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Swann"},"license":"MIT","homepage":"https://cielolimitada.com/moflo","keywords":["moflo","claude","claude-code","anthropic","ai-agents","agent-orchestration","mcp","model-context-protocol","cli","developer-tools","workflow","orchestration"],"repository":{"url":"git+https://github.com/eric-cielo/moflo.git","type":"git"},"description":"MoFlo — AI agent orchestration for Claude Code. A standalone, opinionated toolkit with semantic memory, learned routing, gates, spells, and the /flo issue-execution skill.","maintainers":[{"name":"ericswann","email":"eric@ericswann.org"}],"readme":"<p align=\"center\">\n  <img src=\"https://raw.githubusercontent.com/eric-cielo/moflo/main/docs/Moflo_wide.png?v=7\" alt=\"MoFlo\" />\n</p>\n\n# MoFlo\n\n**A standalone, opinionated AI agent orchestration toolkit for Claude Code, optimized for local development.**\n\n**[Website](https://cielolimitada.com/moflo)** · [npm](https://www.npmjs.com/package/moflo) · [GitHub](https://github.com/eric-cielo/moflo)\n\n## TL;DR\n\nMoFlo makes Claude Code remember what it learns, check what it knows before exploring files, and get smarter over time — all automatically. Install it, run `flo init`, restart Claude Code, and everything just works: your docs and code are indexed on session start so Claude can search them instantly, gates prevent Claude from wasting tokens on blind exploration, task outcomes feed back into routing so it picks the right agent type next time, and context depletion warnings tell you when to start a fresh session. No configuration, no API keys, no cloud services — it all runs locally on your machine.\n\n## Quickstart\n\n```bash\nnpm install --save-dev moflo\nflo init\n```\n\nRestart Claude Code. That's it — memory, indexing, gates, and routing are all active.\n\nOr — just ask Claude to install MoFlo into your project and initialize it!\n\nTo verify everything is running, run the **`/healer`** skill inside Claude Code (or `flo healer` from the CLI) after restarting — it runs full diagnostics. If anything fails, run **`/healer --fix`** to automatically fix issues.\n\n## Next Step: Consult the Eldar\n\nAfter installing moflo, the single highest-leverage thing you can do for the best experience is run **`/eldar`** inside a Claude Code session.\n\nWhere `/healer` (or `flo healer` from the CLI) verifies that *moflo itself* is wired up correctly, **`/eldar` audits how Claude is set up to actually use your project** — guidance docs, CLAUDE.md, memory namespaces, hook/MCP wiring, model routing, and whether every technology in your stack (TypeScript, Python, Rust, Go, etc.) has matching guidance for Claude to lean on. The stack → guidance cross-reference alone is often the difference between *\"Claude feels lost in this codebase\"* and *\"Claude knows this codebase\"*.\n\n```\n/eldar          # Read-only audit; categorized findings, severity-ranked\n/eldar --fix    # Interactive triage — pick what to fix and the Eldar walk you through it\n```\n\nRun it on day one in any new project, any time Claude feels off, or as a periodic health check. Outside of the core install, this is the most impactful thing moflo offers — full details in the **`/eldar`** section [further down](#eldar--consult-the-eldar-project-setup-audit--wizard).\n\n## Opinionated Defaults\n\nMoFlo makes deliberate choices so you don't have to:\n\n- **Fully self-contained** — No external services, no cloud dependencies, no API keys. Everything runs locally on your machine.\n- **Minimal dependencies** — small runtime dep set, all WASM or prebuilt binaries. No native compilation, no `node-gyp`, no platform-specific build steps.\n- **Node.js runtime** — Targets Node.js specifically. All scripts, hooks, and tooling are JavaScript/TypeScript. No Python, no Rust binaries, no native compilation.\n- **node:sqlite (built-in)** — The memory database uses Node 22's built-in SQLite engine. No `better-sqlite3` native bindings to compile, no WASM round-trip, no platform-specific build steps. Works identically on Windows, macOS, and Linux.\n- **Neural embeddings by default** — 384-dimensional embeddings using `all-MiniLM-L6-v2`. No hash fallback, no peer-optional setup, no install prompts — real semantic search works out of the box. A `postinstall` step trims the embedding runtime to your platform and strips GPU-only libraries the runtime never loads, reclaiming roughly 340 MB on Linux and 150 MB on Windows from a fresh install. Set `MOFLO_NO_PRUNE=1` to skip the trim, or `ONNXRUNTIME_NODE_INSTALL_CUDA=true` to keep CUDA GPU support.\n- **Full learning stack wired up OOTB** — All configured and functional from `flo init`, no manual setup:\n  - **SONA** (Self-Optimizing Neural Architecture) — learns from task trajectories\n  - **MicroLoRA** — fast rank-2 weight adaptations from successful patterns\n  - **EWC++** (Elastic Weight Consolidation) — prevents catastrophic forgetting across sessions\n  - **HNSW Vector Search** — fast nearest-neighbor search over your knowledge base\n  - **Semantic Routing** — maps tasks to the right agent via learned patterns (ReasoningBank)\n  - **Trajectory Persistence** — outcomes survive across sessions\n  - All local, no GPU, no API keys, no external services.\n- **Memory-first** — Claude must search what it already knows before exploring files. Enforced by hooks, not just instructions.\n- **Task registration before agents** — Sub-agents can't spawn until work is tracked. Prevents runaway agent proliferation.\n- **Learned routing** — Task outcomes feed back into the routing system automatically. No manual configuration needed — it gets smarter with use.\n- **Incremental indexing** — Guidance and code map indexes run on every session start but skip unchanged files. Fast after the first run.\n- **Claude Code is the only target** — MoFlo is built and shipped for Anthropic's Claude Code (CLI, IDE extensions, web). It is **not** a Claude Desktop integration: nothing reads from or writes to `~/.claude/claude_desktop_config.json` or `%APPDATA%/Claude/`, and adding paths there is always a bug. The MCP tools, memory system, and hooks could in principle work with any MCP-capable client, but Claude Code is the *only* surface we author for, test against, or accept bug reports on.\n- **GitHub-oriented** — The `/flo` skill, PR automation, and issue tracking are built around GitHub. With Claude's help, you can adapt them to your own issue tracker and source control system.\n- **Cross-platform** — Works identically on macOS, Linux, and Windows.\n\n## Features\n\n| Feature | What It Does |\n|---------|-------------|\n| **Semantic Memory** | 384-dim domain-aware embeddings. Store knowledge, search it instantly. |\n| **Reflection** | Distills durable lessons from your sessions into searchable memory — automatically (auto-meditate), or on demand with `/meditate`. |\n| **Cross-Install Sharing** | Durable `learnings` follow you across git worktrees **automatically** (no setup) — and across your own machines or a whole team via `flo memory sync` or a git-tracked artifact. Structural namespaces stay local. [Full documentation →](.claude/guidance/shipped/moflo-cross-install-memory-sharing.md) |\n| **Code Navigation** | Indexes your codebase structure so Claude can answer \"where does X live?\" without Glob/Grep. |\n| **Guidance Indexing** | Chunks your project docs (`.claude/guidance/`, `docs/`) and makes them searchable. |\n| **Gates** | Enforces memory-first and task-creation patterns via Claude Code hooks. Prevents Claude from skipping steps. |\n| **Learned Routing** | Routes tasks to the right agent type. Learns from outcomes — gets better over time. |\n| **Spell Engine** | Define multi-step automations as YAML — shell commands, agent spawns, conditionals, loops, memory ops. [Full documentation →](docs/SPELLS.md) |\n| **`/flo` Skill** | Execute GitHub issues through a full process: research → enhance → implement → test → simplify → PR. (Also available as `/fl`.) |\n| **Spec-Driven Development** | `/flo -sd` runs a spec → plan → implement → verify cycle with memory-indexed artifacts. Opt-in, but once armed **both halves are enforced**: an implement gate blocks source edits until the plan is reviewed, and verify-before-done gates the PR. Human review is optional (`sdd.human_checkpoints`, off by default); spec+plan auto-embed into the PR body (`embed_in_pr`), or point `sdd.specs_dir` at a tracked path. [Details →](#spec-driven-development-sdd) |\n| **Context Tracking** | Monitors context window usage (FRESH → MODERATE → DEPLETED → CRITICAL) and advises accordingly. |\n| **Cross-Platform** | Works on macOS, Linux, and Windows. |\n\n## Getting Started\n\n### 1. Install and init\n\n```bash\nnpm install --save-dev moflo\nflo init\n```\n\n`flo init` automatically scans your project to find where your guidance, code, and tests live, then writes the results into `moflo.yaml`. It looks for:\n\n| What | Directories it checks | Default if none found |\n|------|----------------------|----------------------|\n| **Guidance** | `.claude/guidance`, `docs/guides`, `docs`, `architecture`, `adr`, `.cursor/rules` | `.claude/guidance` |\n| **Source code** | `src`, `packages`, `lib`, `app`, `apps`, `services`, `server`, `client` | `src` |\n| **Tests** | `tests`, `test`, `__tests__`, `spec`, `e2e`, plus `__tests__` dirs inside `src/` | `tests` |\n| **Languages** | Scans detected source dirs for file extensions | `.ts`, `.tsx`, `.js`, `.jsx` |\n\nIt also generates:\n\n| Generated File | Purpose |\n|----------------|---------|\n| `moflo.yaml` | Project config with detected guidance/code locations |\n| `.claude/settings.json` | Gate hooks for Claude Code |\n| `.claude/skills/flo/` | The `/flo` issue execution skill (also `/fl`) |\n| `CLAUDE.md` section | Teaches Claude how to use MoFlo |\n| `.gitignore` entries | Excludes MoFlo state directories |\n\nIn interactive mode (`flo init` without `--yes`), it shows what it found and lets you confirm or adjust before writing.\n\n#### Migrating from Claude Flow / Ruflo\n\nIf `flo init` detects an existing `.claude/settings.json` or `.claude-flow/` directory (from a prior Claude Flow or Ruflo installation), it treats the project as already initialized and runs in **update mode** — merging MoFlo's hooks and configuration into your existing setup without overwriting your data. Specifically:\n\n- **Hooks** — If your `.claude/settings.json` already has MoFlo-style gate hooks (`flo gate`), the hooks step is skipped. Otherwise, MoFlo's hooks are written into the file (existing non-MoFlo hooks are not removed).\n- **MCP servers** — MoFlo registers itself as the `moflo` server in `.mcp.json`. If you had `claude-flow` or `ruflo` MCP servers configured previously, those entries remain untouched — you can remove them manually once you've verified MoFlo is working. The `/healer` skill (or `flo healer` from the CLI) checks for the `moflo` server specifically.\n- **Config files** — `moflo.yaml`, `CLAUDE.md`, and `.claude/skills/flo/` follow the same skip-if-exists logic. Use `--force` to regenerate them.\n\nTo force a clean re-initialization over an existing setup:\n\n```bash\nflo init --force\n```\n\n#### First-run heads-up: brief CPU spike during initial indexing\n\nThe **very first time** MoFlo runs in your project — typically right after `flo init` and the next session start — it builds the initial guidance, code map, and test indexes from scratch and generates 384-dim embeddings for every chunk. On a medium-sized project this takes **one to a few minutes** and you may see elevated CPU during that window. It runs in the background, so you can start working immediately; you just might hear your fans for a bit.\n\nAfter that first pass, indexing is **incremental and lazy** — every subsequent session start only re-processes files that actually changed since the last run, which typically finishes in under a second with no perceptible CPU activity. The big one-time cost is a deliberate trade: pay it once, then every future session opens with your project already searchable by meaning.\n\n> **Tip:** Let that initial indexing finish before running **`/healer`** (or `flo healer`). Healer's embeddings and semantic-quality checks expect the indexes to exist — if you run it mid-build it may flag warnings that resolve themselves the moment indexing completes.\n\n### 2. Review your guidance and code settings\n\nOpen `moflo.yaml` to see what init detected. The two key sections:\n\n**Guidance** — documentation that helps Claude understand your project (conventions, architecture, domain context):\n\n```yaml\nguidance:\n  directories:\n    - .claude/guidance    # project rules, patterns, conventions\n    - docs                # general documentation\n```\n\n**Code map** — source files to index for \"where does X live?\" navigation:\n\n```yaml\ncode_map:\n  directories:\n    - src                 # your source code\n    - packages            # shared packages (monorepo)\n  extensions: [\".ts\", \".tsx\"]\n  exclude: [node_modules, dist, .next, coverage]\n```\n\n**Tests** — test files to index for \"what tests cover X?\" reverse mapping:\n\n```yaml\ntests:\n  directories:\n    - tests               # your test files\n    - __tests__            # jest-style test dirs\n  patterns: [\"*.test.*\", \"*.spec.*\", \"*.test-*\"]\n  extensions: [\".ts\", \".tsx\", \".js\", \".jsx\"]\n  exclude: [node_modules, coverage, dist]\n  namespace: tests\n```\n\nMoFlo chunks your guidance files into semantic embeddings, indexes your code structure, and maps test files back to their source targets — so Claude searches your knowledge base before touching any files. Adjust these directories to match your project:\n\n```yaml\n# Monorepo with shared docs\nguidance:\n  directories: [.claude/guidance, docs, packages/shared/docs]\ncode_map:\n  directories: [packages, apps, libs]\n\n# Backend + frontend\ncode_map:\n  directories: [server/src, client/src]\n```\n\n### 3. Index and verify\n\n```bash\nflo memory index-guidance    # Index your guidance docs\nflo memory code-map          # Index your code structure\nflo healer                   # Verify everything works (alias: flo doctor)\n```\n\nBoth indexes run automatically at session start after this, so you only need to run them manually on first setup or after major structural changes. The first index may take a minute or two on large codebases (1,000+ files) but runs in the background — you can start working immediately. Subsequent indexes are incremental and typically finish in under a second. To reindex everything at once:\n\n```bash\nflo memory refresh           # Reindex all content, rebuild embeddings, cleanup, vacuum\n```\n\n## Auto-Indexing\n\nMoFlo automatically indexes three types of content on every session start, so your AI assistant always has up-to-date knowledge without manual intervention.\n\n### What gets indexed\n\n| Index | Content | What it produces | Namespace |\n|-------|---------|------------------|-----------|\n| **Guidance** | Markdown files in your guidance directories (`.claude/guidance/`, `docs/`, etc.) | Chunked text with 384-dim semantic embeddings — enables natural-language search across your project documentation | `guidance` |\n| **Code map** | Source files in your code directories (`src/`, `packages/`, etc.) | Structural index of exports, classes, functions, and types — enables \"where does X live?\" navigation without Glob/Grep | `code-map` |\n| **Tests** | Test files matching configured patterns (`*.test.*`, `*.spec.*`) | Reverse mapping from test files to their source targets — enables \"what tests cover X?\" lookups | `tests` |\n\n### How it works\n\n1. **Session start hook** — When Claude Code starts a new session, MoFlo's `SessionStart` hook launches the indexers sequentially in a single background process. This runs silently — you can start working immediately.\n2. **Incremental** — Each indexer tracks file modification times. Only files that changed since the last index run are re-processed. The first run on a large codebase may take a minute or two; subsequent runs typically finish in under a second.\n3. **Embedding generation** — Guidance chunks are embedded using MiniLM-L6-v2 (384 dimensions, WASM). These vectors are stored in the SQLite memory database and used for semantic search.\n4. **No blocking** — The indexers run in the background and don't block your session from starting. You can begin working immediately.\n\n### Configuration\n\nEach indexer can be toggled independently in `moflo.yaml`:\n\n```yaml\nauto_index:\n  guidance: true     # Index docs on session start\n  code_map: true     # Index code structure on session start\n  tests: true        # Index test files on session start\n```\n\nSet any to `false` to disable that indexer. The underlying data remains in memory — you just stop refreshing it automatically. You can still run indexers manually:\n\n```bash\nflo memory index-guidance    # Manual guidance reindex\nflo memory code-map          # Manual code map reindex\nflo memory refresh           # Reindex everything + rebuild embeddings + vacuum\n```\n\n### Why this matters\n\nWithout auto-indexing, Claude Code starts every session with a blank slate — it doesn't know what documentation exists, where code lives, or what tests cover which files. It resorts to Glob/Grep exploration, which burns tokens and context window on rediscovery.\n\nWith auto-indexing, Claude can search semantically (\"how does auth work?\") and get relevant documentation chunks ranked by similarity, or ask \"where is the user model defined?\" and get a direct answer from the code map — all without touching the filesystem.\n\n## Learning From Your Sessions\n\nMoFlo turns the work you do into durable knowledge. A lesson worth keeping — a reusable pattern, a gotcha that cost you an hour, a decision and the rationale behind it — lands in the `learnings` memory namespace, where it's embedded and semantically searchable in every future session. Two paths feed that namespace: one you trigger, one that runs on its own.\n\n### `/meditate` — deliberate retrospective\n\nRun **`/meditate`** at the end of a meaningful chunk of work. It reviews the session, distills the handful of lessons that would help a *future* session on a *different* task, deduplicates them against what's already stored, and writes the survivors to `learnings`. It's the curated pass — you choose when to capture, and it keeps only high-signal items (an empty reflection is a valid result, not a failure to pad).\n\n```\n/meditate                  # Review the whole session and store durable lessons\n/meditate --preview        # Show the candidate lessons without writing anything\n/meditate <focus>          # Scope the retrospective to one thread, e.g. \"the auth refactor\"\n```\n\n### Auto-meditate — the automatic counterpart\n\n**Auto-meditate** does the same job without being asked. While you work, a lightweight hook notices when a durable lesson emerges — a correction, an error you fixed, a decision you made. At the next session start, a brief background pass distills those into `learnings` using the same durability bar and dedup-then-store protocol as `/meditate`. It reuses your existing Claude Code session (no extra API key), runs in the background, and **ships on by default**.\n\n```yaml\nauto_meditate:\n  enabled: true            # Set to false to opt out — /meditate still works manually\n```\n\nThe two are complementary: auto-meditate is the always-on safety net, `/meditate` is the deliberate, curated pass. Both write to the same `learnings` namespace and both deduplicate, so neither pollutes the other — and anything they store is available to semantic search from then on.\n\n### Sharing learnings across installations\n\nThe `learnings` (and `knowledge`) namespaces are the **durable** slice of memory — user-authored and worth carrying across checkouts. The rest of the DB (code-map, guidance chunks, run state) is structural or ephemeral and rebuilds cheaply, so it stays local. For ongoing sync MoFlo shares only the durable slice — **never *live-shares* the whole `moflo.db`** between two daemons, which would make each daemon's in-memory search index diverge.\n\nPick the mechanism by topology:\n\n| You want to share across… | Use | How |\n|---------------------------|-----|-----|\n| Git worktrees / Conductor workspaces (same machine) | **Automatic** — nothing to set | Learnings converge across worktrees at session-start (stored at `<git-common-dir>/moflo/durable.db`). Override with `memory.durable_path`; opt out with `memory.worktree_sharing: false` |\n| Your own laptop + desktop + CI | `flo memory sync --to/--from <file>` | Export to a synced folder (Dropbox/iCloud) or a copied file, import on the other machine |\n| A whole team on one repo | `flo memory team-export` → commit `.moflo/shared/learnings.jsonl` | Teammates' session-start import-merges it after `git pull` (first-write-wins; author provenance retained) |\n| A fresh workspace that must be ready fast | `flo memory backup/restore` or `memory.hydrate_from` | Seed a new workspace from a **whole-DB snapshot** so it's searchable on session one — no cold reindex. Safe because each workspace owns its own copy (a one-time restore, not live sharing) |\n\nVerify your setup with `flo doctor -c shared-db` (it warns if you've accidentally pointed at a full `moflo.db` for *live* sharing). Full guide: [`moflo-cross-install-memory-sharing.md`](.claude/guidance/shipped/moflo-cross-install-memory-sharing.md).\n\n## The Gate System\n\nMoFlo installs Claude Code hooks that run on every tool call. Together, these gates create a **feedback loop** that prevents Claude from wasting tokens on blind exploration and ensures it builds on prior knowledge.\n\n### Gates explained\n\n| Gate | What it enforces | When it triggers | Why it matters |\n|------|-----------------|------------------|----------------|\n| **Memory-first** | Claude must search the memory database before using Glob, Grep, or Read on guidance files | Before every Glob/Grep call, and before Read calls targeting `.claude/guidance/` | Prevents the AI from re-exploring files it (or a previous session) already indexed. Forces it to check what it knows first, saving tokens and context window. |\n| **TaskCreate-first** | Claude must call TaskCreate before spawning sub-agents via the Task tool | Before every Task (agent spawn) call | Ensures every piece of delegated work is tracked. Prevents runaway agent proliferation where Claude spawns agents without a clear plan. |\n| **Task-status** *(blocks by default)* | The task list Claude opened must reflect reality before the PR — every task closed, deleted, or explicitly acknowledged as deferred | Before `gh pr create`, whenever the session opened tasks and left some open | A stale task list is worse than none: it reports as not-started work that is about to merge. Every other step here is gated on an artifact; this is the one that gates what the *user is shown*. Deliberate deferrals stay legitimate — the block prints a one-command acknowledgement. Set `task_status_gate: warn` to report without blocking, or `off`; `task_create_first: false` disables both halves. |\n| **Context tracking** | Tracks conversation length and warns about context depletion | On every user prompt (UserPromptSubmit hook) | As conversations grow, AI quality degrades. MoFlo tracks interaction count and assigns a bracket (FRESH → MODERATE → DEPLETED → CRITICAL), advising Claude to checkpoint progress or start a fresh session before quality drops. |\n| **Routing** | Analyzes each prompt and recommends the optimal agent type and model tier | On every user prompt (UserPromptSubmit hook) | Saves cost by suggesting haiku for simple tasks, sonnet for moderate ones, opus for complex reasoning — without you having to think about model selection. |\n| **Verify-before-done** *(on by default)* | Claude must verify the change end-to-end (the `/verify` skill) before `gh pr create` | Before `gh pr create` (docs-only diffs exempt) | Enforces \"prove it works before done.\" On by default since #1294 (`/flo` delegates to `/verify` and reuses its test run — no double verify). Opt out with `verify_before_done: false` or `--no-verify`. Pairs with the [Spec-Driven Development](#spec-driven-development-sdd) cycle, which gives verification its acceptance criteria. |\n| **Implement gate (SDD front half)** | When a run is armed for SDD, Claude must author a spec and get its plan reviewed before editing source | Before every source `Write`/`Edit`, when `-sd`/`sdd.default` armed the run | Makes the SDD front half enforced, not advisory (#1297): a spec-gated run can't skip to implementation. No-op for non-SDD work. Opt out per-project with `sdd_gate: false`, per-run with `--no-sdd`. Pairs with verify-before-done to gate both ends of the cycle. |\n\n### Smart classification\n\nThe memory-first gate doesn't blindly block every request. It classifies each prompt:\n\n- **Simple directives** (e.g., \"commit\", \"yes\", \"continue\", \"looks good\") — skip the gate entirely, no memory search required\n- **Task-oriented prompts** (e.g., \"fix the auth bug\", \"add pagination to the API\") — gate enforced, must search memory first\n\n### Escape hatch\n\nPrefix any prompt with `@@` to bypass the memory-first gate for that turn. Useful for conversational questions, thinking out loud, or discussions that don't need prior context:\n\n```\n@@ what do you think about this approach?\n@@ question — is there a better way to handle auth tokens?\n```\n\nThe `@@` prefix is stripped before Claude sees the prompt, so it won't affect the response.\n\n### Disabling gates\n\nAll gates are configurable in `moflo.yaml`:\n\n```yaml\ngates:\n  memory_first: true          # Set to false to disable memory-first enforcement\n  task_create_first: true     # Set to false to disable TaskCreate enforcement (disables task_status_gate too)\n  task_status_gate: block     # Open tasks block `gh pr create`; warn → report only; off → silent\n  context_tracking: true      # Set to false to disable the context-usage notice\n  # context_limit: 200k       # Optional. Your model's window, so the notice can quote a %.\n                              # Unset (default) = report raw tokens; moflo never guesses a window.\n  verify_before_done: true    # On by default (#1294); set false to skip /verify before `gh pr create`\n```\n\nYou can also disable individual hooks in `.claude/settings.json` by removing the corresponding hook entries.\n\n## The `/flo` Skill\n\nInside Claude Code, the `/flo` (or `/fl`) slash command drives GitHub issue execution:\n\n```\n/flo <issue>                  # Full process (research → implement → test → PR)\n/flo -t <issue>               # Ticket only (research and update ticket, then stop)\n/flo -r <issue>               # Research only (analyze issue, output findings)\n/flo -s <issue>               # Swarm mode (multi-agent coordination)\n/flo -h <issue>               # Hive-mind mode (consensus-based coordination)\n/flo -n <issue>               # Normal mode (default, single agent, no swarm)\n/flo -w <issue>               # Worktree: run the work in a fresh git worktree (aliases: -wt, --worktree)\n/flo -sd <issue>              # SDD: spec → plan → implement → verify (implies --verify)\n/flo -v <issue>               # Verify-before-done only (no spec/plan front-half)\n/flo -m <issue>               # Auto-merge the PR once required checks pass\n```\n\nFlags compose: e.g. `/flo -sd -m <issue>` runs the SDD cycle and auto-merges. Each modifier has a `--no-*` form (`--no-sdd`, `--no-verify`, `--no-merge`) to override a `moflo.yaml` default for a single run — including `--no-verify`, since verify-before-done is on by default. For full options and details, type `/flo` with no arguments — Claude Code will display the complete skill documentation. Also available as `/fl`.\n\n### Provisioned worktrees (`-w` / `flo worktree`)\n\nRunning two tickets at once means two worktrees, and a bare `git worktree add` gives you a valid\ncheckout that you cannot actually run: no `node_modules`, none of your gitignored `.env` files, and\ndev servers that fight the primary checkout over the same ports. `/flo -w` drives `flo worktree add`,\nwhich creates the worktree **and** provisions it.\n\nProvisioning is opt-in per project. **With no `worktree:` block in `moflo.yaml`, `flo worktree add`\ncreates the worktree and provisions nothing** — exactly what a plain `git worktree add` would do.\n\n```yaml\nworktree:\n  dir: ../myrepo-worktrees   # default: <repo-parent>/<repo>-worktrees\n  copy: [\".env\", \".env.*\"]   # gitignored files copied from the primary checkout\n  link: [\"node_modules\"]     # symlinked (junctioned on Windows) from the primary checkout\n  setup: \"npm ci\"            # run inside the new worktree after copy/link\n```\n\n| Key | Reach for it when | Watch out for |\n|-----|-------------------|---------------|\n| `copy` | A fresh checkout is missing gitignored config your build needs | It relocates **secrets** outside the repo, and outside its `.gitignore`. Sources must live inside the primary checkout — `../secrets` is refused. |\n| `link` | `node_modules` is large and you are not using npm workspaces | A symlinked root `node_modules` is fragile under npm/yarn workspaces — prefer `setup: npm ci` there. An existing path is never clobbered. |\n| `setup` | Install or build steps must run per workspace | A non-zero exit marks the provision failed but leaves the worktree in place. |\n\n**Ports.** MoFlo cannot rewrite your hardcoded ports — it has no way to know which files hold them.\nInstead each worktree gets a small integer, unique among live worktrees and reused when one is\nremoved, exported to the `setup` command as `MOFLO_WORKTREE_INDEX`. Offset your own ports from it:\n\n```yaml\nworktree:\n  setup: \"npm ci && node -e \\\"require('fs').writeFileSync('.env.local','PORT='+(3000+Number(process.env.MOFLO_WORKTREE_INDEX)*20))\\\"\"\n```\n\n`flo worktree remove` refuses a tree with uncommitted changes unless you pass `--force`, and names\nany gitignored files it discarded that provisioning did not create. MoFlo's own\n`.moflo/worktree.json` never counts as \"uncommitted work\" — otherwise every worktree it created\nwould demand `--force` — but un-pushed specs under `.moflo/specs/` do.\n\nMemory needs no setup at all: durable learnings already converge across a repo's worktrees\nautomatically — see [Sharing learnings across installations](#sharing-learnings-across-installations).\n\n#### Running it inside a Claude session\n\n`flo worktree` is a plain CLI command with no MCP wrapper, so it works the same whether you type it\nin a terminal or Claude runs it through Bash. `/flo -w` takes the second path — that is all the flag\ndoes.\n\nOne thing to know if you drive it yourself from a session, and the reason `/flo -w` handles it for\nyou: **Claude Code resets the Bash working directory to the project root after every call.** Two\nconsequences, both silent when you get them wrong:\n\n```bash\n# ✗ the cd is gone by the next call — this resolves the WRONG repo\ncd path/to/repo\nflo worktree add feature/42-thing --json\n\n# ✓ bind the directory to the call\ncd path/to/repo && flo worktree add feature/42-thing --json\n```\n\n```bash\n# ✗ runs the tests in the PRIMARY checkout; the run goes green and the PR is empty\ncd \"$WORKTREE\"\nnpm test\n\n# ✓ bind it, or skip cd entirely where the tool supports it\ncd \"$WORKTREE\" && npm test\ngit -C \"$WORKTREE\" status\n```\n\n`flo worktree` resolves the repository from its working directory, so a call made from the wrong\nplace targets a different repository — usually reported as `Not a registered worktree of this repo`,\noccasionally as work landing somewhere you did not intend. When editing files in the worktree, use\nabsolute paths under the path `add` printed rather than repo-relative ones.\n\nRead the worktree location from `--json` rather than reconstructing it; the sibling-directory\nconvention lives in one tested function, and a second copy of that rule will drift from it.\n\nIf you are on a `flo` older than the skills synced into `.claude/` — which happens in a MoFlo source\ncheckout before a change is published, or when a global `flo` lags the project's devDependency —\nthe command reports `Unknown command: worktree`. `/flo -w` falls back to a plain `git worktree add`\nand tells you provisioning was skipped, rather than failing the run.\n\n### Spec-Driven Development (SDD)\n\n`/flo` can run the full **spec → plan → (review) → implement → verify** cycle — the 2026 agentic-coding pattern — with two independent modifiers. Turning SDD on is opt-in, but once a run is armed for it (via `-sd` or `sdd.default`) **both halves are enforced**: the front half by an implement gate, the back half by verify-before-done.\n\n- **`-sd` / `--sdd`** *(opt-in; enforced once on)* — author a **spec** (the *what* + acceptance criteria) and a **plan** (the *steps*) before implementing. When armed, the **`check-before-implement` gate blocks every source `Write`/`Edit`** until the spec exists and its plan is reviewed (#1297) — a run can't skip straight to code. Artifacts persist as Markdown at `<specs_dir>/<slug>/{spec,plan}.md` (default `.moflo/specs`) and are indexed into memory, so prior specs are searchable across sessions. Implies `--verify`.\n- **`-v` / `--verify`** *(on by default)* — the verify half: a normal run plus the [verify-before-done gate](#the-gate-system). It runs the **`/verify`** skill, which exercises the change end-to-end against its acceptance criteria and reports a per-criterion PASS/FAIL, reusing the run's own tests (no double verify). Runs by default; `--no-verify` skips it. Separable from SDD, so you get \"prove it works\" without the spec ceremony.\n\n**Human review is optional and off by default.** moflo stays autonomous: the front half self-advances its spec/plan review checkpoints without stopping. Set `sdd.human_checkpoints: true` to sit in the loop and approve each artifact by hand before the cycle proceeds.\n\nBoth compose with execution mode (`-n`/`-s`/`-h`) and `--worktree`, and default from `moflo.yaml`:\n\n```yaml\nsdd:\n  default: false              # true → every /flo run uses the SDD cycle unless --no-sdd\n  specs_dir: .moflo/specs     # where spec/plan artifacts are written (see below)\n  human_checkpoints: false    # true → pause for human approval at spec & plan review (default: autonomous)\n  embed_in_pr: true           # true → append spec+plan to the PR body so reasoning is reviewable\ngates:\n  verify_before_done: true    # on by default (#1294); false → skip /verify unless -v. Per-run: --no-verify\n  sdd_gate: true              # on by default (#1297); false → don't enforce the spec→plan front half\n```\n\nOn upgrade, consumers with no `verify_before_done` key start enforcing verify-before-done; an explicit value is preserved. `sdd_gate` only bites when a run is actually armed for SDD, so non-SDD work is unaffected. Docs-only diffs are exempt, so a pure-docs PR is never blocked.\n\n**Where specs live — and making them reviewable.** By default spec/plan artifacts are written under `.moflo/specs`, which `flo init` gitignores — so they stay **local and never bloat source control** — and (with `embed_in_pr`, the default) the spec + plan are appended to the PR body, so the reasoning is reviewable in the PR **even while the files stay local**. If you'd rather source-control the artifacts, point `sdd.specs_dir` at a **tracked** path (e.g. `docs/specs` or `.specs`) and commit them normally; no gitignore surgery required — the two mechanisms compose. The path is written with `/` and resolved cross-platform. If you set it to a directory already covered by `guidance.directories`, moflo indexes the specs once (as guidance) rather than twice.\n\n`--sdd` implies `--verify` (a spec/plan without an enforced verify step drifts). Manage artifacts directly with `flo sdd` (`spec`, `plan`, `review`, `check`, `embed`, `list`), and start from a fuzzy idea with **`/commune`**, which can hand its synthesized spec straight into the SDD spine. Wiring status is reported by **`/healer`** (and `/eldar`).\n\n### Auto-merge\n\n- **`-m` / `--merge`** — after the PR is opened, await its merge preconditions and merge it, instead of stopping at \"PR opened\". Orthogonal to execution mode (`-n`/`-s`/`-h`), `--worktree`, and `--sdd`/`--verify`, and always runs **after** the quality gates (tests, simplify, learnings, verify) have let `gh pr create` through — so `--merge` never bypasses a gate.\n\nIt prefers GitHub-native auto-merge, falls back to poll-then-merge once required checks are green, and — when the *only* remaining blocker is review-required on a repo you administer (e.g. a solo repo where GitHub blocks self-approval) — auto-attempts an admin squash-merge. If an unattended admin merge is denied by Claude Code's permission classifier (headless/cron runs), it hands you a copy-paste command rather than looping. It re-confirms checks are green before any admin merge, and never `--admin` over a red or pending required check.\n\nDefault seeds from `moflo.yaml`; the per-run flag overrides, and `--no-merge` opts a single run out:\n\n```yaml\nmerge:\n  auto: false                 # true → every /flo run auto-merges its PR unless --no-merge\n```\n\n### Epic handling\n\nWhen you pass an issue number, `/flo` automatically checks if it's an epic — no extra flag needed. An issue is treated as an epic if any of these are true:\n\n- It has a label matching `epic`, `tracking`, `parent`, or `umbrella` (case-insensitive)\n- Its body contains a `## Stories` or `## Tasks` section\n- Its body has checklist-linked issues: `- [ ] #101`\n- Its body has numbered issue references: `1. #101`\n- The issue has GitHub sub-issues (via the API)\n\nWhen an epic is detected, `/flo` processes each child story sequentially — full process per story (research → implement → test → PR), one at a time, in the order listed.\n\nFor simple epics with independent stories, `/flo <epic>` is all you need. For complex features where you want state tracking, resume capability, and auto-merge between stories, use `flo epic` instead.\n\n### Feature Orchestration (`flo epic`)\n\n`flo epic` is the robust epic runner — it adds persistent state, resume from failure, and per-story auto-merge on top of `/flo`. It takes a GitHub epic issue number:\n\n```bash\nflo epic 42                                # Fetch epic #42, run all stories sequentially\nflo epic 42 --dry-run                      # Preview execution plan without running\nflo epic 42 --strategy auto-merge          # Per-story PRs with auto-merge between stories\nflo epic status 42                         # Check progress (which stories passed/failed)\nflo epic reset 42                          # Reset state for re-run\n```\n\n`flo epic` fetches the epic from GitHub, extracts child stories from checklists, numbered references, and `## Stories` / `## Tasks` sections, then runs each through `/flo` with state tracking. If a story fails, you can fix the issue and re-run `flo epic 42` — it resumes from where it left off, skipping already-passed stories. (`flo epic run 42` is an explicit alias for the same shorthand.)\n\n| | `/flo <epic>` | `flo epic <epic>` |\n|---|---|---|\n| **State tracking** | No | Yes (`epic-state` memory namespace) |\n| **Resume from failure** | No | Yes (skips passed stories) |\n| **Auto-merge PRs** | No | Yes (`--strategy auto-merge`) |\n| **Dry-run preview** | No | Yes |\n\n## Spells\n\n### What are spells?\n\nSpells are declarative YAML automations composed of pluggable step commands. They exist because shell scripts drift, ad-hoc prompts aren't reproducible, and CI/CD pipelines are the wrong tool for local automation. A spell is **deterministic** (same inputs → same steps), **reviewable** (a YAML file you read like a recipe), and **replayable** (re-cast it tomorrow and it behaves the same). Spells run from the CLI (`flo spell cast`), from an MCP tool call inside Claude Code, or on a schedule.\n\n### How do they work?\n\nEach cast goes through the same lifecycle:\n\n1. **Parse & validate** — YAML is parsed and every step's `config` is checked against its command's schema.\n2. **Resolve capabilities** — every step declares what it needs (`shell`, `net`, `fs:read`, `fs:write`, `memory`, `credentials`, `browser`, `agent`). Undeclared access is rejected before execution.\n3. **Execute the step graph** — steps run sequentially by default, or in parallel groups, with `depends_on` for ordering and `condition`/`loop` for flow control.\n4. **Outputs flow forward** — any step can reference a prior step's output as `{stepId.field}`, so later steps can consume earlier results.\n5. **Persistence** — memory writes, artifacts, and per-step logs persist between runs; pause/resume and dry-run are supported.\n\n```bash\nflo spell cast -n development            # Cast a named spell\nflo spell cast -f ./my-spell.yaml        # Cast from a file\nflo spell cast -n sa --dry-run           # Validate without casting\nflo spell list                           # List available spells and recent runs\nflo spell grimoire list                  # Browse built-in spell templates\nflo spell schedule list                  # List scheduled spells\n```\n\n### Defining spells\n\n```yaml\nname: my-spell\nsteps:\n  - name: lint\n    command: npm run lint\n  - name: test\n    command: npm test\n  - name: deploy\n    command: ./deploy.sh\n    depends_on: [lint, test]\n```\n\nSteps support shell (`bash`), agent spawns, memory reads/writes, conditionals, loops, parallel groups, browser automation, GitHub/IMAP/Outlook/Slack/MCP integrations, prompts, waits, graphs, and composite steps. See [docs/SPELLS.md](docs/SPELLS.md) for the full schema.\n\n### Sandboxing and security\n\nSpells run with **least-privilege access**. Each step command declares the capabilities it needs (`shell`, `net`, `fs:read`, `fs:write`, `memory`, `credentials`, `browser`, `browser:evaluate`, `agent`), and the runner blocks any undeclared access. Spell authors can further restrict capabilities per step — e.g. `fs:read: [\"./config/\"]` or `shell: [\"cat\", \"jq\"]` — but never expand them.\n\nBash steps also run inside an OS sandbox when one is available. MoFlo auto-selects the best tier installed on your machine:\n\n| Tier | Platform | Isolation |\n|------|----------|-----------|\n| Docker | all | Container, strictest |\n| bwrap | Linux | User namespaces |\n| sandbox-exec | macOS | Apple seatbelt profile |\n| none | fallback | Capability-only enforcement |\n\nThe sandbox is `network-off` by default; a step must explicitly declare `net` to reach the outside world. Credentials referenced as `{credentials.X}` are resolved from the encrypted credential store, masked in logs, and never written to disk. A destructive-pattern checker refuses to run bash commands that look like `rm -rf /`, unscoped `git push --force`, and similar footguns. See [docs/SPELL-SANDBOXING.md](docs/SPELL-SANDBOXING.md) for the full model.\n\n### Reusability\n\nYou interact with spells at three tiers:\n\n1. **Shipped spells** — bundled with MoFlo and ready to cast. Browse them with `flo spell grimoire list`.\n2. **User spells** — YAML files you drop in `.claude/spells/`. Override the location in `moflo.yaml`:\n   ```yaml\n   spells:\n     userDirs:\n       - .claude/spells\n       - my/project/spells\n   ```\n   A user spell with the same `name` as a shipped one wins — that's how you customize a shipped spell without forking.\n3. **Custom step commands and connectors** — drop TypeScript/JavaScript files in `.claude/spells/steps/` (new step types) and `.claude/spells/connectors/` (new connectors). They're auto-discovered at startup. Connectors that wrap heavy SDKs (IMAP, MCP) declare those SDKs as `optionalDependencies`; install them only if your spells use them.\n\n### Scheduling\n\nSpells can run on a schedule. The MoFlo background daemon polls for due spells once a minute and casts them — no external cron, no extra services.\n\n**Three timing options:**\n\n```bash\n# Cron (5 fields: minute hour day-of-month month day-of-week)\nflo spell schedule create -n nightly-audit --cron \"0 2 * * *\"\n\n# Interval (e.g., 90s, 30m, 6h, 1d)\nflo spell schedule create -n health-check --interval 30m\n\n# One-time (ISO 8601 datetime)\nflo spell schedule create -n migration --at 2026-04-15T09:00:00Z\n```\n\nYou can also declare a schedule directly inside the spell YAML — that registers it on every daemon start:\n\n```yaml\nname: nightly-audit\nschedule:\n  cron: \"0 2 * * *\"\nsteps:\n  - id: audit\n    type: bash\n    config:\n      command: ./scripts/audit.sh\n```\n\n**Daemon prerequisite.** Schedules only fire while the daemon is running. To survive reboot:\n\n```bash\nflo daemon install   # registers an OS-level autostart service\nflo daemon status    # shows whether the service is registered AND running\n```\n\n`flo spell schedule create` warns when the daemon isn't installed so you don't quietly miss runs.\n\n**Monitoring.** **[The Luminarium](#the-luminarium)** — moflo's localhost daemon dashboard — surfaces live schedules, recent executions, and per-schedule controls (disable / re-enable / run now), alongside worker health, memory stats, and Claude Code session stats. Ask `/luminarium` in your Claude session and it'll print the link.\n\nFor full configuration (`scheduler:` block in `moflo.yaml`), event types, and the catch-up window after restarts, see [docs/SPELLS.md#scheduling](docs/SPELLS.md#scheduling).\n\n### Building spells with the `/spell-builder` skill\n\nInside Claude Code, use the `/spell-builder` skill to create, edit, and validate spell definitions interactively. The skill understands the full spell schema and available step commands, so you can describe what you want in natural language and it will generate the YAML:\n\n```\n/spell-builder                           # Start the spell builder\n```\n\n### Other AI-client skills shipped with MoFlo\n\nBeyond `/flo`, `/spell-builder`, and `/eldar`, MoFlo ships a handful of focused slash-command skills that work in any consumer project once you `flo init`:\n\n| Skill | Purpose |\n|-------|---------|\n| `/guidance` | Author and audit guidance docs. Default writes guidance for Claude into `.claude/guidance/` as Markdown applying moflo's universal rules. `-h` switches the audience to humans (lighter ruleset, writes into `docs/`). `--html` emits HTML with a minimal default stylesheet instead of Markdown. `-a` audits every doc in `.claude/guidance/` against the universal rules. |\n| `/flo-simplify` (alias `/distill`) | Adaptive code review on the current diff. Tier-based fan-out — trivial edits get a self-review, small diffs get one routed agent, cross-cutting refactors get three parallel agents. Routes through the moflo model router for cost-aware execution. (Named `/flo-simplify` to avoid colliding with Claude Code's built-in `/simplify`; also available as `/distill` for a more wizardy feel.) |\n| `/quicken` (alias `/perf-audit`) | Ad-hoc performance audit — \"quicken the codebase\". Reveals N+1 queries, needless re-renders, missing caching, memory leaks, and redundant computation, then prescribes the fix **inline in the session**. Scopes to your current diff by default (or a path you name), so it never re-audits the whole tree. Replaces the old always-on `optimize` daemon worker. |\n| `/ward` (alias `/test-gaps`) | Ad-hoc test-gap audit — \"ward the codebase\". Reveals untested functions, uncovered edge cases, and missing error-handling/integration tests, then conjures ready-to-paste test skeletons in your framework **inline in the session**. Scopes to your current diff by default (or a path you name). Replaces the old always-on `testgaps` daemon worker. |\n| `/commune` | Socratic requirements elicitation. Turns a fuzzy \"I'm not sure exactly what I want yet\" idea into a concrete spec through a short Q&A, then hands the result off to a `/flo` ticket, a spell, or memory. The pre-execution counterpart to `/meditate` — use it to *open* a unit of work. |\n| `/divine` | Multi-hop web research with explicit confidence gating. Plans the inquiry, searches the web, scores its own confidence, and keeps digging until the answer is well-supported (or a hop cap is hit) — then returns a cited synthesis and remembers what worked so the next research run starts smarter. |\n| `/meditate` | Deliberate session retrospective — distills durable lessons into the `learnings` memory namespace, deduped against what's already there. See [Learning From Your Sessions](#learning-from-your-sessions) for the full picture, including its automatic counterpart, auto-meditate. |\n| `/spell-schedule` | Schedule a spell on the local moflo daemon (cron, interval, or one-time) without leaving the chat. For remote Anthropic-cloud agents on a schedule, use Claude Code's built-in `/schedule` instead. |\n\nRun any of them with no arguments to see full usage, or browse the source in `.claude/skills/` (each skill is a single `SKILL.md` file).\n\n### Epics\n\nEpics are a specialized process for handling GitHub issues that contain multiple child stories. When you pass a GitHub issue to `/flo` and it's detected as an epic, MoFlo processes each child story sequentially through the full `/flo` process (research → implement → test → PR).\n\nFor simple epics, `/flo <epic-number>` is all you need. For complex features requiring state tracking, resume from failure, and auto-merge between stories, use the dedicated `flo epic` command:\n\n```bash\nflo epic 42                              # Run all stories in epic #42\nflo epic 42 --strategy auto-merge        # Per-story PRs with auto-merge\nflo epic 42 --dry-run                    # Preview execution plan\nflo epic status 42                       # Check progress\nflo epic reset 42                        # Reset state for re-run\n```\n\nSee the [Epic handling](#epic-handling) section above for detection criteria and the comparison between `/flo <epic>` and `flo epic run`.\n\n## The Luminarium\n\nThe Luminarium is moflo's localhost daemon dashboard. It boots automatically with the background daemon (no extra service to install) and stays running as long as the daemon is up.\n\n### Finding the URL\n\nInside a Claude Code session in a moflo project, ask **`/luminarium`** — the skill prints the dashboard URL for the current project. `flo daemon status` prints the same URL alongside the health summary. Each project binds its own port so two projects on the same machine never collide.\n\n### What it shows\n\n| Tab | What you see |\n|-----|--------------|\n| **Workers** | Live agent processes the daemon is running (statusline updater, indexer, embedder, etc.) |\n| **Schedules** | All registered spell schedules (cron / interval / one-time), with run-now and disable controls |\n| **Executions** | Recent spell runs — duration, exit code, step-by-step output |\n| **Memory** | Memory namespace breakdown, vector count, embedder backend, HNSW index health |\n| **Claude Stats** | Per-session Claude Code transcript stats — tokens (with a subagent-token subtotal that splits main-loop context from Task-tool-spawned subagent context), tools called, files touched (local primary sessions only) |\n\n### Flags\n\n- `flo daemon start --no-dashboard` — disable the HTTP server entirely (the daemon itself still runs)\n- `flo daemon start --dashboard-port <N>` — pin to a specific port, overriding the per-project default. Also accepts the `MOFLO_DAEMON_PORT` env var, which the rest of moflo respects when talking to the daemon\n\n## Commands\n\nYou don't need to run these for normal use — `flo init` sets everything up, and the hooks handle memory, routing, and learning automatically. These commands are here for manual setup, debugging, and tweaking.\n\n### Memory\n\n```bash\nflo memory store -k \"key\" --value \"data\"    # Store with 384-dim embedding\nflo memory search -q \"auth patterns\"         # Semantic search\nflo memory index-guidance                    # Index guidance docs\nflo memory code-map                          # Index code structure\nflo memory rebuild-index                     # Regenerate all embeddings\nflo memory refresh                           # Reindex all + rebuild + cleanup + vacuum\nflo memory stats                             # Show statistics\n```\n\n### Routing & Learning\n\n```bash\nflo hooks route --task \"description\"          # Route task to optimal agent\nflo hooks learn --pattern \"...\" --domain \".\"  # Store a pattern\nflo hooks patterns                            # List learned patterns\nflo hooks consolidate                         # Promote/prune patterns\n```\n\n### Gates\n\n```bash\nflo gate check-before-scan       # Blocks Glob/Grep if memory not searched\nflo gate check-before-agent      # Blocks Agent tool if no TaskCreate\nflo gate prompt-reminder         # Context bracket tracking\nflo gate session-reset           # Reset gate state\n```\n\n### Worktrees\n\n```bash\nflo worktree add feature/123-thing   # Create a worktree and provision it (alias: flo wt)\nflo worktree add feature/123 --json  # {\"path\":…,\"branch\":…,\"index\":0,\"provisioned\":true}\nflo worktree add feature/123 --from v2.1.0    # Branch off a specific ref\nflo worktree add feature/123 --no-provision   # Create it, skip copy/link/setup\nflo worktree list                    # Every worktree and its provisioning state\nflo worktree remove feature/123-thing         # Refuses a dirty tree unless --force\n```\n\n### Diagnostics\n\n```bash\nflo healer                       # Quick health check (environment, deps, config)\nflo healer --fix                 # Auto-fix issues (memory DB, daemon, config, MCP, zombies)\nflo diagnose                     # Full integration test (memory, swarm, hive, hooks, neural)\nflo diagnose --suite memory      # Run only memory tests\nflo diagnose --json              # JSON output for CI/automation\n```\n\n`flo doctor` is still accepted as an alias for `flo healer` — every flag and subcommand below works under either name.\n\n#### `flo healer` — Health Check\n\n`flo healer` runs 38 parallel health checks against your environment and reports pass/warn/fail for each:\n\n| Check | What it verifies |\n|-------|-----------------|\n| **Version Freshness** | Whether your installed MoFlo version matches the latest on npm (detects stale npx cache) |\n| **Node.js Version** | Node.js >= 20 installed |\n| **npm Version** | npm >= 9 installed |\n| **Claude Code CLI** | `claude` command available |\n| **Git** | Git installed |\n| **Git Repository** | Project is inside a git repository |\n| **Config File** | Valid `moflo.yaml` exists |\n| **Status Line** | `statusLine` config wired in `.claude/settings.json` (auto-fixes when missing) |\n| **Daemon Status** | Background daemon running (checks PID, cleans stale locks) |\n| **Memory Database** | SQLite memory DB exists and is accessible |\n| **Embeddings** | Vectors indexed in memory DB, HNSW index present |\n| **Embedding Hygiene** | Indexer writes preserve existing embeddings instead of clobbering them |\n| **Test Directories** | Test dirs from `moflo.yaml` exist on disk, reports auto-index status |\n| **MCP Servers** | `moflo` MCP server configured in `.mcp.json` |\n| **Disk Space** | Sufficient free disk space (warns at 80%, fails at 90%) |\n| **TypeScript** | TypeScript compiler available |\n| **Semantic Quality** | Semantic search returns relevant, varied results with acceptable similarity scores |\n| **Intelligence** | SONA, ReasoningBank, PatternLearner, LoRA, EWC++, and RL subsystems are loaded |\n| **Spell Engine** | Core spell modules, step commands, loaders, and index are present |\n| **Zombie Processes** | No orphaned MoFlo node processes running |\n| **Subagent Health** | Agent lifecycle (spawn → status → terminate) completes successfully |\n| **Spell Execution** | End-to-end spell probe runs a real step and captures output |\n| **MCP Tool Invocation** | MCP tool schemas are loaded and callable |\n| **MCP Spell Integration** | Bridge between MCP tools and spell engine functions correctly |\n| **Hook Execution** | Hook executor is functional and can fire hooks |\n| **Gate Health** | All gate cases, hook bindings, and state file are intact |\n| **MofloDb Bridge** | Memory DB adapter (node:sqlite + HNSW) is wired and routable |\n| **Sandbox Tier** | Detects which sandbox backend is available (Docker / bwrap / sandbox-exec / none) |\n\n**Auto-fix mode** (`flo healer --fix`) attempts to repair each failing check automatically:\n\n| Issue | What `--fix` does |\n|-------|------------------|\n| Missing memory database | Creates `.swarm/` directory and initializes the SQLite DB |\n| Embeddings not initialized | Initializes memory DB and runs `embeddings init` |\n| Missing config file | Runs `config init` to generate defaults |\n| Status line not wired | Adds `statusLine` config block to `.claude/settings.json` |\n| Stale daemon lock | Removes stale `.moflo/daemon.lock` and restarts daemon |\n| Malformed `.mcp.json` (e.g. unescaped Windows paths) | Backs up the broken file as `.mcp.json.malformed-<ts>`, regenerates a clean one, verifies it parses (#1126) |\n| MCP server missing from a valid `.mcp.json` | Runs `claude mcp add moflo` to register the server |\n| Claude Code CLI missing | Installs `@anthropic-ai/claude-code` globally |\n| Zombie processes | Kills orphaned MoFlo processes (tracked + OS-level scan) |\n\nAfter auto-fixing, healer re-runs all checks and shows the updated results. Issues that can't be fixed automatically are listed with manual fix commands.\n\nAdditional flags:\n\n```bash\nflo healer --install             # Auto-install missing Claude Code CLI\nflo healer --kill-zombies        # Find and kill orphaned MoFlo processes\nflo healer -c memory             # Check only a specific component\nflo healer -c embeddings         # Check only embeddings health\nflo healer --verbose             # Verbose output\n```\n\n#### `/eldar` — Consult the Eldar (project setup audit + wizard)\n\nWhere the Healer checks your moflo install, `/eldar` audits how Claude is set up to *use* the project — guidance, CLAUDE.md, memory namespaces, hook/MCP wiring, model routing, and stack-aware guidance gaps — then walks you through fixing whichever findings you pick. Use it when starting in a new project, when Claude feels lost or inefficient, or as a periodic health check.\n\n```\n/eldar                           # Read-only audit; categorized report + top-3 ranked recommendation\n/eldar --fix                     # Audit, then interactive triage menu — pick which findings to address\n```\n\nThe Eldar **consult** the Healer (they call `flo healer --json` as one of the audit checks) — they don't replace it. Categories audited include setup health, index freshness, version skew, model/token routing, CLAUDE.md size + reference integrity, guidance content + structure, memory health, hook/MCP wiring, settings sanity, spell + subagent inventory, **stack → guidance cross-reference** (detects tech from package.json/pyproject.toml/Cargo.toml/go.mod and flags every detected technology with no matching guidance doc — the highest-leverage finding for new adopters), and best-effort anti-pattern detection from history.\n\nIn `--fix` mode, each chosen finding drives the appropriate sub-flow: Healer for setup repair, the `/guidance` skill for guidance authoring (wizard, never autogen), a stack-aware scaffold for missing CLAUDE.md, `flo init --upgrade` for hook/MCP wiring. Every write is confirmed before it lands.\n\n#### `flo diagnose` — Integration Tests\n\nWhile `healer` checks your environment, `diagnose` exercises every subsystem end-to-end: memory CRUD, embedding generation, semantic search, swarm lifecycle, hive-mind consensus, task management, hooks, config, neural patterns, and init idempotency. All test data is cleaned up after each test — nothing is left behind.\n\n### GitHub Repository Setup\n\n```bash\nflo github setup                  # One-shot: generate CI + apply repo settings + branch protection\nflo github setup --dry-run        # Preview everything without making changes\nflo github ci                     # Generate .github/workflows/ci.yml from project config\nflo github ci --dry-run           # Print CI config to stdout\nflo github settings               # Apply repo settings + branch protection via gh CLI\nflo github settings --dry-run     # Preview settings changes\n```\n\n`flo github ci` auto-detects your package manager (npm/pnpm/yarn/bun), TypeScript, and test directories from `moflo.yaml` and `package.json`, then generates a GitHub Actions CI pipeline with install, build, lint, type-check, and test steps.\n\n`flo github settings` applies recommended defaults via `gh` CLI: delete-branch-on-merge, squash merge with PR title/body, auto-merge, linear history, and configurable branch protection (required reviews, dismiss stale reviews, block force pushes). Requires `gh auth login`.\n\n### System\n\n```bash\nflo init                          # Initialize project (one-time setup)\nflo --version                    # Show version\n```\n\n## What Ships Out of the Box\n\n`flo init` wires up the following systems automatically. Here's what each one does, why it matters, and whether it's enabled by default.\n\n### Hooks (enabled OOTB)\n\nHooks are shell commands that Claude Code runs automatically at specific points in its lifecycle. MoFlo installs 26 hook bindings across 8 lifecycle events. You don't invoke these — they fire automatically.\n\n| Hook Event | What fires | What it does | Enabled OOTB |\n|------------|-----------|-------------|:---:|\n| **PreToolUse: Write/Edit** | `flo hooks pre-edit` | Records which file is about to be edited, captures before-state for learning | Yes |\n| **PreToolUse: Glob/Grep** | `flo gate check-before-scan` | Memory-first gate — blocks file exploration until memory is searched | Yes |\n| **PreToolUse: Read** | `flo gate check-before-read` | Blocks reading guidance files directly until memory is searched | Yes |\n| **PreToolUse: Bash** | `flo gate check-dangerous-command` | Safety check on shell commands | Yes |\n| **PreToolUse: Bash** | `flo gate check-before-pr` | Validates PR readiness before `gh pr create` | Yes |\n| **PostToolUse: Write/Edit** | `flo hooks post-edit` | Records edit outcome, optionally trains neural patterns | Yes |\n| **PostToolUse: Write/Edit** | `flo gate reset-edit-gates` | Resets edit-related gate state after the write completes | Yes |\n| **PostToolUse: Agent** | `flo hooks post-task` | Records task completion, feeds outcome into routing learner | Yes |\n| **PostToolUse: TaskCreate** | `flo gate record-task-created` | Records that a task was registered (clears TaskCreate gate) | Yes |\n| **PostToolUse: Bash** | `flo gate check-bash-memory` | Detects memory search commands in Bash (clears memory gate) | Yes |\n| **PostToolUse: Bash** | `flo gate record-test-run` | Records test runs from Bash for the test-output gate | Yes |\n| **PostToolUse: Skill** | `flo gate record-skill-run` | Records that a skill was invoked (clears skill-related gates) | Yes |\n| **PostToolUse: memory_search** | `flo gate record-memory-searched` | Records that memory was searched (clears memory-first gate) | Yes |\n| **PostToolUse: memory_store** | `flo gate record-learnings-stored` | Records that learnings were persisted to memory | Yes |\n| **UserPromptSubmit** | `prompt-hook.mjs` | Resets per-prompt gate state, tracks context bracket, routes task to agent | Yes |\n| **UserPromptSubmit** | `meditate-capture.mjs meditate-detect` | Auto-meditate: notices when a durable lesson emerges in the live session and queues it for distillation | Yes |\n| **SubagentStart** | `subagent-start` | Injects context and guidance into spawned sub-agents | Yes |\n| **SessionStart** | `session-start-launcher.mjs` | Launches auto-indexers (guidance, code map, tests), restores session state, fires the auto-meditate distillation pass | Yes |\n| **SessionStart** | `auto-memory-hook.mjs` | Imports auto-memory entries from Claude's persistent memory | Yes |\n| **Stop** | `flo hooks session-end` | Persists session metrics, exports learning data | Yes |\n| **Stop** | `auto-memory-hook.mjs` | Syncs auto-memory state on session close | Yes |\n| **Stop** | `session-continuity.mjs capture` | Captures a \"where you left off\" session digest for relevance-gated injection at the next session start | Yes |\n| **Stop** | `meditate-capture.mjs meditate-scrape` | Auto-meditate: scrapes the lessons recognized this session into the distillation queue | Yes |\n| **PreCompact** | `flo gate compact-guidance` | Injects guidance summary before context compaction | Yes |\n| **Notification** | `flo hooks notification` | Routes Claude Code notifications through MoFlo | Yes |\n\n### Systems (enabled OOTB)\n\nThese are the backend systems that hooks and commands interact with.\n\n| System | What It Does | Why It Matters | Enabled OOTB |\n|--------|-------------|----------------|:---:|\n| **Semantic Memory** | SQLite database (Node's built-in `node:sqlite`) storing knowledge entries with 384-dim vector embeddings | Your AI assistant accumulates project knowledge across sessions instead of starting from scratch each time | Yes |\n| **HNSW Vector Search** | Hierarchical Navigable Small World index for fast nearest-neighbor search | Searches across thousands of stored entries return in milliseconds instead of scanning linearly | Yes |\n| **Guidance Indexing** | Chunks markdown docs into overlapping segments, embeds each with MiniLM-L6-v2 | Your project documentation becomes searchable by meaning (\"how does auth work?\") not just keywords | Yes |\n| **Code Map** | Parses source files for exports, classes, functions, types | The AI can answer \"where is X defined?\" from the index instead of running Glob/Grep | Yes |\n| **Test Indexing** | Maps test files to their source targets based on naming patterns | The AI can answer \"what tests cover X?\" and identify untested code | Yes |\n| **Gates** | Hook-based enforcement of memory-first and task-registration patterns | Prevents the AI from wasting tokens on blind exploration and untracked agent spawns | Yes |\n| **Context Tracking** | Interaction counter with bracket classification (FRESH/MODERATE/DEPLETED/CRITICAL) | Warns before context quality degrades, suggests when to checkpoint or start fresh | Yes |\n| **Semantic Routing** | Matches task descriptions to agent types using vector similarity against 12 built-in patterns | Routes work to the right specialist (security-architect, tester, coder, etc.) automatically | Yes |\n| **Learned Routing** | Records task outcomes (agent type + success/failure) and feeds them back into routing | Routing gets smarter over time — successful patterns are weighted higher in future recommendations | Yes |\n| **SONA Learning** | Self-Optimizing Neural Architecture that learns from task trajectories | Adapts routing weights based on actual outcomes, not just key","readmeFilename":"README.md"}