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organized into context-bounded cells for LLMs coding alongside humans.","maintainers":[{"name":"henrythdu","email":"henry.thdu@protonmail.com"}],"readme":"# Cells\n\n> New issues and PRs from new contributors are auto-closed by default.\n> Maintainers review auto-closed issues daily. See [CONTRIBUTING.md](CONTRIBUTING.md).\n\n[![npm version](https://img.shields.io/npm/v/@henrythdu/cells?style=flat-square)](https://www.npmjs.com/package/@henrythdu/cells)\n\nThere are many ways to keep a codebase's architecture consistent. Cells is one: the architecture is **authored and visible**, so every agent — every session, every model — shares the same declared structure instead of re-deriving its own.\n\n- Every file has a named home — **a cell**.\n- Every cell has a written contract — **a membrane** (`name`, `purpose`, `provides`, `requires`).\n- Every cross-cell dependency is a **derived crossing** — computed from real imports, never hand-written.\n\nThe dependency checks are inspired by Clean Architecture (dependencies point toward the core; no cycles) — applied as visible warnings, not academic ceremony.\n\n---\n\n## Install\n\n```bash\nnpm install -g @henrythdu/cells\n```\n\nRequires Node (ESM). Git and npm versions always match — every npm publish is tagged in git.\n\n**From source:**\n\n```bash\ngit clone https://github.com/henrythdu/cells.git\ncd cells\npnpm install # installs deps + builds dist/ via prepare\nnpm link # live symlink into dist/ for local edits\n```\n\nRuntime dependencies (`smol-toml`, `minimatch`, `web-tree-sitter`; grammar WASMs bundled in `grammars/`) install automatically.\n\n---\n\n## Quickstart\n\n```bash\ncells init # create .cells/ — detects your language (code-exts/code-dirs)\ncells plan # propose a partition: crates / npm packages / Python packages become one cell each (review, then curate)\ncells plan --apply # or create the proposed cells + ownership mechanically (dry-run: add --dry-run)\ncells assign parser src/parser.ts # assign a file to a cell (records ownership; stubs the declaration)\n$EDITOR .cells/parser.cell.toml # author the membrane: purpose / provides / requires\ncells health # the gate: every check at once (integrity + crossings + grammars + structure + size)\ncells list # see the whole partition\n```\n\n`assign` records ownership **and** creates a declaration stub if the cell is new. Ownership is *non-overlapping* — a file belongs to exactly one cell (the file itself isn't relocated on disk; only its owning cell changes).\n\n---\n\n## Handing work to an agent\n\nPoint it at a repo and tell it to run `cells help` — the tool is self-documenting, and that's the whole handoff. The loop it will follow: `list` (orient) → `show` (zoom) → `payload` (retrieve) → `impact` (assess) → edit inside the membrane → `health` (check). You review partition and membrane changes; it works the cells.\n\n---\n\n## The mental model\n\n| term | meaning |\n| --- | --- |\n| **Cell** | a context-bounded unit of code that solves ONE problem and fits a context window. Has a *membrane* (contract) + *owned files* (body). |\n| **Partition** | the complete, non-overlapping assignment of every code file to exactly one cell. (A file is the atomic unit.) |\n| **Membrane** | a cell's declaration — `name`, `purpose`, `provides`, `requires`. What you read first to understand a cell. |\n| **Crossing** | a real dependency from one cell's code into another's (derived from imports). The seams between cells. |\n| **Payload** | what a model consumes to work a cell — its membrane + owned files + its neighbors' membranes. Measured in tokens (~chars/3). |\n| **Metrics** | per-cell **fan-in** / **fan-out** (distinct cells it's depended-on-by / depends-on) and **instability** I = fan-out ÷ (fan-in + fan-out): 0 = stable, 1 = unstable. Shown in `list` and `show`; derived from crossings, free. |\n\n**Three storage truths:**\n\n- **Ownership is *tracked*** — `ownership.toml`, machine-managed by `assign`.\n- **Declarations are *authored*** — `*.cell.toml`, you write the membrane.\n- **Crossings are *derived*** — computed from real imports, never hand-written.\n\n**One principle:** *visibility over enforcement.* Cells shows you the structure and its problems; it rarely blocks. (The exceptions are integrity, undeclared leakage, and broken grammars — see Rules.)\n\n---\n\n## Commands\n\n
\nFull command reference (also in cells help)\n\n| command | what it does |\n| --- | --- |\n| `cells init [--dry-run]` | bootstrap `.cells/` — detects your language (code-exts/code-dirs) (idempotent; `--dry-run` previews) |\n| `cells plan [--apply] [--dry-run]` | propose a cell partition: crates / npm packages / Python **init** packages become one cell each, other files group by directory (prints declarations + ownership to review — writes nothing). `--apply` creates the cells + adopts the files mechanically (never overwrites existing cells or steals curated ownership); `--dry-run` previews |\n| `cells assign ` | assign file(s) to a cell (records ownership; stubs declaration if new) |\n| `cells new [--purpose \"...\"] [--provides a,b] [--requires a,b] [--layer N]` | scaffold a cell declaration (`.cell.toml`) — declare the contract first, then `assign` files into it |\n| `cells prune-stale [--apply]` | remove requires that are declared but never imported (stale); dry-run by default, `--apply` rewrites the declaration files |\n| `cells unassign ` | remove file(s) from their cell (→ orphan) |\n| `cells rename ` | rename a cell across the store (file, ownership keys, requires refs) |\n| `cells remove [--force]` | delete a cell's declaration (ownership freed → orphans unless `--force` also clears them) |\n| `cells owns ` | which cell owns this file? (reverse lookup; orphan-aware) |\n| `cells list [--verbose]` | partition overview: each cell's files / size / fan-in·fan-out / requires + orphans; `--verbose` adds a per-cell health line (size%, stale provides, unresolved) |\n| `cells show [--verbose]` | one cell's membrane + in/out crossings (aggregated past 8 edges; `--verbose` for raw) + fan-in/fan-out/instability + size + dead-at-boundary files + change-coupled partners + stale provides + unresolved imports |\n| `cells surface ` | print the cell's export-like declaration lines (file:line) — the starting point for populating the membrane `signatures` field |\n| `cells impact ` | blast radius: cells that transitively depend on this one (change-safety) |\n| `cells payload ` | print a cell's full payload (membrane + code + neighbors + the cells that depend on you) — the context to work it |\n| `cells health [--verbose] [--summary]` | **the gate** — all checks at once: integrity (duplicates, dangling refs, undeclared cells) + crossings (**undeclared** leakage gate-fails; **stale** is informational) + a broken packaged grammar WASM + structure (cycles / direction) + size. Exits 1 only on integrity + undeclared leakage + grammars (strict gate); size/structure are exit-0 warnings (⚠). `--verbose` names failing undeclared edges inline (saves the `crossings` round-trip); `--summary` collapses unresolved entries into per-file groups (the triage unit for high-unresolved repos). Output ends with a machine-parseable `health: X.Xs` timing line. |\n| `cells crossings [--diff] [--verbose] [--json] [--warnings]` | derived cross-cell imports + **leakage** check; `--diff` shows crossings your uncommitted edits added/removed; `--warnings` = leakage + unresolved only (no pair listing — the actionable tail on a big repo); `--verbose` names off-membrane symbols inline; `--json` is the machine surface |\n| `cells imports [--json]` | raw file→file import graph (resolved edges + unresolved specifiers) — the machine surface for tooling |\n| `cells size` | context-fit: each cell's payload vs the ceiling (warning); over-ceiling cells list **peel candidates** — biggest files few others import. A cell can declare its own ceiling (`ceiling = N` in its `.cell.toml`) — same check, its own number |\n| `cells config [set max-payload-tokens ]` | read the effective config (defaults where the file omits); `set` edits the global ceiling in place — comments and other keys preserved |\n| `cells structure [--summary]` | layer tiers + ADP (no cycles) + Direction (deps point toward core) + SDP (deps run toward stability) — the dependency rule, checked. All info/warnings; cycles suggest the cheapest edge to cut. `--summary` is the triage view: one line per cycle (size + cheapest edges) + counts |\n| `cells graph [--mermaid]` | the cell dependency graph (ASCII tree default; `--mermaid` for Mermaid source) |\n| `cells help` | this text (also `--help`, `-h`) — the tool's self-documentation; run it first in any repo |\n\n
\n\n---\n\n## The `.cells/` directory\n\n```text\n.cells/\n .cell.toml # declarations (authored) — one per cell\n ownership.toml # file → cell map (tracked)\n config.toml # settings (optional)\n ignore # gitignore-style patterns (optional)\n```\n\n### `.cell.toml` — a cell's membrane\n\n```toml\nname = \"parser\"\npurpose = \"Turn a .cell declaration file into a checked Cell AST.\"\nprovides = [\"parseCell\", \"Cell\"] # authored docs of the cell's surface (shown in show/payload; reference-checked when symbol-shaped — stale/unread info; prose tolerated)\nrequires = [\"token\", \"diagnostic\"] # neighbor CELL names\n# optional — couplings static analysis can't see (data files, runtime loading, shared\n# schema). Integrity-checked and included in payloads; never import-audited:\ndata-requires = [\"translations\"]\nlayer = 0 # optional — 0 = core; higher = more peripheral (direction)\n```\n\n### `ownership.toml` — the file→cell map\n\n```toml\n[parser]\nfiles = [\n \"src/parser.ts\",\n]\n\n[cli]\nfiles = [\n \"src/cli.ts\",\n \"test/cli.test.ts\",\n]\n```\n\nSerialized deterministically (sorted cells, sorted files, one per line) so parallel\nbranches that touch different cells merge cleanly.\n\n### `config.toml` — settings\n\n```toml\nmax-payload-tokens = 16000 # context-fit ceiling — the per-repo knob for cell size (default 16000); edit in place or `cells config set max-payload-tokens `\n# One cell can declare its own ceiling — add `ceiling = N` to its .cell.toml for a\n# legitimately-big unit (a huge crate) without raising the bar for every cell.\n# It's still a budget: over it, size/health flag it just like any over-ceiling cell.\n# [layers] # optional legend (rank → label); 0 = core, higher = peripheral\n# 0 = \"domain\"\n# 1 = \"application\"\n# 2 = \"infrastructure\"\ncode-dirs = [\"src\", \"test\"] # dirs scanned for code (`cells init` auto-detects)\ncode-exts = [\".ts\"] # extensions counted (`cells init` auto-detects; set per language)\n# skip-dirs = [] # dir names the census never walks (node_modules, dist, build,\n# # target, .git, .cells, vendor, .venv, ...). Setting this REPLACES\n# # the defaults — the unhide path for a real internal/build package.\n```\n\n### `ignore` — intentionally cell-free files\n\ngitignore-style globs (a trailing `/` marks a directory → its whole tree, like gitignore's `dir/`).\nMatched files aren't counted as code and never surface as orphans (examples, scratch, scripts):\n\n```text\nexamples/**\n*.tmp\nvendor/\n```\n\n---\n\n## Language support\n\n**Partition, payload, size, and owns** are language-agnostic — set `code-dirs` and `code-exts` in `config.toml` to point Cells at your code (e.g. `[\"lib\", \"cmd\"]` + `[\".go\"]`).\n\n**Crossings and structure** (leakage, ADP, direction, metrics) analyze *real imports*:\n\n- **TypeScript/JavaScript/TSX** via `tree-sitter` (WASM; tsconfig `paths` aliases, workspace `package.json` resolution, `.js`→`.ts` remaps).\n- **Python** via `tree-sitter` (WASM; bundled grammar, no native build).\n- **Rust** via `tree-sitter` (WASM; handles `use`/`super`/`self`, groups, re-exports).\n- **Go** via `tree-sitter` (WASM; package→directory resolution, nested `go.mod` sub-modules).\n- **C/C++** via `tree-sitter` (WASM; `#include` → file resolution: quoted = local, angle = external unless owned; probes importer-dir + repo `-I` roots derived from the census).\n- **Java** via `tree-sitter` (WASM; fully-qualified class imports → package-decl resolution, layout-agnostic; wildcards → one representative edge per package).\n- Other languages need an importer — one per language, selected automatically by file extension.\n\n**What importers can't see (static-analysis blind spots, named per language):** Python — `importlib`, `__import__`, string-built module names; Rust — proc-macro-expanded paths; Go — `reflect`-based coupling and generator→generated relationships; Java — static imports only, nothing beyond the repo's own sources; C/C++ — `#include` only, no macro-computed paths; TypeScript — string-built specifiers (plugin loaders) are not resolved. The derived graph is honest about what it derived: when a coupling the importer can't see matters, say so in the membrane — the authored declaration is the tool's only source of invisible-channel truth.\n\n**Named-symbol visibility** (what the membrane check can audit): TypeScript/JavaScript/TSX — named imports (`import { a, b } from '…'`, aliases stripped to the exported name) plus namespace-attribute uses (`import * as ns` + `ns.portion` → `portion`, first tail segment; default-import attributes excluded — sub-export granularity); Python — `from M import a, b` names; Rust — `use`-path tail items (`use a::b::Item` → `Item`). Module-level dependencies and C/C++/Go/Java edges carry no symbols — exempt by construction, listed here rather than hidden.\n\nAdding a language: write an importer spec in `src/languages/` (tree-sitter langs: a spec for the\nshared factory in `src/languages/tree-sitter.ts`; otherwise a custom `extract`) + one line in\n`DEFAULT_IMPORTERS` in `src/importers.ts`. The repo's own cells show the pattern — `cells new`\nthe language cell declare-first, then `cells health` enforces the declaration.\n\nResolution doesn't chase the filesystem or require the repo to build/install: it derives a module→file map from ownership, so it runs on source you're just reading.\n\n---\n\n## The rules\n\n| rule | severity | what it catches |\n| --- | --- | --- |\n| **Leakage (undeclared)** | **gate** (exit 1) | a cell imports another it doesn't `require` — a hidden dependency |\n| **Leakage (stale)** | info (exit 0) | a cell `requires` one it never imports — remove it, or move it to `data-requires` if the coupling is real but invisible to static analysis (shown, doesn't fail the gate) |\n| **Integrity** | **gate** (exit 1) | a file in two cells; an owned file missing from disk; a requires or ownership key pointing at an undeclared cell |\n| **Size** | warning (exit 0) | a cell's payload exceeds its ceiling — `max-payload-tokens` (default 16000 — configurable via `cells config set` or `config.toml`), or the cell's own `ceiling = N` — consider dividing |\n| **Structure** | warning (exit 0) | a cycle (ADP), an edge to a higher layer (Direction), or a stable cell depending on a less-stable one (SDP) |\n| **Membrane** | warning (exit 0) | a cell imports **named symbols** the target's `provides` doesn't list (an empty `provides` on a consumed cell = membrane incomplete) — `cells crossings --verbose` names them; converge the list |\n| **Orphans** | visibility (not a violation) | unowned files — shown by `list`; `.cells/ignore` declares the intentional ones |\n\nPayload tokens are estimated at chars/3 (a rough, consistent proxy across models — not exact for any of them). The ceiling is a budget, not a limit: nothing breaks when a cell exceeds it. A cell at 1.5× the ceiling is often the right call for a coherent unit; the gate doesn't care, it's your judgment that matters. The low default is also a module-size discipline — small enough that any current model can hold the payload — and per-cell `ceiling = N` opts a legitimately-big cell out without raising the bar for everyone.\n\n---\n\n*Cells dogfoods itself: this codebase is partitioned into 32 cells. Run `cells list` to see.*\n","readmeFilename":""}