooks/enforce-graph-first-read.sh +94 -0
core/hooks/enforce-memory-check.sh +128 -0
core/hooks/enforce-rename-plan.sh +78 -0
core/hooks/enforce-scaffold-boundary.sh +68 -0
core/hooks/enforce-skill.sh +125 -0
core/hooks/enforce-task-body.sh +52 -0
core/hooks/enforce-task-start.sh +81 -0
core/hooks/enforce-task-transition.sh +75 -0
core/hooks/enforce-template.sh +143 -0
core/hooks/enforce-verify.sh +112 -0
core/hooks/enforce-wip-limit.sh +43 -0
core/hooks/enforce-zoom.sh +69 -0
core/hooks/ensure-hub-up.sh +67 -0
core/hooks/inject-mcp-caller-session.sh +70 -0
core/hooks/jit-recall.sh +65 -0
core/hooks/link-commit-to-task.sh +143 -0
core/hooks/lint-task.sh +40 -0
core/hooks/nudge-docs-first.sh +71 -0
core/hooks/nudge-git-mode.sh +29 -0
core/hooks/nudge-graph-os.sh +118 -0
core/hooks/nudge-learn-narrative.sh +36 -0
core/hooks/nudge-model-routing.sh +32 -0
core/hooks/nudge-reentry.sh +101 -0
core/hooks/nudge-reuse-first.sh +68 -0
core/hooks/nudge-task-discovery.sh +81 -0
core/hooks/nudge-thinking-os.sh +109 -0
core/hooks/pr-reap.sh +23 -0
core/hooks/reclaim-sweep.sh +58 -0
core/hooks/record-verify-auto.sh +77 -0
core/hooks/record-verify.sh +74 -0
core/hooks/regen-reminder.sh +104 -0
core/hooks/registry.yaml +1262 -0
core/hooks/remind-daily.sh +27 -0
core/hooks/remind-dogfood.sh +70 -0
core/hooks/remind-learn-validate.sh +94 -0
core/hooks/rules-primer.sh +50 -0
core/hooks/search-enforce-inventory.sh +108 -0
core/hooks/search-verify-remaining.sh +132 -0
core/hooks/session-context.sh +729 -0
core/hooks/session-end.sh +145 -0
core/hooks/session-skill-primer.sh +43 -0
core/hooks/snapshot-transcript.sh +56 -0
core/hooks/sync-task-current.sh +85 -0
core/hooks/test-first-reminder.sh +120 -0
core/hooks/test-governor.sh +173 -0
core/hooks/thinking_os-gate.sh +52 -0
core/hooks/track-backtrack.sh +35 -0
core/hooks/track-discovery.sh +121 -0
core/hooks/track-skill.sh +53 -0
core/hooks/validate-task-frontmatter.sh +49 -0
core/hooks/verify-rename-callers.sh +119 -0
core/hooks/warn-abandoned-task.sh +99 -0
core/hooks/warn-destructive-edit.sh +64 -0
core/hooks/warn-diff-size.sh +43 -0
core/hooks/warn-graph-empty.sh +81 -0
core/hooks/warn-mcp-down.sh +190 -0
core/hooks/write-state.sh +55 -0
core/logging_os/__init__.py +33 -0
core/logging_os/api.py +127 -0
core/logging_os/bridge.py +80 -0
core/logging_os/config.py +172 -0
core/logging_os/fingerprint.py +25 -0
core/logging_os/redact.py +53 -0
core/logging_os/render.py +83 -0
core/logging_os/sinks.py +164 -0
core/rules/anti-overengineering.md +44 -0
core/rules/api-contract-discipline.md +41 -0
core/rules/dimension-registry.md +155 -0
core/rules/git-workflow.md +57 -0
core/rules/memory.md +46 -0
core/rules/model-routing.md +22 -0
core/rules/skill-enforcement.md +75 -0
core/rules/test-discipline.md +38 -0
core/rules/thinking_os.md +48 -0
core/rules/transparency-banner.md +37 -0
core/runtime_paths.yaml +36 -0
core/scaffold_manifest.json +14430 -0
core/scheduled/__init__.py +0 -0
core/scheduled/_activity.py +126 -0
core/scheduled/_state.py +113 -0
core/scheduled/config.py +86 -0
core/scheduled/dep_reconcile.py +135 -0
core/scheduled/error_sweep.py +137 -0
core/scheduled/nightly.py +930 -0
core/scheduled/responsive_extract.py +65 -0
core/schemas/adapter.schema.json +269 -0
core/schemas/preset.schema.json +50 -0
core/schemas/skill.schema.json +81 -0
core/schemas/stack.schema.json +404 -0
core/scripts/_lib.sh +9 -0
core/scripts/docs-lint.sh +228 -0
core/scripts/docs-nav-fix.sh +133 -0
core/scripts/docs-staleness-check.sh +154 -0
core/scripts/install-adapter.sh +266 -0
core/scripts/link-stack-skills.sh +52 -0
core/scripts/log-latest.sh +106 -0
core/scripts/log-search.sh +89 -0
core/scripts/log-write.sh +134 -0
core/scripts/ref-resolve.sh +71 -0
core/skills/a11y/SKILL.md +305 -0
core/skills/a11y/assets/a11y-checklist.md +137 -0
core/skills/a11y/references/aria-and-focus.md +247 -0
core/skills/a11y/references/rn-accessibility.md +343 -0
core/skills/a11y/references/screen-reader-testing.md +190 -0
core/skills/agent-memory/SKILL.md +191 -0
core/skills/agent-memory/assets/memory-checklist.md +21 -0
core/skills/agent-memory/references/memory-recipes.md +57 -0
core/skills/api-design/SKILL.md +232 -0
core/skills/api-design/assets/api-design-checklist.md +110 -0
core/skills/api-design/references/error-envelope.md +381 -0
core/skills/api-design/references/idempotency-pagination.md +312 -0
core/skills/api-design/references/rest-contracts.md +426 -0
core/skills/auth-patterns/SKILL.md +352 -0
core/skills/auth-patterns/assets/auth-checklist.md +118 -0
core/skills/auth-patterns/references/jwt-and-service-tokens.md +343 -0
core/skills/auth-patterns/references/passkeys-2fa.md +289 -0
core/skills/auth-patterns/references/sessions-vs-jwt.md +230 -0
core/skills/auth-patterns/scripts/cookie-flag-check.py +146 -0
core/skills/backend-fundamentals/SKILL.md +238 -0
core/skills/backend-fundamentals/assets/backend-checklist.md +27 -0
core/skills/backend-fundamentals/references/backend-patterns.md +56 -0
core/skills/backend-fundamentals/scripts/check_layering.py +83 -0
core/skills/clean-code/SKILL.md +642 -0
core/skills/clean-code/scripts/audit-fail-closed.py +167 -0
core/skills/codebase-explorer/SKILL.md +89 -0
core/skills/codebase-explorer/assets/reading-checklist.md +24 -0
core/skills/codebase-explorer/references/reading-strategies.md +52 -0
core/skills/codebase-explorer/scripts/outline.py +99 -0
core/skills/db-design/SKILL.md +327 -0
core/skills/db-design/assets/migration-template.sql +49 -0
core/skills/db-design/references/migration-discipline.md +290 -0
core/skills/db-design/references/postgres-patterns.md +340 -0
core/skills/db-design/scripts/migration-safety.sh +150 -0
core/skills/deployment-cicd/SKILL.md +260 -0
core/skills/deployment-cicd/assets/deploy-checklist.md +26 -0
core/skills/deployment-cicd/references/pipeline-and-release.md +54 -0
core/skills/deployment-cicd/scripts/lint_workflow.py +79 -0
core/skills/docker/SKILL.md +114 -0
core/skills/docker/assets/dockerfile-checklist.md +31 -0
core/skills/docker/references/compose-patterns.md +66 -0
core/skills/docker/references/dockerfile-optimization.md +64 -0
core/skills/docker/scripts/lint_dockerfile.sh +48 -0
core/skills/docker/versions.json +16 -0
core/skills/end-to-end-testing/SKILL.md +101 -0
core/skills/end-to-end-testing/assets/e2e-checklist.md +23 -0
core/skills/end-to-end-testing/references/maestro.md +63 -0
core/skills/end-to-end-testing/references/playwright.md +68 -0
core/skills/end-to-end-testing/scripts/lint_e2e.py +88 -0
core/skills/end-to-end-testing/versions.json +16 -0
core/skills/frontend-design/SKILL.md +76 -0
core/skills/frontend-design/assets/design-checklist.md +29 -0
core/skills/frontend-design/references/design-principles.md +65 -0
core/skills/frontend-design/scripts/check_contrast.py +89 -0
core/skills/frontend-fundamentals/SKILL.md +213 -0
core/skills/frontend-fundamentals/assets/frontend-checklist.md +25 -0
core/skills/frontend-fundamentals/references/rendering-and-state.md +66 -0
core/skills/frontend-fundamentals/scripts/check_frontend.py +86 -0
core/skills/graph-explorer/SKILL.md +215 -0
core/skills/graph-explorer/scripts/explain-impact.sh +64 -0
core/skills/graphql/SKILL.md +187 -0
core/skills/grpc-microservices/SKILL.md +174 -0
core/skills/hexagonal-architecture/SKILL.md +199 -0
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templates/svelte-sveltekit/scaffold-boundary.yaml +29 -0
templates/svelte-sveltekit/skills/svelte/SKILL.md +90 -0
templates/svelte-sveltekit/skills/svelte/references/anatomy.md +62 -0
templates/svelte-sveltekit/stack.yaml +70 -0
templates/typescript-plain/scaffold/src/index.ts +3 -0
templates/typescript-plain/scaffold/tsconfig.json +13 -0
templates/typescript-plain/scaffold-boundary.yaml +22 -0
templates/typescript-plain/stack.yaml +44 -0
templates/vue-nuxt/rules/frontend.md +19 -0
templates/vue-nuxt/scaffold/docs/engineering/nuxt-rules.md +30 -0
templates/vue-nuxt/scaffold/docs/playbooks/nuxt-app.md +29 -0
templates/vue-nuxt/scaffold/src/frontend/app.vue +3 -0
templates/vue-nuxt/scaffold/src/frontend/nuxt.config.ts +11 -0
templates/vue-nuxt/scaffold/src/frontend/package.json +20 -0
templates/vue-nuxt/scaffold/src/frontend/pages/index.test.ts +19 -0
templates/vue-nuxt/scaffold/src/frontend/pages/index.vue +11 -0
templates/vue-nuxt/scaffold/src/frontend/vitest.config.ts +12 -0
templates/vue-nuxt/scaffold-boundary.yaml +26 -0
templates/vue-nuxt/skills/vue-nuxt/SKILL.md +57 -0
templates/vue-nuxt/skills/vue-nuxt/references/anatomy.md +60 -0
templates/vue-nuxt/stack.yaml +61 -0
templates/wordpress/rules/backend.md +19 -0
templates/wordpress/scaffold/docs/engineering/wordpress-rules.md +28 -0
templates/wordpress/scaffold/docs/playbooks/wordpress-service.md +29 -0
templates/wordpress/scaffold/src/backend/composer.json +17 -0
templates/wordpress/scaffold/src/backend/phpcs.xml.dist +11 -0
templates/wordpress/scaffold/src/backend/phpunit.xml +10 -0
templates/wordpress/scaffold/src/backend/plugin/inc/health.php +8 -0
templates/wordpress/scaffold/src/backend/plugin/plugin.php +28 -0
templates/wordpress/scaffold/src/backend/tests/HealthStatusTest.php +15 -0
templates/wordpress/scaffold/src/backend/theme/functions.php +18 -0
templates/wordpress/scaffold/src/backend/theme/style.css +11 -0
templates/wordpress/scaffold-boundary.yaml +23 -0
templates/wordpress/skills/wordpress/SKILL.md +110 -0
templates/wordpress/skills/wordpress/assets/wp-checklist.md +28 -0
templates/wordpress/skills/wordpress/references/wp-development.md +75 -0
templates/wordpress/skills/wordpress/references/wp-security.md +68 -0
templates/wordpress/skills/wordpress/scripts/scan_wp_smells.py +91 -0
templates/wordpress/skills/wordpress/versions.json +16 -0
templates/wordpress/stack.yaml +60 -0
thinking_os/__init__.py +1 -0
thinking_os/_agent_markers.py +32 -0
thinking_os/background.py +405 -0
thinking_os/bootstrap_outcomes.py +200 -0
thinking_os/budget.py +302 -0
thinking_os/capture.py +495 -0
thinking_os/cognition.py +516 -0
thinking_os/cognition_schemas.py +517 -0
thinking_os/compress.py +192 -0
thinking_os/concepts.py +233 -0
thinking_os/dashboard.py +159 -0
thinking_os/database.py +2883 -0
thinking_os/decay.py +393 -0
thinking_os/digest.py +295 -0
thinking_os/dispatcher.py +192 -0
thinking_os/dispatcher_helpers.py +48 -0
thinking_os/dispatchers/__init__.py +3 -0
thinking_os/dispatchers/default.py +47 -0
thinking_os/distill.py +192 -0
thinking_os/doc_indexer.py +905 -0
thinking_os/embeddings.py +943 -0
thinking_os/formula_composer.py +556 -0
thinking_os/gate_marker.py +75 -0
thinking_os/graph.py +296 -0
thinking_os/graph_indexer.py +360 -0
thinking_os/health_check.py +517 -0
thinking_os/impact.py +119 -0
thinking_os/memory_gc.py +356 -0
thinking_os/migrator_embeddings.py +318 -0
thinking_os/precision.py +194 -0
thinking_os/record_outcome.py +399 -0
thinking_os/repair.py +105 -0
thinking_os/retrieval_quality.py +239 -0
thinking_os/roles_state.py +168 -0
thinking_os/sanitizer.py +320 -0
thinking_os/server.py +3160 -0
thinking_os/session_enrich.py +272 -0
thinking_os/session_observe_worker.py +111 -0
thinking_os/session_startup.py +74 -0
thinking_os/session_summary.py +245 -0
thinking_os/task_analyzer.py +462 -0
thinking_os/task_parser.py +342 -0
thinking_os/task_sync.py +73 -0
thinking_os/tools/__init__.py +6 -0
thinking_os/tools/_shared.py +947 -0
thinking_os/tools/cognition.py +1867 -0
thinking_os/tools/docs.py +770 -0
thinking_os/tools/learning.py +2078 -0
thinking_os/tools/logs.py +79 -0
thinking_os/tools/memory.py +840 -0
thinking_os/tools/metrics.py +200 -0
thinking_os/tools/retrieve.py +415 -0
thinking_os/tools/routing.py +658 -0
thinking_os/tools/tasks.py +449 -0
thinking_os/tools/trajectory.py +181 -0
thinking_os/tracing.py +235 -0
web/__init__.py +5 -0
web/_cache.py +118 -0
web/_deps.py +56 -0
web/_envelope.py +85 -0
web/_project_context.py +140 -0
web/chat_providers.py +108 -0
web/init_jobs.py +216 -0
web/routes/__init__.py +25 -0
web/routes/_bounded_read.py +76 -0
web/routes/board.py +1089 -0
web/routes/cognition.py +1838 -0
web/routes/config.py +635 -0
web/routes/graph.py +513 -0
web/routes/health.py +180 -0
web/routes/hooks.py +288 -0
web/routes/hub.py +1219 -0
web/routes/logs.py +374 -0
web/routes/metrics.py +43 -0
web/routes/observability.py +400 -0
web/routes/patterns.py +227 -0
web/routes/presence.py +609 -0
web/routes/roles.py +446 -0
web/routes/scheduled.py +261 -0
web/routes/search.py +238 -0
web/routes/sessions.py +220 -0
web/routes/settings.py +363 -0
web/routes/stream.py +547 -0
web/security.py +157 -0
web/server.py +283 -0

graph_os/extractors/md_links.py ADDED Viewed

@@ -0,0 +1,890 @@
+"""graph_os — markdown link + heading + frontmatter extractor (I.2).
+DEPENDS:  stdlib regex; frontmatter is parsed from the HTML comment or
+          YAML-fence convention used across coding-os docs.
+"""
+from __future__ import annotations
+import hashlib
+import logging
+import re
+from dataclasses import dataclass, field
+from pathlib import Path, PurePosixPath
+from ..types import GraphEdge, GraphNode
+logger = logging.getLogger("graph_os.extractors.md_links")
+EXTRACTOR_ID = "md_links@v1"
+# Match `[text](target)` — target may contain nested parens via the
+# balanced pattern below. Stops at unescaped `)`.
+_INLINE_LINK_RE = re.compile(r"\[(?P<text>[^\]]*)\]\((?P<target>[^)\s]+(?:\s+\"[^\"]*\")?)\)")
+# `[[wikilink]]` or `[[wikilink|alias]]`.
+_WIKI_LINK_RE = re.compile(r"\[\[(?P<target>[^\]|]+)(?:\|[^\]]+)?\]\]")
+# ATX-style heading: `##  Title`. Setext headings are rare in this repo so
+# we skip them for simplicity.
+_HEADING_RE = re.compile(r"^(?P<level>#{1,6})\s+(?P<title>.+?)\s*#*\s*$")
+# Frontmatter HTML comment used across coding-os docs:
+# `<!-- domain:backend | layer:engineering | ssot:true | updated:... -->`
+_HTML_FRONTMATTER_RE = re.compile(r"<!--\s*(?P<body>[^-]+(?:-(?!->)[^-]*)*)\s*-->")
+# YAML fence: lines between `---` at file start.
+_YAML_FENCE_RE = re.compile(r"^---\s*\n(?P<body>.*?)\n---\s*", re.DOTALL)
+# Fenced code blocks: ```...``` — stripped before link extraction.
+_FENCED_CODE_RE = re.compile(r"```[\s\S]*?```", re.MULTILINE)
+# Opening-block "Read next:" lines. Long form lives plain in the
+# body; short form lives inside a blockquote (`> N: …`). Both produce
+# read_next edges to every comma-separated target.
+_OPENING_READ_NEXT_RE = re.compile(
+    r"^(?:Read next:|>\s*N:)\s*(?P<targets>.+?)\s*$",
+    re.MULTILINE,
+)
+# Strip markdown link wrapper `[label](href)` to keep only the href.
+_LINK_HREF_RE = re.compile(r"\[[^\]]+\]\(([^)]+)\)")
+# W6.5 (X7): valid path target must match this — no spaces, must look like
+# a path / URL / fragment. Rejects garbage prose fragments captured by
+# the previous lenient `_split_read_targets` (Round 3 root cause of 386
+# stale_paths + ranking pollution from doc:file:"…prose…" uids).
+_PATH_LIKE_RE = re.compile(r"^[\w./\-:#?&=%~+]+$")
+def _split_read_targets(raw: str) -> list[str]:
+    """Split a comma-or-bracket list of read_next targets into clean paths."""
+    text = raw.strip()
+    # Only collapse the wrapping brackets when the whole value is `[…]` —
+    # short-form `reads:[a, b]`. Markdown links like `[a](a.md), [b](b.md)`
+    # must keep their `[`/`]` so the link regex can still match.
+    if text.startswith("[") and text.endswith("]") and "](" not in text:
+        text = text[1:-1]
+    if not text:
+        return []
+    fragments = [frag.strip() for frag in text.split(",") if frag.strip()]
+    out: list[str] = []
+    seen: set[str] = set()
+    for frag in fragments:
+        match = _LINK_HREF_RE.search(frag)
+        href = (match.group(1) if match else frag).strip()
+        href = href.strip("`").strip()
+        if not href or href in seen:
+            continue
+        # W6.5 (X7): reject prose fragments — only accept path-like strings.
+        # Prevents `Relevant ADR in ../architecture/adr/ or the domain doc.`
+        # from becoming a doc:file: uid.
+        if not _PATH_LIKE_RE.match(href):
+            continue
+        seen.add(href)
+        out.append(href)
+    return out
+# Repo-root prefixes — a read_next target starting with one of these is
+# already repo-rooted and used verbatim; anything else (bare filename or
+# `./`/`../`) is resolved against the source doc's directory.
+_REPO_ROOT_PREFIXES = ("docs/", "src/", "tests/", "infrastructure/", "scripts/")
+def _resolve_read_target(path: str, target_path: str) -> str | None:
+    """Resolve a read_next / opening-block target to a clean uid.
+    Bare filenames + `./`/`../` paths anchor against the source doc dir
+    (R4 follow-up: a bare `accessibility-checklist.md` used to mint a
+    repo-root `doc:file:accessibility-checklist.md` stub that never
+    existed). Repo-rooted `docs/...`/`src/...` targets pass through.
+    """
+    if target_path.startswith(("http://", "https://")):
+        return f"doc:external:{target_path}"
+    if target_path.startswith(("../", "./")):
+        resolved = _resolve_link(path, target_path)
+        return resolved or None
+    if target_path.startswith(_REPO_ROOT_PREFIXES):
+        normalised = _normalize_path(target_path)
+        if normalised.endswith((".md", ".mdx")) and not Path(normalised).is_file():
+            # Same existence gate as _resolve_link (roadmap §6) — a
+            # repo-rooted read_next target that is gone mints a stale stub.
+            return None
+        normalised = _resolve_through_symlink(normalised)
+        if not normalised:
+            return None
+        return f"doc:file:{normalised}"
+    # Bare relative name — anchor against the source doc's directory.
+    resolved = _resolve_link(path, target_path)
+    return resolved or None
+def _emit_read_next_targets(
+    path: str,
+    raw_value: str,
+    result: ExtractionResult,
+    *,
+    source: str,
+) -> None:
+    """Emit one ``read_next`` edge per parsed target in ``raw_value``."""
+    for target_path in _split_read_targets(raw_value):
+        target_uid = _resolve_read_target(path, target_path)
+        if not target_uid:
+            continue
+        result.edges.append(
+            GraphEdge(
+                source_uid=file_uid(path),
+                target_uid=target_uid,
+                edge_type="read_next",
+                extractor=EXTRACTOR_ID,
+                confidence=0.9,
+                source_span=f"{_normalize_path(path)}:{source}",
+            )
+        )
+def _extract_opening_block_reads(path: str, content: str, result: ExtractionResult) -> None:
+    """Parse opening-block ``Read next:`` (long) and ``> N:`` (short)."""
+    seen_targets: set[str] = set()
+    for match in _OPENING_READ_NEXT_RE.finditer(content):
+        for target_path in _split_read_targets(match.group("targets")):
+            if target_path in seen_targets:
+                continue
+            seen_targets.add(target_path)
+            target_uid = _resolve_read_target(path, target_path)
+            if not target_uid:
+                continue
+            result.edges.append(
+                GraphEdge(
+                    source_uid=file_uid(path),
+                    target_uid=target_uid,
+                    edge_type="read_next",
+                    extractor=EXTRACTOR_ID,
+                    confidence=0.9,
+                    source_span=f"{_normalize_path(path)}:opening-block",
+                )
+            )
+@dataclass(frozen=True)
+class ParseError:
+    """Non-fatal extractor warning (e.g. malformed frontmatter)."""
+    kind: str
+    detail: str
+    line: int | None = None
+@dataclass
+class ExtractionResult:
+    """Nodes, edges, parse_errors returned from extract()."""
+    nodes: list[GraphNode] = field(default_factory=list)
+    edges: list[GraphEdge] = field(default_factory=list)
+    parse_errors: list[ParseError] = field(default_factory=list)
+# ---------------------------------------------------------------------------
+# Slug / uid helpers
+# ---------------------------------------------------------------------------
+def slugify(heading: str) -> str:
+    """Compute a stable URL-anchor slug from a heading title.
+    Rules match GitHub-flavored Markdown: lowercase, strip non-alnum,
+    collapse dashes. Deterministic — same input → same slug across
+    platforms and runs (required by the P-I-11 determinism principle).
+    """
+    lowered = heading.lower()
+    cleaned = re.sub(r"[^\w\s-]", "", lowered)
+    return re.sub(r"[\s_]+", "-", cleaned).strip("-")
+def file_uid(path: str) -> str:
+    return f"doc:file:{_normalize_path(path)}"
+def heading_uid(path: str, slug: str, level: int, occurrence: int) -> str:
+    # occurrence disambiguates repeated headings under different parents.
+    suffix = f":{occurrence}" if occurrence > 0 else ""
+    return f"doc:heading:{_normalize_path(path)}#{slug}:{level}{suffix}"
+def frontmatter_key_uid(path: str, key: str) -> str:
+    return f"doc:frontmatter:{_normalize_path(path)}::{key}"
+def _normalize_path(path: str) -> str:
+    """Forward-slash, no trailing slash — stable across platforms."""
+    return str(PurePosixPath(path.replace("\\", "/")))
+def _classify_governance_path(normalised: str) -> tuple[str | None, str | None]:
+    parts = normalised.split("/")
+    if len(parts) >= 4 and parts[-1] == "SKILL.md" and "skills" in parts:
+        skills_idx = parts.index("skills")
+        if skills_idx + 1 < len(parts) - 1:
+            return ("cos:skill", parts[skills_idx + 1])
+    if (
+        len(parts) >= 3
+        and parts[-1].endswith(".md")
+        and "rules" in parts
+        and parts[-1] != "SKILL.md"
+    ):
+        rules_idx = parts.index("rules")
+        if rules_idx + 1 == len(parts) - 1:
+            return ("cos:rule", parts[-1][:-3])
+    return (None, None)
+_ASSET_SUFFIXES = frozenset(
+    {
+        ".png",
+        ".jpg",
+        ".jpeg",
+        ".gif",
+        ".svg",
+        ".webp",
+        ".ico",
+        ".bmp",
+        ".pdf",
+        ".mp4",
+        ".mov",
+        ".webm",
+        ".mp3",
+        ".woff",
+        ".woff2",
+        ".ttf",
+        ".eot",
+        ".zip",
+    }
+)
+def _resolve_through_symlink(normalised: str) -> str:
+    # In-repo symlink target (CLAUDE.md → AGENTS.md): land the edge on the
+    # real file — walk_local skips symlinks, so a symlink-path node has no
+    # owner and doctor flags it malformed (roadmap §6). A symlink escaping
+    # the repo root resolves to "" (caller drops it).
+    path = Path(normalised)
+    if not normalised or not path.is_symlink():
+        return normalised
+    try:
+        return path.resolve().relative_to(Path.cwd().resolve()).as_posix()
+    except (OSError, ValueError):
+        return ""
+def _resolve_link(origin_path: str, target: str) -> str:
+    """Resolve a link (possibly relative) to an absolute repo-rooted path.
+    Returns the target as a doc:file uid when it points to a filesystem
+    path, or a canonical external URL for http(s) links.
+    """
+    target = target.strip()
+    if target.startswith(("http://", "https://", "mailto:")):
+        return f"doc:external:{target}"
+    # W6.5 (X7) residual: reject targets carrying regex / markup
+    # metacharacters — a prose regex like `[module](?P<module>[^'"]+)`
+    # matches the inline-link regex and used to mint a garbage
+    # `doc:file:?P<module>...` stub. Real paths never contain these.
+    if any(c in target for c in "<>\"'{}^*|`"):
+        return ""
+    # Discard `"title"` suffix after a space.
+    target = target.split(" ")[0]
+    # Split off `#anchor`.
+    path_part, _, anchor = target.partition("#")
+    # If the link is to the same file's anchor only, resolve to self.
+    if path_part == "":
+        return f"doc:file:{_normalize_path(origin_path)}#{anchor}" if anchor else ""
+    origin_dir = PurePosixPath(_normalize_path(origin_path)).parent
+    resolved = (origin_dir / path_part).as_posix()
+    # Collapse `./` and `../` — PurePosixPath already handles this in
+    # most cases; normalise for Windows-style edge cases.
+    parts: list[str] = []
+    for part in resolved.split("/"):
+        if part in ("", "."):
+            continue
+        if part == "..":
+            if parts:
+                parts.pop()
+            continue
+        parts.append(part)
+    normalised = "/".join(parts)
+    # Repo-root fallback: a doc nested deep in the meta-repo can
+    # author a consumer-relative link (`../../docs/x`) that collapses to a
+    # nonexistent `src/docs/x` here while the real file is `docs/x` at repo
+    # root. If the collapsed path is missing but a repo-rooted variant of
+    # the raw target exists, prefer the real file. Mirrors the bare-name
+    # anchoring in _resolve_read_target; kills the stale_paths churn that
+    # doctor --fix can only paper over.
+    if normalised and not Path(normalised).exists():
+        bare = path_part.lstrip("./")
+        if bare and bare != normalised and Path(bare).is_file():
+            normalised = bare
+    normalised = _resolve_through_symlink(normalised)
+    if not normalised:
+        return ""
+    # Markdown links can target any artefact in the repo; route them to
+    # the right uid namespace by extension so a `.md → .py` link does
+    # not create a ghost `doc:file` stub that duplicates the real
+    # `code:file` node the code extractors emit.
+    suffix = PurePosixPath(normalised).suffix.lower()
+    # Image / binary asset links are not code or doc references — drop them
+    # so a relative `![x](diagram.png)` never mints a code:file node.
+    if suffix in _ASSET_SUFFIXES:
+        return ""
+    if suffix == "" and normalised and Path(normalised).is_dir():
+        # Directory target → existing folder node, not a phantom doc:file:<dir>.
+        return f"folder:{normalised}"
+    if suffix == "" and not Path(normalised).is_file():
+        # Extensionless target that is neither a real dir nor a real file is a
+        # placeholder / prose fragment ('relative/path', 'docs/_meta/path',
+        # unicode-ellipsis truncations) — minting a node for it created
+        # permanent stale/orphan junk invisible to the doctor.
+        return ""
+    if suffix in {".md", ".mdx"} and not Path(normalised).is_file():
+        # Broken doc link (target moved/deleted/consumer-only) — same drop
+        # policy as the extensionless placeholders above; minting a stub
+        # here is permanent stale_paths churn (existence gate: roadmap §6).
+        return ""
+    if suffix not in {".md", ".mdx", ""} and not Path(normalised).is_file():
+        # Non-doc local target (.yaml/.py/.json/…) that does not exist on
+        # disk — a broken/stale link (e.g. a render-dir COPY whose relative
+        # path resolves one level short → code:file:core/hooks/registry.yaml).
+        # The .md gate above already drops missing doc links; widen the same
+        # existence gate to every extension so no broken code:file stub is
+        # minted (roadmap §6, TASK-410).
+        return ""
+    if suffix in {".md", ".mdx", ""}:
+        base = f"doc:file:{normalised}"
+    elif normalised.startswith("docs/tasks/"):
+        base = f"task:file:{normalised}"
+    else:
+        # Code-file nodes carry no line/heading anchor (the uid scheme has no
+        # line numbers): a `foo.py#L954` link resolves to the file node, not a
+        # phantom `code:file:...#L954` that pollutes similarity.
+        return f"code:file:{normalised}"
+    return f"{base}#{anchor}" if anchor else base
+# ---------------------------------------------------------------------------
+# Main entry point
+# ---------------------------------------------------------------------------
+def extract(
+    path: str,
+    content: str,
+) -> ExtractionResult:
+    """Parse a Markdown document → nodes + edges."""
+    result = ExtractionResult()
+    try:
+        content_hash = hashlib.sha256(content.encode("utf-8")).hexdigest()[:16]
+        normalised = _normalize_path(path)
+        special_kind, special_label = _classify_governance_path(normalised)
+        file_node = GraphNode(
+            uid=file_uid(path),
+            kind=special_kind or "doc:file",
+            label=special_label or PurePosixPath(normalised).name,
+            file_path=normalised,
+            lang="md",
+            doc_blob=_extract_doc_blob(content),
+            content_hash=content_hash,
+            metadata={"extractor": EXTRACTOR_ID},
+        )
+        result.nodes.append(file_node)
+        # Frontmatter FIRST so linked docs get ssot/read_next edges even
+        # when headings / body parsing fails later.
+        _extract_frontmatter(path, content, result)
+        # Opening-block "Read next:" / "> N:" → read_next edges. Runs after
+        # frontmatter so duplicate-href dedupe inside the scan only fires
+        # within the body. Frontmatter `reads:[…]` is handled inline via
+        # `_emit_read_next_targets` to keep both forms graph-symmetric.
+        # Strip fenced code first — so a `Read next:` line
+        # that lives inside a ```bash``` block does not produce a false edge.
+        _opening_block_content = _FENCED_CODE_RE.sub("", content)
+        _extract_opening_block_reads(path, _opening_block_content, result)
+        # Heading scan builds the containment tree AND a slug→uid map
+        # for subsequent in-page fragment resolution.
+        headings = _extract_headings(path, content, result)
+        # Strip fenced code before link scan so ``[x](y)`` inside a code
+        # block does not produce a false edge.
+        cleaned = _FENCED_CODE_RE.sub("", content)
+        _extract_links(path, cleaned, headings, result)
+        # S3: attach Folder→...→File spine so the SPA tree-view always
+        # has a connected root. Idempotent on uid — parallel extractors
+        # emit identical folder uids and bulk_upsert de-dupes.
+        emit_contains_spine(
+            file_path=path,
+            file_uid_=file_node.uid,
+            result=result,
+            extractor_id=EXTRACTOR_ID,
+        )
+        # Promote any edge-only uid (link target the extractor does not
+        # own the source for) into a stub node so the backend's edge
+        # write does not raise ValueError for unknown uids. Upserting
+        # the extracted nodes in another pass will replace the stub
+        # with the real row — uid is the join key.
+        _promote_stubs(result)
+        return result
+    except Exception as exc:
+        logger.debug("md_links.extract(%s) fatal error: %s", path, exc)
+        result.parse_errors.append(ParseError(kind="fatal", detail=str(exc)))
+        return result
+# ---------------------------------------------------------------------------
+# Internals
+# ---------------------------------------------------------------------------
+def folder_uid(path: str) -> str:
+    """Stable uid for a repo-rooted folder.
+    Empty / ``.`` / ``/`` path collapse to the synthetic repo root uid.
+    Matches the convention used by the backend's bulk_upsert — so
+    parallel extractors emit the SAME uid for the same folder and the
+    upsert de-duplicates.
+    """
+    normalised = _normalize_path(path)
+    if normalised in ("", ".", "/"):
+        return "folder:."
+    return f"folder:{normalised}"
+def emit_contains_spine(
+    *,
+    file_path: str,
+    file_uid_: str,
+    result: ExtractionResult,
+    extractor_id: str,
+) -> None:
+    """Append folder nodes + Folder→Folder → Folder→File ``contains`` edges."""
+    normalised = _normalize_path(file_path)
+    if not normalised or normalised in (".", "/"):
+        return
+    # Walk up the directory chain → list of (uid, label, parent_uid).
+    parts = [p for p in normalised.split("/") if p]
+    if not parts:
+        return
+    # Drop the filename — we only want directory segments.
+    directory_parts = parts[:-1]
+    # Always emit the repo root folder (parent of every top-level dir).
+    # uid stays `folder:.` for stability across rebuilds and idempotency;
+    # the label is the PROJECT NAME (cwd directory name — extraction runs
+    # from the project root by convention) so the spine anchors on
+    # something a human recognises ("coding-os"), not the technical
+    # "repo-root" placeholder (TASK-406). uid is the contract, label is
+    # presentation.
+    try:
+        project_label = Path.cwd().name or "repo-root"
+    except OSError:
+        project_label = "repo-root"
+    root_uid = folder_uid(".")
+    root_node = GraphNode(
+        uid=root_uid,
+        kind="folder",
+        label=project_label,
+        file_path=None,
+        metadata={"extractor": extractor_id, "repo_root": True},
+    )
+    result.nodes.append(root_node)
+    # Emit one folder node per directory segment, and a contains edge
+    # from its parent. Parent of first segment is the repo root.
+    previous_uid = root_uid
+    accumulated: list[str] = []
+    for segment in directory_parts:
+        accumulated.append(segment)
+        this_path = "/".join(accumulated)
+        this_uid = folder_uid(this_path)
+        result.nodes.append(
+            GraphNode(
+                uid=this_uid,
+                kind="folder",
+                label=segment,
+                file_path=this_path,
+                metadata={"extractor": extractor_id},
+            )
+        )
+        result.edges.append(
+            GraphEdge(
+                source_uid=previous_uid,
+                target_uid=this_uid,
+                edge_type="contains",
+                extractor=extractor_id,
+                confidence=1.0,
+            )
+        )
+        previous_uid = this_uid
+    # Finally the deepest folder → file edge.
+    result.edges.append(
+        GraphEdge(
+            source_uid=previous_uid,
+            target_uid=file_uid_,
+            edge_type="contains",
+            extractor=extractor_id,
+            confidence=1.0,
+        )
+    )
+def _promote_stubs(result: ExtractionResult) -> None:
+    """Emit a minimal stub node for every edge target we do not own."""
+    known = {n.uid for n in result.nodes}
+    seen_extra: set[str] = set()
+    for edge in result.edges:
+        for uid in (edge.source_uid, edge.target_uid):
+            if uid in known or uid in seen_extra:
+                continue
+            seen_extra.add(uid)
+            result.nodes.append(_stub_for_uid(uid))
+def _stub_for_uid(uid: str) -> GraphNode:
+    if uid.startswith("folder:"):
+        path = uid[len("folder:") :]
+        label = PurePosixPath(path).name if path not in ("", ".") else "."
+        return GraphNode(
+            uid=uid,
+            kind="folder",
+            label=label or path or ".",
+            file_path=path if path not in ("", ".") else None,
+            metadata={"stub": True, "extractor": EXTRACTOR_ID},
+        )
+    if uid.startswith("doc:file:"):
+        rest = uid[len("doc:file:") :]
+        path, _, anchor = rest.partition("#")
+        label = PurePosixPath(path).name if path else anchor
+        return GraphNode(
+            uid=uid,
+            kind="doc:file",
+            label=label or uid,
+            file_path=path or None,
+            lang="md",
+            metadata={"stub": True, "extractor": EXTRACTOR_ID},
+        )
+    if uid.startswith("doc:heading:"):
+        return GraphNode(
+            uid=uid,
+            kind="doc:heading",
+            label=uid.split("#", 1)[-1] or uid,
+            lang="md",
+            metadata={"stub": True, "extractor": EXTRACTOR_ID},
+        )
+    if uid.startswith("doc:external:"):
+        return GraphNode(
+            uid=uid,
+            kind="doc:external",
+            label=uid[len("doc:external:") :],
+            metadata={"stub": True, "extractor": EXTRACTOR_ID},
+        )
+    # Infer kind from any standard `<kind>:<sub>:...` prefix so cross-
+    # extractor edge targets (code symbols, mcp tools, routes, tasks)
+    # keep the correct kind when synthesised as stubs. Falls through to
+    # doc:external only when the prefix is genuinely unknown.
+    head, sep, rest = uid.partition(":")
+    if sep and head in {"code", "doc", "cos", "task"}:
+        sub, sep2, tail = rest.partition(":")
+        if sep2:
+            kind = f"{head}:{sub}"
+            label = tail.split("::", 1)[-1] or tail or uid
+            return GraphNode(
+                uid=uid,
+                kind=kind,
+                label=label,
+                metadata={"stub": True, "extractor": EXTRACTOR_ID},
+            )
+    return GraphNode(
+        uid=uid,
+        kind="doc:external",
+        label=uid,
+        metadata={"stub": True, "extractor": EXTRACTOR_ID},
+    )
+def _extract_doc_blob(content: str, *, cap: int = 4000) -> str:
+    """Flat preview of the doc's body, trimmed to keep nodes lean."""
+    stripped = _FENCED_CODE_RE.sub("", content)
+    stripped = re.sub(r"<!--.*?-->", "", stripped, flags=re.DOTALL)
+    compact = re.sub(r"\s+", " ", stripped).strip()
+    return compact[:cap]
+def _extract_frontmatter(path: str, content: str, result: ExtractionResult) -> None:
+    """Pull out HTML-comment and/or YAML-fence frontmatter keys."""
+    candidates: list[str] = []
+    yaml_match = _YAML_FENCE_RE.match(content)
+    if yaml_match:
+        candidates.append(yaml_match.group("body"))
+    html_match = _HTML_FRONTMATTER_RE.search(content[:4000])  # cap scan range
+    if html_match:
+        body = html_match.group("body")
+        # The coding-os convention is pipe-separated key:value pairs; accept
+        # both the multi-key style ("domain:x | layer:y") and a single-key
+        # HTML comment ("<!-- ssot_of:path -->") so ssot/read_next edges
+        # survive even in minimal frontmatter.
+        candidates.append(body)
+    for body in candidates:
+        for raw in body.splitlines() if "\n" in body else body.split("|"):
+            if ":" not in raw:
+                continue
+            key, _, value = raw.strip().partition(":")
+            key = key.strip().lower()
+            value = value.strip().strip('"').strip("'")
+            if not key or not value:
+                continue
+            # Frontmatter keys are simple identifiers. Reject anything
+            # that looks like prose / markdown (heading `#`, backtick,
+            # whitespace, braces) — the HTML-comment scan otherwise
+            # mis-parses a `# `output_format={type|...}`` code line as a
+            # key:value pair and mints a malformed doc:frontmatter node.
+            if not re.fullmatch(r"[a-z0-9_]+", key):
+                continue
+            # `reads:[a, b, c]` short-form vector — emit one read_next edge
+            # per target instead of a single key node carrying the literal
+            # bracket-string. Short-form authors get the same graph
+            # surface as long-form `read_next:path` keys.
+            if key == "reads":
+                _emit_read_next_targets(path, value, result, source="frontmatter:reads")
+                continue
+            node = GraphNode(
+                uid=frontmatter_key_uid(path, key),
+                kind="doc:frontmatter_key",
+                label=f"{key}={value}",
+                file_path=_normalize_path(path),
+                lang="md",
+                metadata={"key": key, "value": value, "extractor": EXTRACTOR_ID},
+            )
+            result.nodes.append(node)
+            result.edges.append(
+                GraphEdge(
+                    source_uid=file_uid(path),
+                    target_uid=node.uid,
+                    edge_type="contains",
+                    extractor=EXTRACTOR_ID,
+                    confidence=1.0,
+                )
+            )
+            # Special-case: ssot_of, read_next, read_before are cross-
+            # file relations declared via frontmatter — emit the
+            # directed edge in addition to the containment one.
+            # Frontmatter values use REPO-ROOTED paths (e.g.
+            # `docs/core/rules.md`), not relative — this matches how
+            # every doc in this repo currently authors them.
+            if key in {"ssot_of", "read_next", "read_before"}:
+                target_path = value.split()[0]
+                if target_path.startswith(("http://", "https://")):
+                    target_uid = f"doc:external:{target_path}"
+                elif target_path.startswith(("../", "./")):
+                    # F13 / Audit #4: frontmatter values are usually
+                    # repo-rooted, but some docs ship relative paths.
+                    # Anchor those against the source doc instead of
+                    # emitting a `doc:file:../...` stub.
+                    target_uid = _resolve_link(path, target_path)
+                    if not target_uid:
+                        continue
+                else:
+                    target_uid = f"doc:file:{_normalize_path(target_path)}"
+                result.edges.append(
+                    GraphEdge(
+                        source_uid=file_uid(path),
+                        target_uid=target_uid,
+                        edge_type=key,
+                        extractor=EXTRACTOR_ID,
+                        confidence=0.9,
+                        source_span=f"{_normalize_path(path)}:frontmatter",
+                    )
+                )
+def _extract_headings(
+    path: str, content: str, result: ExtractionResult
+) -> list[tuple[str, int, str]]:
+    """Produce heading nodes + contains edges + a list of (uid, level, slug).
+    Returns a list in document order so link resolution can point to the
+    nearest preceding heading when the link has an anchor.
+    """
+    headings: list[tuple[str, int, str]] = []
+    stack: list[tuple[int, str]] = [(0, file_uid(path))]
+    slug_counts: dict[str, int] = {}
+    for lineno, line in enumerate(content.splitlines(), start=1):
+        # Skip ATX headings inside fenced code — approximate by checking
+        # balanced backticks up to this line.
+        m = _HEADING_RE.match(line)
+        if not m:
+            continue
+        level = len(m.group("level"))
+        title = m.group("title").strip()
+        if not title:
+            continue
+        slug = slugify(title)
+        if not slug:
+            slug = hashlib.sha1(title.encode("utf-8")).hexdigest()[:8]
+        occurrence = slug_counts.get(slug, 0)
+        slug_counts[slug] = occurrence + 1
+        uid = heading_uid(path, slug, level, occurrence)
+        node = GraphNode(
+            uid=uid,
+            kind="doc:heading",
+            label=title,
+            file_path=_normalize_path(path),
+            start_line=lineno,
+            lang="md",
+            metadata={
+                "level": level,
+                "slug": slug,
+                "occurrence": occurrence,
+                "extractor": EXTRACTOR_ID,
+            },
+        )
+        result.nodes.append(node)
+        # Walk up the stack until we find a parent whose level is lower.
+        while stack[-1][0] >= level:
+            stack.pop()
+        parent_uid = stack[-1][1]
+        result.edges.append(
+            GraphEdge(
+                source_uid=parent_uid,
+                target_uid=uid,
+                edge_type="contains",
+                extractor=EXTRACTOR_ID,
+                confidence=1.0,
+                source_span=f"{_normalize_path(path)}:{lineno}",
+            )
+        )
+        stack.append((level, uid))
+        headings.append((uid, level, slug))
+    return headings
+def _extract_links(
+    path: str,
+    cleaned_content: str,
+    headings: list[tuple[str, int, str]],
+    result: ExtractionResult,
+) -> None:
+    """Emit links_to + cites_heading edges.
+    Headings list is consumed for in-page anchor → heading-node
+    resolution (so `[text](#slug)` lands on the heading, not the file).
+    """
+    slug_to_uid: dict[str, str] = {}
+    for uid, _level, slug in headings:
+        # First occurrence wins for in-page links — same convention as
+        # GitHub anchors.
+        slug_to_uid.setdefault(slug, uid)
+    # Inline links.
+    for match in _INLINE_LINK_RE.finditer(cleaned_content):
+        target = match.group("target").strip()
+        if not target:
+            continue
+        resolved = _resolve_link(path, target)
+        if not resolved:
+            continue
+        # Heading anchor inside THIS file — emit cites_heading.
+        if resolved.startswith(f"doc:file:{_normalize_path(path)}#"):
+            anchor = resolved.rsplit("#", 1)[1]
+            heading_uid_resolved = slug_to_uid.get(anchor)
+            if heading_uid_resolved:
+                result.edges.append(
+                    GraphEdge(
+                        source_uid=file_uid(path),
+                        target_uid=heading_uid_resolved,
+                        edge_type="cites_heading",
+                        extractor=EXTRACTOR_ID,
+                        confidence=0.95,
+                    )
+                )
+                continue
+        # Cross-file heading anchor — cites_heading to the target file's
+        # heading node (target_uid assumes the other file will have the
+        # heading indexed in the same run; if not, the edge dangles
+        # until the cross-file reindex catches up).
+        if "#" in resolved and resolved.startswith("doc:file:"):
+            base_path, anchor = resolved.split("#", 1)
+            target_file = base_path  # keep doc:file prefix
+            target_heading = f"doc:heading:{base_path[len('doc:file:') :]}#{anchor}"
+            result.edges.append(
+                GraphEdge(
+                    source_uid=file_uid(path),
+                    target_uid=target_heading,
+                    edge_type="cites_heading",
+                    extractor=EXTRACTOR_ID,
+                    confidence=0.7,  # lower — target heading may not exist
+                    source_span=f"{_normalize_path(path)}",
+                )
+            )
+            result.edges.append(
+                GraphEdge(
+                    source_uid=file_uid(path),
+                    target_uid=target_file,
+                    edge_type="links_to",
+                    extractor=EXTRACTOR_ID,
+                    confidence=0.9,
+                )
+            )
+            continue
+        # Plain link — file-level references_to.
+        result.edges.append(
+            GraphEdge(
+                source_uid=file_uid(path),
+                target_uid=resolved,
+                edge_type="links_to",
+                extractor=EXTRACTOR_ID,
+                confidence=0.9 if resolved.startswith("doc:file:") else 0.6,
+            )
+        )
+    # Wiki links.
+    for match in _WIKI_LINK_RE.finditer(cleaned_content):
+        target = match.group("target").strip()
+        if not target:
+            continue
+        if target.endswith(".md"):
+            resolved = _resolve_link(path, target)
+        else:
+            resolved = _resolve_link(path, target + ".md")
+        if not resolved:
+            continue
+        result.edges.append(
+            GraphEdge(
+                source_uid=file_uid(path),
+                target_uid=resolved,
+                edge_type="links_to",
+                extractor=EXTRACTOR_ID,
+                confidence=0.8,
+                source_span=f"{_normalize_path(path)}:wikilink",
+            )
+        )
+__all__ = [
+    "EXTRACTOR_ID",
+    "ExtractionResult",
+    "ParseError",
+    "emit_contains_spine",
+    "extract",
+    "file_uid",
+    "folder_uid",
+    "frontmatter_key_uid",
+    "heading_uid",
+    "slugify",
+]