loki-mode 11.3.0 → 11.3.2

package/docs/CLI-REFERENCE.md

@@ -1,6 +1,6 @@
 # CLI reference
 
-Generated from `loki-ts/src/cli/registry.ts` by `scripts/generate-stale-zero.sh` for v11.3.0. Do not edit by hand.
+Generated from `loki-ts/src/cli/registry.ts` by `scripts/generate-stale-zero.sh` for v11.3.2. Do not edit by hand.
 Hidden and legacy-only commands are omitted; see `docs/v10/CLI-MODERN.md` for the full inventory.
 
 | Command | Description |
@@ -15,6 +15,8 @@ Hidden and legacy-only commands are omitted; see `docs/v10/CLI-MODERN.md` for th
 | `loki memory` | Cross-project learnings |
 | `loki memory list` | All learnings |
 | `loki memory index` | Show or rebuild the memory index |
+| `loki memory learn` | Learn lessons from a merged PR's review comments |
+| `loki memory lessons` | List PR review lessons with uses and outcomes |
 | `loki memory show` | Show one learning |
 | `loki memory search` | Search learnings |
 | `loki memory stats` | Memory statistics |
@@ -55,6 +57,14 @@ Hidden and legacy-only commands are omitted; see `docs/v10/CLI-MODERN.md` for th
 | `loki start` | Run the autonomous build |
 | `loki slack` | Slack inbound handler |
 | `loki slack serve` | Serve the Slack handler |
+| `loki queue` | Overnight issue queue with a morning digest |
+| `loki queue add` | Queue issue refs |
+| `loki queue list` | Show the queue |
+| `loki queue run` | Process the queue |
+| `loki issues` | Run every open issue in a repo and open PRs |
+| `loki issues run` | Triage and run open issues; split too-large ones into stacked PRs |
+| `loki undo` | Plan or apply an undo of a run |
+| `loki verify-pr` | Verify a PR against its linked issue in a sandbox |
 | `loki answer` | Resume a BLOCKED run with an answer |
 | `loki engine10` | v10 engine router |
 | `loki engine10 run` | Run the v10 engine |

package/docs/COMPONENTS.md

@@ -0,0 +1,447 @@
+# Loki Mode Components
+
+This document maps the major components of the loki-mode codebase: each one's
+purpose, key files, public interface, and dependencies on other components.
+
+Loki Mode is an autonomous spec-to-product system. It takes a spec (PRD, GitHub
+issue, OpenAPI/JSON/YAML, or one-line brief) to a deployed product through the
+RARV-C closure loop (Reason - Act - Reflect - Verify - Close) with 8 quality
+gates. It is provider-agnostic (Claude Code, OpenAI Codex CLI, Cline, Aider).
+
+## Component Map
+
+| Component | Language | Role |
+|---|---|---|
+| `autonomy/` | Bash + Python | CLI and orchestration engine (RARV loop) |
+| `loki-ts/` | TypeScript (Bun) | Modern runner: CLI, runner, council, providers, metrics |
+| `memory/` | Python | Episodic/semantic/procedural memory with vector search |
+| `providers/` | Bash + Python | Multi-provider config and model registry |
+| `dashboard/` | Python (FastAPI) | Web dashboard API and control plane |
+| `packages/control-plane/` | TypeScript | Control Plane (browser UI and service) |
+| `web-app/` | Python + JS | Purple Lab web app (deprecated v7.44.0) |
+| `mcp/` | Python | MCP server (tools, resources, prompts) |
+| `api/` | TypeScript (Deno) | REST API surface and services |
+| `events/` | Python + TS + Bash | Unified event bus |
+| `agents/` | Python + JSON | Agent type registry and hub install |
+| `skills/` | Markdown | On-demand skill modules (progressive disclosure) |
+| `references/` | Markdown | Detailed documentation |
+| `templates/` | Markdown | PRD templates per project archetype |
+| `benchmarks/` | Bash + Python | SWE-bench and HumanEval benchmark harness |
+| `plugins/` | JSON + Markdown | Claude Code plugin packaging |
+
+---
+
+## autonomy/
+
+The CLI and orchestration engine. This is the heart of the bash route: the
+RARV loop, completion detection, code review, healing, and all runtime state
+management.
+
+**Purpose:** Drive autonomous execution from spec to verified completion.
+
+**Key files:**
+- `loki` - Main CLI (~23K lines, 100+ `cmd_` functions, dispatch in `main()`).
+- `run.sh` - Orchestration engine (~12K lines). Hosts the RARV iteration loop
+  (`run_autonomous()`), prompt construction (`build_prompt()`), state
+  persistence (`save_state()`), code review (`run_code_review()`), checkpoints,
+  and budget/rate-limit circuit breakers.
+- `completion-council.sh` - Completion detection via council voting
+  (`council_should_stop()`).
+- `council-v2.sh` - Reviewer council pipeline.
+- `app-runner.sh` - Manages the generated app's run/healthcheck lifecycle.
+- `checklist-verify.py`, `prd-checklist.sh`, `prd-analyzer.py` - PRD parsing
+  and checklist verification.
+- `context-tracker.py`, `notification-checker.py` - Context window tracking and
+  notification triggers.
+- `crash.sh`, `grill.sh`, `docker-run.sh`, `playwright-verify.sh` - Crash
+  capture, spec interrogation, containerized runs, and smoke testing.
+- `hooks/` - Lifecycle hooks: `migration-hooks.sh` (healing safety gates),
+  `quality-gate.sh`, `session-init.sh`, `store-episode.sh`, `track-metrics.sh`,
+  `validate-bash.sh`.
+- `lib/` - Helper library: proof/evidence generation (`proof-generator.py`,
+  `proof-verify.py`, `proof-pr.sh`, `proof_redact.py`), crash redaction
+  (`crash_capture.py`, `crash_redact.py`), claude flags, MCP config, locks,
+  launch kit, project graph, PRD enrichment.
+- `issue-parser.sh`, `issue-providers.sh` - GitHub issue import.
+- `CONSTITUTION.md` - Behavioral constitution for the autonomous agent.
+
+**Public interface:**
+- CLI commands: `loki start`, `loki verify`, `loki spec`, `loki grill`,
+  `loki heal` / `loki modernize heal`, `loki preview` / `loki open`,
+  `loki deploy`, `loki docker`, `loki mcp`, `loki memory`, `loki plan`,
+  `loki quickstart`, `loki demo`, `loki status`, `loki stop`, `loki doctor`.
+- `.loki/` filesystem state files (session, queue, memory, checkpoints,
+  findings, healing artifacts) that all other components read and write.
+
+**Dependencies:**
+- `providers/` for provider-aware invocation and model selection.
+- `memory/` for episodic trace storage and context retrieval.
+- `events/` for event emission.
+- `loki-ts/` as the default modern runner (bash route is the fallback via
+  `LOKI_LEGACY_BASH=1`).
+
+---
+
+## loki-ts/
+
+The modern Bun/TypeScript runner. Default execution path; mirrors the bash
+route's behavior with strict parity (checked by the parity suites under `tests/`).
+
+**Purpose:** Fast, typed implementation of the runner, CLI, council,
+provider abstraction, and metrics.
+
+**Key files:**
+- `src/cli.ts` - CLI entry.
+- `src/version.ts` - Version reporting.
+- `src/runner/` - Autonomous run loop, state, RARV phasing.
+- `src/runner/providers.ts` - Provider abstraction with automatic failover.
+- `src/runner/council.ts` - Completion-council hook: convergence tracking, the stagnation and done-signal force-stop valves, and the v8 confidence-spike re-check.
+- `src/runner/goal_score.ts` - Goal-measurability scoring (v8.0.0). Advisory only; flags a goal the loop cannot hill-climb. Byte-mirrored in `autonomy/run.sh`.
+- `src/runner/retry_class.ts` - Failure classification (v8.0.0). Separates transient failures from positively-identified permanent ones; unrecognized failures stay transient.
+- `src/council/` - Reviewer council and verdict logic.
+- `src/commands/` - Command implementations.
+- `src/metrics/` - Efficiency and reward metrics.
+- `src/project_graph.ts` - Project/codebase graph.
+- `src/util/` - Shared utilities.
+- `tests/` - Bun test suite; `stryker.config.json` for mutation testing.
+
+**Public interface:**
+- The `loki` binary behavior (parity with the bash CLI).
+- Provider invocation contract consumed by the orchestration layer.
+
+**Dependencies:**
+- `providers/` (shared model catalog and provider semantics).
+- `.loki/` state (shared with the bash route, byte-identical where required).
+
+---
+
+## memory/
+
+The memory system: episodic interaction traces, generalized semantic patterns,
+learned procedural skills, with optional vector search and cross-project recall.
+
+**Purpose:** Persist and retrieve task-relevant context across iterations and
+across projects.
+
+**Key files:**
+- `engine.py` - Memory orchestrator.
+- `schemas.py` - Pydantic schemas (includes healing `FrictionPoint`,
+  `FailureMode`).
+- `storage.py` - File-based storage backend (`.loki/memory/`).
+- `retrieval.py` - Task-aware retrieval.
+- `consolidation.py` - Episodic-to-semantic consolidation pipeline.
+- `token_economics.py` - Discovery vs read token accounting.
+- `embeddings.py`, `vector_index.py` - Optional embedding-based similarity.
+- `cross_project.py`, `knowledge_graph.py`, `rag_injector.py` - Cross-project
+  recall, knowledge graph, and RAG prompt injection (v7.1.0+).
+- `app_graph.py`, `error_log.py`, `ingest.py`, `namespace.py`, `replay.py`,
+  `unified_access.py` - Supporting modules.
+- `layers/` - Progressive disclosure (index, timeline, full detail).
+- `managed_memory/` - Managed memory client, gated on
+  `LOKI_MANAGED_MEMORY=true`.
+- `tests/` - Memory test suite.
+
+**Public interface:**
+- `loki memory index|timeline|consolidate|economics|retrieve|episode|pattern|skill|vectors`.
+- REST endpoints at `/api/memory/*` (via the API/dashboard layers).
+- Python package API consumed by the runner and MCP server.
+
+**Dependencies:**
+- Consumed by `autonomy/` (trace storage bridge), `mcp/`, `dashboard/`,
+  and `api/`.
+- Optional `sentence-transformers` for vector search.
+
+---
+
+## providers/
+
+Multi-provider support. Shell-sourceable provider configs and a model registry
+shared by both the bash route and loki-ts.
+
+**Purpose:** Abstract over Claude Code, Cline, Codex CLI, and Aider with tiered
+capability degradation.
+
+**Key files:**
+- `claude.sh` - Claude Code (Tier 1: full features).
+- `cline.sh` - Cline (Tier 2: reduced parallelism).
+- `codex.sh` - OpenAI Codex CLI (Tier 3: degraded, sequential).
+- `aider.sh` - Aider (Tier 3: degraded).
+- `loader.sh` - Provider loader utility.
+- `models.sh`, `model_catalog.json` - Model name registry and catalog.
+- `managed.py` - Managed provider client.
+
+Note: Gemini CLI was deprecated in v7.5.18; `LOKI_PROVIDER=gemini` exits with a
+migration message.
+
+**Public interface:**
+- `--provider <name>` flag, `LOKI_PROVIDER` env var.
+- Sourceable shell functions consumed by `autonomy/run.sh`.
+
+**Dependencies:**
+- Consumed by `autonomy/` and `loki-ts/src/runner/providers.ts`.
+
+---
+
+## dashboard/
+
+The FastAPI web dashboard: a control plane and observability surface for live
+runs, plus auth, tenancy, telemetry, and migration tooling.
+
+**Purpose:** Visualize and control autonomous runs from the browser.
+
+**Key files:**
+- `server.py` - FastAPI app (~6K lines, 100+ endpoints, WebSocket).
+- `api_v2.py`, `control.py`, `runs.py` - Run control and v2 API.
+- `auth.py`, `api_keys.py`, `tenants.py`, `app_secrets.py` - Auth, API keys,
+  multi-tenancy, secret storage.
+- `database.py`, `models.py`, `registry.py` - Persistence and models.
+- `activity_logger.py`, `audit.py`, `telemetry.py` - Logging and telemetry.
+- `failure_extractor.py`, `prompt_optimizer.py`, `migration_engine.py`,
+  `rigour_integration.py` - Failure analysis, prompt tuning, healing/migration.
+- `static/` - Built frontend (`index.html`, served by the API).
+- `frontend/` - Frontend source assets.
+- `run.py`, `Dockerfile`, `docker-compose.yml`, `requirements.txt` - Runtime.
+
+**Public interface:**
+- HTTP/WebSocket endpoints (run status, control, memory, council, cost,
+  context, escalations, notifications, app runner, migration).
+- Served by `loki web` / `loki start --api`.
+
+**Dependencies:**
+- `memory/` for memory views.
+- `events/` for live event streaming.
+- `.loki/` state from `autonomy/` runs.
+
+---
+
+## Removed: legacy dashboard UI
+
+The legacy browser UI source and its bundle were deleted in CPE-24. The browser UI is the Control Plane (`packages/control-plane`); `dashboard/server.py` serves the `/api/*` routes only.
+
+---
+
+## web-app/
+
+The Purple Lab web app (deprecated v7.44.0; source kept, still in the tarball
+during phased removal). Provided a multi-project lab surface with browser-based
+PRD input.
+
+**Purpose:** Legacy lab UI (superseded by the single dashboard web surface).
+
+**Key files:**
+- `auth.py`, `crypto.py`, `models.py`, `migrations/`, `alembic.ini` - Backend.
+- `index.html`, `package.json`, `playwright.config.ts` - Frontend.
+- `Dockerfile`, `docker-compose.purple-lab.yml`, `deploy/` - Deployment.
+
+**Dependencies:**
+- Historically consumed `autonomy/` runs; being retired.
+
+---
+
+## mcp/
+
+The Model Context Protocol server. Exposes Loki capabilities (including code
+search) to MCP clients.
+
+**Purpose:** Make Loki's memory, tools, and search available over MCP.
+
+**Key files:**
+- `server.py` - MCP server (47 tools: 31 in-file + magic + gated managed + 8 cp; plus
+  3 resources, 2 prompts).
+- `tools.py` - Core tool implementations.
+- `magic_tools.py` - Magic Modules tools.
+- `cp_tools.py` - Read-only Control Plane data tools (`cp_*`, GET only; the CP URL
+  and token come from the MCP child env and are never returned).
+- `managed_tools.py` - Managed-memory tool (`loki_memory_redact`, gated on
+  `LOKI_MANAGED_AGENTS=true` and `LOKI_MANAGED_MEMORY=true`).
+- `resources.py` - MCP resources.
+- `lsp_proxy.py` - LSP proxy (find references, go to definition, symbol lookup).
+- `learning_collector.py` - Learning signal collection.
+- `_sdk_loader.py` - Bootstraps the Python MCP SDK on first run.
+- `tests/` - MCP test suite.
+
+**Public interface:**
+- MCP tools, resources, and prompts. Launched via `loki mcp`.
+
+**Dependencies:**
+- `memory/` for memory tools.
+- ChromaDB for code search.
+- On-PATH language servers for the LSP proxy.
+
+---
+
+## api/
+
+The REST API surface (Deno/TypeScript): routes, middleware, and services that
+bridge to the CLI and event bus.
+
+**Purpose:** Programmatic HTTP access to runs, memory, learning, and events.
+
+**Key files:**
+- `server.ts`, `mod.ts`, `client.ts` - Server, module entry, client.
+- `routes/` - `events.ts`, `health.ts`, `learning.ts`, `memory.ts`,
+  `sessions.ts`, `tasks.ts`.
+- `middleware/` - `auth.ts`, `cors.ts`, `error.ts`, `timing.ts`.
+- `services/` - `cli-bridge.ts`, `event-bus.ts`, `learning-collector.ts`,
+  `state-notifications.ts`, `state-watcher.ts`.
+- `types/` - `api.ts`, `events.ts`, `memory.ts`.
+- `openapi.yaml` - API specification.
+
+**Public interface:**
+- HTTP routes documented in `openapi.yaml`.
+
+**Dependencies:**
+- `autonomy/` CLI via `cli-bridge.ts`.
+- `events/` via `event-bus.ts`.
+- `memory/` via the memory route.
+
+---
+
+## events/
+
+The unified event bus. Multi-language so any component can emit and consume
+events.
+
+**Purpose:** Decouple components via a shared event stream.
+
+**Key files:**
+- `bus.py` - Python event bus.
+- `bus.ts` - TypeScript event bus.
+- `emit.sh` - Bash helper for emitting events.
+
+**Public interface:**
+- `emit`/subscribe APIs in each language binding.
+
+**Dependencies:**
+- Consumed by `autonomy/`, `api/`, and `dashboard/`.
+
+---
+
+## agents/
+
+The agent type registry and installation tooling.
+
+**Purpose:** Define the specialized agent roles the orchestrator adopts per
+phase.
+
+**Key files:**
+- `types.json` - Agent type definitions (41 agent types across 8 domains).
+- `hub_install.py` - Agent hub install.
+- `managed_registry.py` - Managed agent registry.
+
+**Public interface:**
+- Agent type definitions consumed during prompt construction.
+
+**Dependencies:**
+- Consumed by `autonomy/` (prompt building) and `loki-ts/`.
+
+---
+
+## skills/
+
+On-demand skill modules following the progressive-disclosure architecture
+(v3.0). Loaded selectively by the orchestrator.
+
+**Purpose:** Provide modular operational knowledge without bloating the core
+skill file.
+
+**Key files:**
+- `00-index.md` - Module selection rules and routing.
+- `quality-gates.md` - The canonical 8-gate table and RARV-C flags.
+- `model-selection.md`, `providers.md`, `healing.md`, `testing.md`,
+  `production.md`, `troubleshooting.md`, `agents.md`, `artifacts.md`,
+  `patterns-advanced.md`, `parallel-workflows.md`, `github-integration.md`,
+  `sdlc-fleet.md`, `memory.md`, `documentation.md`, `compound-learning.md`,
+  `magic-modules.md`, `mirofish-integration.md`, `openspec-integration.md`.
+
+**Dependencies:**
+- Referenced by `SKILL.md` and read at runtime by the orchestrator.
+
+---
+
+## references/
+
+Detailed reference documentation backing the slim skill modules.
+
+**Purpose:** Deep-dive docs for patterns, research foundations, and subsystems.
+
+**Key files:**
+- `core-workflow.md`, `sdlc-phases.md`, `task-queue.md`, `deployment.md`.
+- `legacy-healing-patterns.md`, `quality-control.md`, `confidence-routing.md`.
+- `memory-system.md`, `mcp-integration.md`, `multi-provider.md`.
+- `openai-patterns.md`, `lab-research-patterns.md`, `advanced-patterns.md`,
+  `tool-orchestration.md`, `agent-types.md`, `competitive-analysis.md`,
+  `cursor-learnings.md`, `prompt-repetition.md`, `business-ops.md`,
+  `invariant-checks.md`, `magic-modules-patterns.md`,
+  `magic-rarv-integration.md`, `production-patterns.md`.
+
+**Dependencies:**
+- Linked from `skills/` and `CLAUDE.md`.
+
+---
+
+## templates/
+
+PRD templates per project archetype. Used to bootstrap specs.
+
+**Purpose:** Give users a starting PRD shaped to their project type.
+
+**Key files:**
+- One template per archetype: `saas-starter.md`, `cli-tool.md`,
+  `discord-bot.md`, `slack-bot.md`, `rest-api.md`, `rest-api-auth.md`,
+  `api-only.md`, `microservice.md`, `e-commerce.md`, `blog-platform.md`,
+  `ai-chatbot.md`, `chrome-extension.md`, `mobile-app.md`, `game.md`,
+  `data-pipeline.md`, `web-scraper.md`, `dashboard.md`, `npm-library.md`,
+  `static-landing-page.md`, `simple-todo-app.md`, `full-stack-demo.md`.
+- `clusters/` - Grouped template clusters.
+
+**Dependencies:**
+- Consumed by `loki quickstart` and `loki start`.
+
+---
+
+## benchmarks/
+
+The SWE-bench and HumanEval benchmark harness.
+
+**Purpose:** Measure Loki's performance on standard coding benchmarks.
+
+**Key files:**
+- `run-benchmarks.sh` - Entry point (`humaneval`, `swebench`).
+- `embedding-benchmark.py`, `prepare-submission.sh` - Embedding bench and
+  submission prep.
+- `datasets/`, `tasks/`, `results/`, `swebench/`, `swebench-pro-pilot/`,
+  `magic-ab/`, `bench/` - Data, tasks, and outputs.
+- `SCHEMA-adapter.md`, `SCHEMA-result.md`, `submission-template/` - Schemas.
+
+**Public interface:**
+- `./benchmarks/run-benchmarks.sh humaneval|swebench --execute --loki`.
+
+**Dependencies:**
+- `autonomy/` CLI for executing builds.
+
+---
+
+## plugins/
+
+Claude Code plugin packaging and marketplace metadata.
+
+**Purpose:** Distribute Loki Mode as a Claude Code plugin.
+
+**Key files:**
+- `loki-mode/.claude-plugin/plugin.json` - Plugin manifest (version pinned to
+  `VERSION`).
+- `.claude-plugin/marketplace.json` (repo root) - Marketplace entry.
+
+**Dependencies:**
+- Packages `SKILL.md`, `skills/`, and `references/`.
+
+---
+
+## Cross-cutting state: `.loki/`
+
+Not a source directory, but the integration substrate. The orchestrator,
+dashboard, API, memory, and MCP server all communicate through filesystem
+state under `.loki/` (session, queue, memory, checkpoints, findings, metrics,
+healing artifacts, verify evidence). This file-based contract is what keeps the
+bash route and the loki-ts runner interchangeable.

package/docs/DEPLOYMENT.md

@@ -69,7 +69,7 @@ Better, for anything real: set `secrets.create=false` and
 External Secrets Operator or a Vault injector. Values passed with `--set` land
 in Helm release history and often in a git-tracked values file.
 
-Compose: put both in `.env` next to `docker-compose.yml`.
+Compose: put both in `.env` at the repo root (`docker/docker-compose.yml` reads `../.env`).
 
 ```
 GITHUB_WEBHOOK_SECRET=<that value>
@@ -168,7 +168,7 @@ Then watch the worker:
 
 ```bash
 kubectl logs -l app.kubernetes.io/component=worker -f     # Kubernetes
-docker compose --profile service logs -f worker           # Compose
+docker compose -f docker/docker-compose.yml --profile service logs -f worker           # Compose
 ```
 
 You are looking for `[queue-consumer] starting build: spec=owner/repo#N`.
@@ -191,7 +191,7 @@ kubectl exec -it deploy/loki-redis-master -- \
 Compose:
 
 ```bash
-docker compose --profile service exec redis \
+docker compose -f docker/docker-compose.yml --profile service exec redis \
   redis-cli RPUSH loki-builds 'owner/repo#123'
 ```
 
@@ -256,7 +256,7 @@ ground manually today.
 ## Kubernetes (Helm)
 
 No `helm dependency build` step: the chart has no subchart dependencies. Redis
-is a plain Deployment on `redis:7-alpine`, the same image `docker-compose.yml`
+is a plain Deployment on `redis:7-alpine`, the same image `docker/docker-compose.yml`
 uses.
 
 The default image tag is the chart's `appVersion`, which tracks `VERSION` and so
@@ -457,21 +457,21 @@ cluster is a NAT gateway, firewall or proxy you run.
 ## Single node (Docker Compose)
 
 ```bash
-cp .env.example .env
+cp docker/.env.example .env
 # set GITHUB_WEBHOOK_SECRET and ANTHROPIC_API_KEY
 
-docker compose --profile service up -d
-docker compose --profile service ps
+docker compose -f docker/docker-compose.yml --profile service up -d
+docker compose -f docker/docker-compose.yml --profile service ps
 ```
 
 The `service` profile is what separates the build service from the one-shot
-path. Without it, `docker compose run loki start prd.md` still does exactly
+path. Without it, `docker compose -f docker/docker-compose.yml run loki start prd.md` still does exactly
 what it always did -- one build, right now, in the current directory.
 
 Scale workers:
 
 ```bash
-docker compose --profile service up -d --scale worker=4
+docker compose -f docker/docker-compose.yml --profile service up -d --scale worker=4
 ```
 
 Same tenancy caveat as Kubernetes: each worker gets its own named volume, and