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agent-independent prompt, multi-language code-index, cleanup, and verification companion with project agent guidance.","maintainers":[{"name":"mercmobily","email":"tonymobily@gmail.com"}],"readme":"# Genesis\n\nGenesis is an agent-independent prompt, code-index, and verification companion\nfor local codebases. It combines product intent, concise codebase explanation,\nselected technology guidance, an existing-function inventory, and an optional\nuser request into a complete prompt for the coding agent you already use.\n\nGenesis outputs text. The agent or host you already use owns execution and\ninteraction.\n\nThe useful mental model is:\n\n- **Genesis describes** the product, selected technology, project operations,\n  existing code, and checks.\n- **Your coding agent implements** the application and follows the prompts\n  Genesis returns.\n- **The relevant tool or host executes** setup, run, preview, deployment, and\n  other consumer-owned operations. Genesis itself executes only the commands\n  explicitly listed under `## Verification`.\n\n## Project files\n\n```text\ngenesis/\n  version            project-file format version used for deterministic migrations\n  blueprint.md       non-technical product intent\n  collaboration.md   project-wide communication choices and authored requirements\n  engineering.md     selected engineering profile and project-specific requirements\n  stack.md           selected components, resources, verification, and project-owned operation contracts\n  stack/             optional per-component Description, Guidance, Adoption, Post-change, and Deslop customization\n  subsystems.md      authored responsibilities, Program membership, and data ownership/use\n  program/           concise public-operation explanations\n.agents/skills/\n  genesis-*          Genesis workflow skills\n  <technology>/      authoritative skills installed by selected Stack pieces\n.codex/hooks.json    project-local Codex lifecycle integration\n.claude/settings.json project-local Claude Code lifecycle integration\n.opencode/plugins/   project-local OpenCode lifecycle integration\n.genesis/\n  machine-city.json  derived detailed source and function map\n  program-city.json  derived simple subsystem and operation map\n```\n\nProgram paths describe public operations rather than languages or source\nlayout:\n\n```text\ngenesis/program/notes/list-notes.md\ngenesis/program/notes/create-note.md\n```\n\nThe directory is a conceptual subsystem. Each file describes one public\noperation provided by that subsystem: an exported method, API action, route,\ncommand, UI operation, or equivalent entry point. Each module cites one or more\nreal files under `## Sources`. There is no 1:1 source mapping: one operation may\nspan several files, helper files may be omitted, and one source may support\nmultiple operations.\n\nAn optional `## Implementation map` records only the internal helpers and seams\nthat materially help a future agent change or debug that operation. It is\ninformational, not part of the public contract, and `check` does not pretend to\nprove it current. Program omits incidental framework glue, generated files,\ntests, fixtures, and migrations. It is useful documentation, not proof that it\ncompletely or correctly explains the implementation.\n\n## Quick start\n\nFor ready-made applications and the shared new/existing-project workflow, see\n[Project opening and templates](docs/templates.md). Templates belong to Genesis\nand work through the CLI or Vibe64's Preview pane.\n\nGenesis requires Node.js 22 or newer and Git.\n\nInstall the framework-neutral compiler and the optional first-party technology\ncatalog as separate packages:\n\n```bash\nnpm install --global genesis-compiler genesis-stack\n```\n\n`genesis-compiler` has no dependency on `genesis-stack` or on any framework.\nThe catalog is static Markdown and contains the complete curated set of\nlanguage, database, UI, and framework pieces. A host may supply another catalog\nthrough the same contract.\n\n### Try a new project with Codex, Claude Code or OpenCode\n\nCreate an ordinary empty Git repository:\n\n```bash\nmkdir genesis-jskit-test\ncd genesis-jskit-test\ngit init\ngenesis init\n```\n\nStart Codex, Claude Code or OpenCode in that directory. For a useful discovery test, begin\nwith a deliberately incomplete request:\n\n> I want to build something with JSKIT.\n\nThe agent should not start surveying frameworks or creating source. It should\nfirst ask what is being built, who or what will use it, and the first useful\nobservable outcome. When it recognizes `jskit` in the live Stack catalog, it\nshould ask before adding it.\n\nFor a faster end-to-end test, give it the important product facts directly:\n\n> Build a private contact manager with JSKIT and MySQL. Signed-in people can\n> create, edit, search, and delete their own contacts. The first useful outcome\n> is registering, signing in, and saving one contact.\n\nThe agent should propose the matching Stack selection and wait for confirmation.\nAfter you answer yes, it should run `genesis stack add`, receive the preparation\nprompt as command output, and continue that prompt in the same task. There is no\nsynthetic follow-up turn.\n\nIf you prefer to drive the CLI yourself, the equivalent shortest selection is:\n\n```bash\ngenesis stack list\ngenesis stack add jskit-mysql\n```\n\n`jskit-mysql` brings in its declared dependencies: `mysql`, `jskit`, and\n`nodejs`. The second command changes `genesis/stack.md`, synchronizes any\ncomponent-declared Agent Skills, and prints one preparation prompt. Genesis\ndoes not execute that prompt or start an AI. Paste it into your agent if you ran\nthe command yourself; if the agent ran the command, it already has the output.\n\nReview the resulting source and contracts, then inspect and verify them:\n\n```bash\ngit diff\ngenesis check\ngenesis inspect environment\ngenesis inspect section Outputs\ngenesis verify\n```\n\n`check` reports structure and recorded evidence. `verify` runs only the finite\ncommands recorded under the project's `## Verification` section; neither\ncommand claims that the whole product is correct.\n\n### Adopt an existing codebase\n\nFor an existing codebase, `adopt` is the direct entry point:\n\n```bash\ncd my-existing-project\ngit init                         # if needed\ngenesis adopt \"Optional product guidance\"\n```\n\nIt preserves the implementation, initializes the Genesis files and local\nhooks, and prints the `adopt` prompt. That prompt imports the existing\napplication's factual Stack declarations—including environment/resources,\nverification, and consumer-owned opaque sections—then creates the first useful\nBlueprint and Program. Give it to the agent already working in the repository.\nAdoption edits Genesis metadata only; implementation modernization remains a\nseparate, explicitly approved port. “Adopt” never moves the project.\n\nYou may write `genesis/blueprint.md` yourself, but normal new-project use can\nlet the opening conversation establish it from your answers before source is\ncreated.\n\nCodex users may also install Genesis's optional discovery plugin once:\n\n```bash\ngenesis codex install\n```\n\nWhen Codex opens a nonempty Git project without `genesis/blueprint.md`, the\nplugin's `SessionStart` hook runs before the first user prompt and asks the\nassistant to recommend preparing the existing project for guided editing in\nproduct language. Codex cannot display an ordinary assistant reply until the\nuser speaks, so the recommendation appears in its first reply. If approved, the\nassistant runs `genesis adopt`; the person need not know Genesis terminology or\ntype a command. It never runs adoption without approval and does nothing in an\nempty or already-adopted project.\n\n`genesis init` creates an empty Blueprint, a focused engineering approach, an\nempty optional Stack, the current `genesis/version`, three project Agent Skills,\nand project-local guidance adapters for Codex, Claude Code and OpenCode. The skills are ordinary\n[Agent Skills](https://agentskills.io): `genesis-project`, `genesis-program`,\nand `genesis-deslop`, each with standard `SKILL.md` and `agents/openai.yaml`\nmetadata. Open `/hooks` once in Codex to review and trust the guidance hook;\nClaude Code loads its project hooks and OpenCode discovers its local project plugin automatically. All three use the same\nGenesis-owned operating guide for new sessions and after compaction. When the\noptional first-party catalog is installed beside Genesis, that guide includes\nonly its current component ids. If a named technology exactly matches an\nunselected component, the agent asks before selecting it, then loads its Stack\ncontext and any skill it declares. No technology is assumed until you confirm\nStack selection:\n\n```bash\ngenesis stack add nodejs\n# or, with dependencies resolved automatically:\ngenesis stack add jskit-mysql\n```\n\nGenesis does not install substitute generic `nodejs`, `vue`, `php`, or similar\nskills. Official, user, or host skills retain their normal names. A Stack piece\nmay instead name one authoritative technology skill; Genesis copies that\ncomplete directory into `.agents/skills/`, including its `references/`,\n`scripts/`, `assets/`, and agent metadata. Every relative Markdown link and image\nmust resolve within that same Skill directory after relocation; a missing\ntarget or path that escapes the Skill root makes the Skill invalid. The agent\nloads valid resources only when the Skill requires them. A technology does not\nneed a Skill to be selectable: the curated JSKIT and Vue pieces link their\nauthoritative framework documentation through Stack prose and declare no Skill.\nA piece's optional `## Guidance` is concise supplemental\nproject-work guidance; it does not create or replace a generic technology\nskill.\n\n`.agents/skills/.genesis-managed.json` records only copies Genesis owns.\nGenesis never overwrites an unmanaged skill and preserves locally modified\nmanaged skills. `genesis check` and `genesis inspect skills` distinguish outdated\nmanaged copies from local customizations. After updating Genesis or a selected\nskill package, run `genesis skills sync` to refresh only those skill directories\nand their ownership manifest. Repeating it makes no changes. It does not install\npackages, initialize project files, migrate contracts, rebuild indexes, or run\nverification.\n\nProjects that declare `genesis-compiler` use the skills from that installed\nproject dependency, including when a host embeds a different compiler. An\nunprepared declared dependency is reported instead of substituting the host's\nversion. Other projects use the running compiler's packaged skills. Package\nupgrades remain explicit dependency changes.\n\nInspection, context generation, and session hooks remain read-only and report\nskill maintenance diagnostics. An assistant that already loaded old skills\nneeds its supported context refresh before using their replacement; changing\nfiles alone does not refresh its existing context.\n\n## Commands at a glance\n\n| Command | What it does |\n| --- | --- |\n| `genesis init` | Initializes Genesis files, workflow skills, code indexes, and local Codex/Claude Code/OpenCode guidance in a new or current-format project. It selects no technology. |\n| `genesis adopt [guidance...]` | Initializes an existing codebase and prints the prompt for describing its real product and operational contracts without moving or modernizing source. |\n| `genesis codex install` | Installs the optional Codex discovery plugin that recommends adoption for nonempty projects without Genesis. |\n| `genesis engineering list` | Lists the installed engineering profiles. |\n| `genesis engineering show [profile]` | Shows one profile, or the current project profile when omitted. |\n| `genesis engineering set <profile>` | Records the selected engineering profile while preserving project-specific requirements. |\n| `genesis stack list` | Lists technology components from the installed Stack catalog. |\n| `genesis stack add <piece...>` | Resolves component dependencies/conflicts, records the selection, materializes missing project contracts, synchronizes declared skills, and prints the one-time preparation prompt. It does not install application packages or run an agent. |\n| `genesis skills sync` | Refreshes selected, unmodified managed skills while preserving customized and unmanaged copies. |\n| `genesis context <path...>` | Returns path-focused Program explanations, indexed functions, selected technology guidance, exact project contracts, and relevant skills. |\n| `genesis index [function-or-path...]` | Regenerates the derived code indexes and optionally searches the existing function/method inventory. |\n| `genesis inspect environment` | Reports declared resources, public defaults, missing input names, and environment-file paths without returning secret values. |\n| `genesis inspect skills` | Reports selected skill freshness and ownership without changing files. |\n| `genesis inspect section <name>` | Returns one exact consumer-owned Stack section without interpreting or executing it. |\n| `genesis prompt [request...]` | Generates the ordinary implementation prompt. Use `--task` for opening, adoption, Deslop, explanation, review, and other explicit prompt tasks. |\n| `genesis verify` | Executes only the ordered finite commands in `## Verification` and records exact evidence. |\n| `genesis check` | Performs a read-only structural check of project format, Blueprint, Stack, skills, Program, resources, and verification evidence. |\n| `genesis migrate` | Advances recognized older Genesis project files deterministically and refreshes managed skills, hooks, and indexes. |\n\nProject-scoped options follow the command, for example\n`genesis check --project-root /path/to/project`. Commands support `--json` when\na host or script needs the normalized result. Run `genesis --help` for the\ncompact CLI synopsis.\n\n## Collaboration approach\n\nGenesis keeps project-wide communication guidance in ordinary source rather\nthan in a host-private policy or a repeated user-message prefix:\n\n```markdown\n# Collaboration approach\n\n## Tone\n\n- `encouraging`\n\n## Response length\n\n- `concise`\n\n## Assumed experience\n\n- `comfortable`\n\n## Explanation style\n\n- `concise`\n\n## Project requirements\n\n- Nothing.\n```\n\nInspect or change it without parsing Markdown yourself:\n\n```bash\ngenesis collaboration show\ngenesis collaboration set direct balanced expert conclusions \"Be candid.\"\n```\n\nGenesis owns the supported choices and their concise expansions. Authored\nproject requirements receive one fixed framing sentence and are otherwise\npreserved. They are omitted when the source says `- Nothing.`.\nThe configured style applies to progress updates as well as final answers,\nwith technical depth and terminology matched to the selected experience level.\nUpdates should describe actual progress, findings, decisions, or blockers,\nrather than announce compliance with guidance or reassure the user about\nunrelated behavior staying unchanged.\n\nPersistent hosts should install `projectSessionContext()` once when a provider\nconversation is created or refreshed. They may then generate task prompts with\n`sessionContextInstalled: true`, preventing the stable Collaboration and\nEngineering guidance from being repeated in each task. A host can supply one\nexplicit session/turn driver; Genesis performs no driver discovery and labels\nturn output untrusted. If the project-local Codex, Claude Code or OpenCode adapter runs in a\nseparate process, the host may set `GENESIS_HOST_CONTEXT_RESOLVER` to one\nexecutable and optionally supply opaque JSON in\n`GENESIS_HOST_CONTEXT_RESOLVER_DATA`. Session and turn hooks pass only the\nrequested lane, native provider session id, and that configured data to the\nexecutable. Session output is composed into stable context; a nonempty turn\nresult is capped at 512 bytes, labeled untrusted, and kept separate from the\nauthored user message. This is a single process bridge, not a plugin registry.\n\n## Engineering approach\n\nEvery profile inherits one universal rule: implementation must remain easy to\nreason about and be the smallest targeted change that satisfies current\nrequirements. Speculative abstractions, infrastructure, compatibility paths,\ndistributed patterns, cryptography, and similarly advanced machinery are not\nallowed. When a concrete requirement makes material complexity necessary, the\nagent must explain why a direct design is insufficient and ask before writing\nthat complexity.\n\nThe installed, versioned profile descriptions live in\n`profiles/engineering/*.md`. Straight Genesis users can inspect and select them\nwithout editing Markdown grammar:\n\n```bash\ngenesis engineering list\ngenesis engineering show focused.v1\ngenesis engineering set durable.v1\n```\n\n`focused.v1` is the default for small direct product work. `durable.v1` adds\nexplicit compatibility and operational care for long-lived products.\n`high-assurance.v1` adds risk-driven security and reliability discipline. None\nof them mandates complexity without a concrete need.\n\nThe selection and any explicit project overrides are portable source:\n\n```markdown\n# Engineering approach\n\n## Profile\n\n- `focused.v1`\n\n## Project requirements\n\n- Nothing.\n```\n\nPeople may edit `## Project requirements` to name obligations the presets do\nnot capture, including a specific organizational, compliance, cryptographic,\nor scale constraint. `genesis engineering set` changes only the profile and\npreserves those requirements. Generated prompts, path-focused context, Codex\nsession guidance, implementation Post-change work, and Deslop all receive the effective\napproach. A project upgraded from an older Genesis release safely uses\n`focused.v1` until `genesis init` or `genesis engineering set focused.v1`\nrecords the file.\n\nHosts that manage project environments can call `inspectEnvironment()`.\nConcrete Stack integrations may propose public, non-secret Environment\ndefaults such as the database driver selected by that integration. `genesis\nstack add` copies those proposals into the project's `## Environment defaults`\ncontract; explicit host or user values still take precedence. The catalog's\nJSKIT MySQL and PostgreSQL pieces propose `DB_CLIENT=mysql2` and\n`DB_CLIENT=pg`. Laravel database integrations also propose their conventional\nconnection, host, port, database, and username while leaving passwords and\nother secrets unset.\nA project may edit its complete `## Resources` and `## Environment defaults`\nsections in `genesis/stack.md` so an imported C++, PHP, Python, older, or\ndeliberately customized application keeps its real names and public constants.\nAn optional readable `## Environment files` section declares safe\nproject-relative dotenv projections such as `.env`. Selection materializes\nthe component proposal once, after which the project declaration is\nauthoritative and may use `- Nothing.`. Genesis reports public defaults, resource declarations,\nvalue-free missing-input diagnostics, and paths. It never returns supplied\nenvironment values, writes files, stores secrets, or decides which resolved\nhost values should be materialized.\n\nConsumers may define additional `##` sections in a project Stack, while Stack\ncomponents may propose initial bodies for them. Selection materializes each\nunambiguous proposal into `genesis/stack.md` and returns one preparation prompt\nthat asks the current agent to make every heading true. Existing project\nsections are preserved and identified for evidence-based review. Thereafter\nthe exact project text is durable across catalog upgrades, participates in\nStack identity and prompt context, and is exposed through\n`inspectStackSection()`. The body is opaque: Genesis does not parse its\ncommands, infer its purpose, or execute it. Competing proposals are reported\nmechanically unless the project already records its decision.\n\nThis is the boundary for every consumer-specific operation. The consumer that\nnames a section owns its schema, validation, runtime mapping, execution, and\nproof of success. Genesis has no model of starting, preparing, deploying,\npackaging, migrating, serving, probing, or supervising a project. A web host,\nnative toolchain, firmware publisher, desktop signer, or any future consumer\ncan define different sections without a Genesis compiler change.\n\nStandalone and non-Node hosts can inspect these same normalized contracts\nwithout importing the JavaScript API or parsing Markdown:\n\n```bash\ngenesis inspect environment --json\ngenesis inspect section 'Consumer operation' --json\n```\n\nWithout `--json`, the commands print concise human-readable summaries. They\nnever interpret or execute a consumer-owned section.\n\nAt session start, Codex receives only a short explanation of how Genesis is\norganized. After it locates the source involved in a request, it can load the\nspecific explanatory and technology context with:\n\n```bash\ngenesis context src/path/to/file\n```\n\nBefore introducing another helper or public operation, query the current\nfunction inventory:\n\n```bash\ngenesis index normalizeNote\ngenesis index src/notes\n```\n\nThis is not merely a README suggestion. The new-session and post-compaction\nguide, generated work prompts, and the installed `genesis-project` skill tell\nthe agent to run `genesis context` after locating relevant source and to run\n`genesis index` before adding another helper or public operation. Genesis\ncannot force a model to obey a prompt, so this is not a hidden command gate.\nThe delivered prompt is tested, and the transcript plus ordinary Git review\nremain the way to confirm that a particular agent followed it.\n\n`genesis index` answers a structural question—what indexed functions or methods\nalready exist by name or path. It does not prove semantic equivalence. The\nagent must still inspect the implementation and direct call sites before\nreusing or consolidating behavior.\n\n`genesis index` regenerates two deterministic projections. Machine City is the\ndetailed physical view: indexed files, line and byte weights, public and\ninternal functions or methods, signatures, source/test role, language, and\nextractor provenance. Program City is intentionally smaller: conceptual\nsubsystems, Program operations, informational helper maps, and links to their\nimplementing source files.\nBoth are derived JSON, not receipts, authority, or correctness claims. An\nextractor warning does not stop ordinary work.\n\nThe selected Stack decides which structural extractors run. Genesis uses the\nTree-sitter-backed [ast-grep JavaScript API](https://ast-grep.github.io/guide/api-usage/js-api.html)\nthrough one shared engine. Built-in adapters cover JavaScript/TypeScript,\nPython, Java, C#, C/C++, PHP, Go, Rust, Ruby, Kotlin, and Shell. A future technology\nadds its adapter through its Stack piece rather than teaching Genesis prompts\nto parse that language.\n\nThe project Codex and Claude Code hooks and OpenCode plugin use the same short operating guide\nfor a new session and after compaction. They record no conversation message,\nblock no completion, and request no follow-up turn. Implementation prompts\ncompose selected Stack `Post-change` guidance into the original implementation\nturn, and the project skill keeps intentional Blueprint and affected Program\nchanges aligned there.\n\nDeslop runs only when explicitly requested. With no stated scope it reviews the\nagent's own changes for the current task across preceding turns, committed or\nuncommitted. An explicit commit, first-parent count, or range takes precedence\nregardless of authorship. The agent establishes ownership from task and edit\nhistory, preserves unrelated edits and existing staging, and asks for scope\nwhen ownership is unclear. A dirty worktree is allowed, and cleanup remains\nuncommitted for review. Genesis supplies the behavior-preserving boundary and\nscope rules. Selected Stack components add technology-specific Deslop guidance\nwithout weakening or broadening that contract.\n\n### Deslop your changes or specified commits\n\nInside Codex, OpenCode, or another skill-aware coding agent, ask directly:\n\n```text\nDeslop\nDeslop the last commit\nDeslop the last 5 commits\nDeslop commit a1b2c3d\nDeslop a1b2c3d..d4e5f6a\n```\n\nThe installed `genesis-deslop` skill generates the canonical project prompt\nonce when the request was not already generated by Genesis. It follows that\nprompt in the same agent turn; it does not start another agent or create a\nsynthetic follow-up turn.\n\nFor a host integration, shell workflow, or agent without automatic skill\nselection, generate the same complete prompt explicitly:\n\n```bash\ngenesis prompt --task deslop\ngenesis prompt --task deslop \"Deslop the last commit\"\ngenesis prompt --task deslop \"Deslop the last 5 commits\"\ngenesis prompt --task deslop \"Deslop commit a1b2c3d\"\ngenesis prompt --task deslop \"Deslop a1b2c3d..d4e5f6a\"\n```\n\nGive the printed prompt to the coding agent that has access to the repository.\nGenesis packages four relevant layers: the explicit scope request; the\nportable behavior-preserving contract from `genesis-deslop`; the selected\nengineering approach; and the effective `Deslop` prose from every selected\nStack component. Project additions or overrides from\n`genesis/stack/<component>.md` are applied before that Stack prose is composed.\nThe main `genesis/stack.md` records component selection and durable project\noperations; it intentionally does not duplicate installed guidance bodies.\n\nThe whole dirty diff is not automatically the agent's work. Deslop preserves\nthe user's and other agents' changes, including edits in the same files. With\nno changes of its own for the task, it reports that there is nothing to clean\nup; it does not silently select the latest commit. Its result is a normal\nuncommitted diff for review and a later commit. It never amends selected commits,\nsilently fixes newly discovered defects, or runs as an automatic completion phase.\n\nProjects can customize a selected technology through its matching file, such\nas `genesis/stack/jskit.md`:\n\n```markdown\n# Stack customization: jskit\n\n## Add\n\n### Description\n\nAdditional project-specific context about how JSKIT is used here.\n\n### Guidance\n\n- Additional project-specific implementation and review guidance.\n\n### Post-change\n\n- Additional project-specific work to perform before the implementation turn completes.\n\n### Deslop\n\n- Additional project-specific cleanup guidance.\n\n## Override\n\n### Description\n\nA replacement for the installed JSKIT description.\n\n### Guidance\n\n- Replacement installed implementation and review guidance.\n\n### Post-change\n\n- Replacement installed post-change work for the implementation turn.\n\n### Deslop\n\n- Replacement installed cleanup guidance.\n```\n\nEvery field is optional. For each field, Genesis uses the installed value,\nreplaces it when `Override` supplies that field, then appends the corresponding\n`Add` content. Customization affects only `Description`, `Guidance`,\n`Adoption`, `Post-change`, and `Deslop`; component dependencies, Agent Skill\nsource, resources, and verification commands retain their installed contracts.\n`genesis stack add` preserves these matching customization files.\n\nPrompt generation remains available for other agents and explicit tasks:\n\n```bash\ngenesis prompt\n```\n\nGive the printed prompt to Vibe64 or another coding agent with access to the\nproject. Review ordinary edits through Git.\n\nAn immediate improvement request can be included directly:\n\n```bash\ngenesis prompt \"Add filtering by note title\"\n```\n\n## Prompt tasks\n\n```bash\ngenesis prompt                                      # implementation work\ngenesis prompt --task start                        # open a new or existing project conversation\ngenesis prompt --task adopt                        # import an existing project's complete contract\ngenesis prompt \"Add filtering by note title\"\ngenesis prompt --task deslop                        # clean up the agent's own task changes\ngenesis prompt --task deslop \"Deslop the last commit\"\ngenesis prompt --task deslop \"Deslop the last 5 commits\"\ngenesis prompt --task deslop \"Deslop commit a1b2c3d\"\ngenesis prompt --task program                       # refresh explanation\ngenesis prompt --task blueprint \"Start on notes\"   # update product intent\ngenesis prompt --task describe                      # create/refresh Blueprint and complete Program\ngenesis prompt --task review                        # compare intent, code, and explanation\n```\n\nThe eight task types are deliberately explicit:\n\n- `start` opens the project conversation. For a new project it establishes what\n  is being built, who or what will use or invoke it, and the first useful\n  observable outcome before presenting relevant choices from the live Stack\n  and engineering-profile catalogs. A partial reply resolves only what it\n  explicitly answers. An existing project receives none of those new-project\n  questions or catalogs. Its opening contains the full Blueprint, concise\n  selected Stack and Program summaries, and full selected Guidance separated by\n  component headings; detailed Program modules, sources, operations, indexes,\n  and skills are loaded later with `genesis context <relevant-path...>`. It\n  checks `genesis stack list` before proposing an additional technology.\n- `adopt` imports an existing application's factual operational and product\n  contracts into Genesis metadata. It composes technology-specific Adoption\n  requirements from the selected Stack and does not change application code.\n- `work` implements the Blueprint and optional request using current code,\n  Program, the selected engineering approach, selected Stack context, and\n  progressively loaded Agent Skills.\n- `deslop` explicitly requests behavior-preserving cleanup of the agent's own\n  task changes, committed or uncommitted. An explicit commit, first-parent\n  count, or range takes precedence. It preserves unrelated work and existing\n  staging, permits a dirty worktree, and leaves its result uncommitted.\n- `program` edits only `genesis/program/` to explain the code that exists, with\n  selected Stack guidance available for technology-specific correctness.\n- `blueprint` edits only `genesis/blueprint.md` from explicit user intent. It\n  must not infer product requirements from accidental implementation behavior.\n- `describe` creates or refreshes both the non-technical Blueprint and the\n  complete useful Program from the current codebase, optional user guidance,\n  and selected Stack guidance where it affects accurate explanation.\n- `review` is read-only. It asks the agent to compare Blueprint, code, Program,\n  and tests, identify contradictions and gaps, and distinguish evidence from\n  inference.\n\nPrompt generation is read-only. Missing external resources are reported in\nthe prompt but do not prevent its generation. Genesis never invents values.\n\nUse `--json` to receive the prompt and its machine-readable context as one\nobject.\n\n## Stack\n\nList and select pieces from the installed optional catalog:\n\n```bash\ngenesis stack list\ngenesis stack add jskit jskit-mysql\n```\n\n### What `stack add` actually does\n\n`genesis stack add` is deterministic project preparation, not an application\ninstaller. It:\n\n1. reads the explicitly installed Stack catalog;\n2. resolves requested components, declared dependencies, and conflicts;\n3. records the owning Stack package and complete resolved component selection;\n4. copies every missing operation proposal into `genesis/stack.md` as a\n   project-owned contract;\n5. synchronizes any authoritative Agent Skill explicitly declared by those\n   components; and\n6. prints one heading-by-heading preparation prompt.\n\nThat final prompt asks the current agent to make the materialized contracts\ntrue: create the necessary source and scripts for a new project, or replace a\ncomplete project section when existing source proves that a proposal is wrong.\nGenesis does not execute the prompt. If the agent ran `stack add`, the prompt is\nalready visible as its command result and the Genesis project instructions tell\nit to continue in the same task. If a person ran the command, they give the\nprinted prompt to their agent. Repeating an already-complete selection prints no\nsecond preparation prompt.\n\n`stack add` itself does **not** run `npm install`, Composer, CMake, a database\nmigration, a development server, or deployment. Those operations belong to the\napplication and the consumer named by the relevant project contract.\n\nFor the ordinary naked CLI, an explicitly installed first-party\n`genesis-stack` package bootstraps an unconfigured project without exposing\ncatalog package plumbing to the agent. Genesis enumerates component ids from\nthat package; it does not hard-code technology names or scan arbitrary npm\npackages. A host can instead supply another catalog explicitly with\n`--stack-package`. Once a selection records its owning package in\n`genesis/stack.md`, ordinary commands use that recorded package directly.\n\n`genesis/stack.md` records the owning Stack package, component ids, and the\nproject-owned operation contracts proposed during selection. After the first\nselection, ordinary commands resolve the recorded package without another\nflag, but later catalog releases never silently rewrite those contracts.\nSelecting no components is valid. `genesis-stack` currently contains C/C++,\nC#, Go, Java, Kotlin, Node.js, PHP, Python, Ruby, Rust, and Shell, plus Vue,\nMySQL, PostgreSQL, JSKIT, JSKIT database integrations, Laravel, and Laravel\ndatabase integrations.\n\n### Why `genesis/stack.md` is deliberately small\n\nThe project Stack is a durable contract, not a copy of every framework manual.\nIt contains only:\n\n- the catalog package that owns the selected component definitions;\n- the resolved component ids;\n- Genesis-owned `Resources`, `Environment defaults`, `Environment files`, and\n  `Verification` contracts that are relevant to this project; and\n- exact consumer-owned sections such as `Workspace setup`, `Outputs`, or\n  `Deployment` when selected components propose them.\n\nConcise technology Guidance, Adoption, Post-change, and Deslop prose stays in\nthe installed catalog, while larger authoritative instructions remain in\ntechnology-owned Agent Skills or official documentation. Genesis composes the\nrelevant guidance into prompts and path-focused context on demand. Application\nsource remains the authority for what actually exists.\n\nSelection copies operation proposals once. From that point onward, the complete\nproject sections in `genesis/stack.md` win: upgrading `genesis-stack` can improve\nguidance for future work but cannot silently change how this application is\ninstalled, checked, run, or deployed.\n\nComponents may contribute:\n\n- a concise description and supplemental Guidance used across relevant tasks;\n- existing-project Adoption requirements used only while importing a codebase;\n- optional Post-change work composed into the original implementation turn;\n- one authoritative Agent Skill directory when the component owns one;\n- generic external-resource requirements;\n- cleanup advice composed on top of the core explicit Deslop contract;\n- structural code indexers used by Machine City and function lookup;\n- default verification commands.\n\nResources, environment declarations, Verification, and opaque consumer\nsections are proposals, not live inherited behavior. `genesis stack add`\nmaterializes them into `genesis/stack.md`, prints a one-time\nheading-by-heading preparation prompt, and expects the implementation or the\ncomplete project section to be made truthful in that same task. Repeating the\nsame selection emits no second preparation prompt.\n\nTechnology-specific supplemental rules intentionally remain in Stack pieces.\nGeneral `Guidance` enriches implementation, review, Program, description, and\ncleanup tasks; `Adoption` adds import-only requirements; `Post-change` adds\nwork to finish in the original implementation turn; `Deslop` adds\ntechnology-specific cleanup rules to Genesis's invariant behavior-preserving\ncontract. When several components contribute one of these prose fields,\nGenesis retains each complete contribution under its component heading in\ndependency-first selected order; it does not blend or semantically deduplicate\ntheir instructions. None shadows an official generic technology skill or assumes that an\nupstream skill contains every rule Genesis needs.\n\nGenesis core contains no Stack pieces and no database, framework, language, or\nplatform dependency. See [Stack components](docs/stack-components.md).\n\n### The current JSKIT command contract\n\nSelecting `jskit` currently proposes the following operations. These are the\nonly commands in the base JSKIT Stack proposal; an application may deliberately\nadd or replace complete project sections when its real scripts differ.\n\n| Project contract | Command or probe | Purpose | Executor |\n| --- | --- | --- | --- |\n| `Workspace setup` | `npm install` | Install development dependencies when `package.json` exists. | The operator or host preparing a workspace, such as Vibe64. |\n| `Outputs` | `npm run develop` | Start the interactive development web application. | The operator or output host. |\n| `Outputs` readiness | `GET /api/health` → `200` | Decide when the development output is ready; preferred port is `3000`. | The output host. |\n| `Verification` | `npm run verify` | Run the application's finite declared checks. | `genesis verify` executes this one directly. |\n| `Deployment` prepare | `npm ci` | Recreate production dependencies from the lockfile. | The deployment consumer. |\n| `Deployment` build | `npm run build` | Produce the deployable application build. | The deployment consumer. |\n| `Deployment` serve | `npm start` | Start the built production application. | The deployment consumer. |\n| `Deployment` readiness | `GET /api/health` → `200` | Prove that the deployed service is ready. | The deployment consumer. |\n\nThe JSKIT proposal also declares `.env` as its environment projection and says\nthat inactive deployment workspaces may recreate `node_modules`; it deliberately\ndoes not mark built output disposable.\n\nSelecting `jskit-mysql` additionally selects `mysql`, `jskit`, and `nodejs`,\nsets the public default `DB_CLIENT=mysql2`, and declares either\n`DB_HOST`/`DB_PORT`/`DB_NAME`/`DB_USER`/`DB_PASSWORD` or `DATABASE_URL` as the\ndatabase input contract, with optional `TEST_DB_NAME`. It does **not** invent a\ndatabase-preparation command. If the application implements a real migration or\nseed script, the agent records that exact command in the complete project\nsections whose consumers need it. Local authentication similarly requires the\napplication to declare `AUTH_LOCAL_SESSION_SECRET` without committing its\nvalue.\n\n### How the Stack contract is enforced\n\nEnforcement deliberately stops at ownership boundaries:\n\n- Genesis strictly parses component ids, dependencies, conflicts, resources,\n  public defaults, environment-file paths, and Verification commands.\n- Current-format projects must contain every project-owned section required by\n  their selected components. Missing materialized contracts make Stack reads\n  and `genesis check` invalid instead of falling back to a newer catalog.\n- `genesis check` validates structure, reports missing declared input names, and\n  reports verification evidence as current, stale, missing, or unconfigured.\n- `genesis verify` executes only the exact argv recorded under\n  `## Verification`, without a shell, and records the passing code and Stack\n  identity.\n- Consumer-owned sections are intentionally opaque to Genesis. The consumer\n  that names `Workspace setup`, `Outputs`, `Deployment`, packaging, signing, or\n  another operation owns its grammar, execution, and proof.\n- The one-time preparation prompt tells the agent to make every heading true,\n  but prompt compliance is not mechanical proof. Source, focused tests, the\n  consumer's validator, runtime behavior, and Git review remain the evidence.\n\n## Verification\n\nRun the Stack's declared checks explicitly:\n\n```bash\ngenesis verify\n```\n\nGenesis applies public Stack defaults beneath explicit environment values,\nevaluates generic resource declarations, and runs each declared Verification\ncommand without a shell. A complete successful run writes only\n`.genesis/verification.json`, recording:\n\n- the exact Git-visible code hash;\n- the selected Stack hash;\n- the commands that passed.\n\nThe evidence becomes stale when code, selected components, declared resources,\nor verification commands change. Description, Guidance, Adoption, Post-change,\nAgent Skill, and Deslop prose do not rewrite what an already-run command proved.\nA failed verification removes prior passing evidence before running.\nVerification does not claim whole-product correctness.\n\nThe project owns the commands in `genesis/stack.md`:\n\n```markdown\n## Verification\n\n- Verify `tests`: `npm` `test`\n- Verify `build`: `npm` `run` `build`\n```\n\n## Inspection\n\n```bash\ngenesis check\n```\n\n`check` is read-only. It reports only structural or recorded facts:\n\n- whether the project format is current, outdated, unversioned, newer than the\n  running CLI, or invalid;\n- Blueprint, engineering approach, and Stack validity;\n- selected Agent Skill presence and structural validity;\n- Program presence and structural validity;\n- environment declarations and consumer-owned Stack extensions as `ready`,\n  `blocked`, or honestly `unconfigured`;\n- missing Stack-declared environment inputs (without claiming the service is\n  reachable);\n- verification evidence as `current`, `stale`, `missing`, `invalid`, or\n  `unconfigured`.\n\nHere, “valid” means parseable and internally consistent: referenced source\nfiles exist, declared environment inputs are non-placeholder, and recorded\nhashes match. It does not mean that the product behavior makes sense. Generate\n`genesis prompt --task review` for that semantic, evidence-based comparison.\n\nGenesis does not label Program semantically current. Program is ordinary\nMarkdown reviewed through Git.\n\nWhen `check` reports an outdated or unversioned project, migrate its Genesis\nfiles to the running CLI's project format:\n\n```bash\ngenesis migrate\n```\n\nMigration is deterministic and forward-only. The format 2 migration snapshots\nthe previously effective Stack operations into project-owned sections before\nremoving component-runtime fallback; format 3 adds the portable Collaboration\ndeclaration. Migration also synchronizes managed skills\nand hooks, regenerates derived indexes, and then returns a fresh `check`\nresult. A newer project is never downgraded. Every project-scoped CLI\ninvocation warns when the recorded format does not match the running CLI, and\nordinary project operations stop until the migration is resolved.\n\n## Public API\n\n```js\nimport {\n  adoptProject,\n  addStack,\n  check,\n  generatePrompt,\n  getContext,\n  indexCodebase,\n  initialize,\n  inspectCollaboration,\n  inspectEngineering,\n  inspectEnvironment,\n  inspectSkills,\n  inspectStackSection,\n  installCodex,\n  listEngineeringProfiles,\n  listStackPieces,\n  listParsers,\n  installParsers,\n  verifyParsers,\n  parserEnvironment,\n  migrate,\n  projectSessionContext,\n  projectTurnContext,\n  setCollaboration,\n  setEngineeringProfile,\n  syncSkills,\n  verify,\n  withTrustedGitRepository,\n} from 'genesis-compiler';\n```\n\n`initialize()` installs the project files, Genesis workflow skills, selected\nStack skills, and local Codex hooks.\nExtra language parsers install on first use, outside the project's dependencies.\nThe CLI can also prepare and verify parsers for an offline host; see\n[language parser management](docs/parsers.md).\n`migrate()` updates recognized older Genesis project-file formats and returns\nthe resulting structural check for hosts such as Vibe64.\n`adoptProject()` also returns the initial `adopt` prompt for an existing\ncodebase. `installCodex()` installs the optional global discovery plugin.\n`listEngineeringProfiles()`, `inspectEngineering()`, and\n`setEngineeringProfile()` expose the same built-in catalog and portable\nproject selection used by the CLI and hosts.\n`inspectCollaboration()` and `setCollaboration()` expose the portable\ncommunication declaration and Genesis-owned choice expansions.\n`inspectSkills()` and `syncSkills()` expose the same inspection and narrow\nsynchronization used by the CLI. Both accept `projectRoot` and `stackPackages`.\nInspection returns aggregate status, per-skill status for valid installed copies,\nand diagnostics for missing, invalid, outdated, customized, or unmanaged skills.\nSynchronization returns changed paths, preservation diagnostics, and the resulting\n`inspection`. Hosts own source-write exclusion and assistant context lifecycle.\n`projectSessionContext()` composes stable project guidance with one explicitly\nsupplied host-driver result. `projectTurnContext()` invokes that same optional\ndriver for the separate untrusted turn lane without accepting user-message\ntext.\n`getContext()` resolves source paths to the Program modules that cite them,\nthe functions already declared there, selected Stack guidance, available Agent\nSkills, and verification commands. `indexCodebase()` regenerates or returns the\ndetailed Machine City and simple Program City projections.\n`inspectEnvironment()` returns normalized Stack resource declarations,\npublic non-secret defaults, value-free missing-input diagnostics, and dotenv\nprojection paths without returning any supplied environment value.\n`inspectStackSection()` returns one exact consumer-owned section without\ninterpreting or executing its contents.\n\nHosts that already validate access to a shared worktree may wrap an operation\nin `withTrustedGitRepository(absoluteWorktreeRoot, () => inspectEnvironment({\nprojectRoot: absoluteWorktreeRoot }))`. This explicitly trusts that one\ncanonical worktree for Genesis's Git subprocesses in the callback's async\ncontext. Concurrent and nested operations remain isolated; it does not change\nglobal Git configuration, repository ownership, or filesystem permissions.\nWithout this explicit host grant, Git's ownership check remains in force and\nan ownership rejection reports `GIT_REPOSITORY_UNTRUSTED`.\n\nNormalized results identify their stable public contract in the `contract`\nfield: `genesis.collaboration.v1`, `genesis.engineering.v1`,\n`genesis.environment.v2`, `genesis.session-context.v1`,\n`genesis.stack-section.v1`, `genesis.turn-context.v1`, or\n`genesis.verification.v1`. A consumer defines any schema embedded inside the\nopaque section body.\n\nA host such as Vibe64 can send the generated prompt to its existing agent:\n\n```js\nconst work = await generatePrompt({\n  projectRoot,\n  task: 'work',\n  request: userMessage,\n});\n\nawait currentAgent.send(work.prompt);\n```\n\nThe host retains model choice, conversation context, reasoning presentation,\nsteering, interruption, permissions, and lifecycle ownership.\n\n## Promise\n\nGenesis generates transparent context-rich prompts, performs deterministic\nproject operations, and records exact verification evidence. Code, tests, Git\nreview, and the user's chosen agent remain responsible for implementation. It\ndoes not claim universal semantic convergence, exhaustive coverage, or\nwhole-product correctness.\n\n## Authored subsystems (version zero)\n\n`genesis/subsystems.md` is the single authored map connecting architectural\nresponsibilities to Program operations and data. Program directories are only\nnavigation; Genesis never infers subsystem membership from them. Blueprint\nremains non-technical product intent. Source, migrations and runtime behavior\nremain evidence; the map does not define application behavior or database DDL.\n\n```markdown\n# Subsystems\n\n## `forms` Forms\n\nOwns reusable form authoring, rendering, and answer validation.\n\n### Program\n- `genesis/program/forms/render.md`\n\n### Data owned\n- Table `database` `default` `form_definitions`\n\n### Data used\n- Nothing.\n```\n\nEach subsystem has a unique lowercase hyphenated id, title, responsibility\nprose, and exactly the three shown sections. Each Program module is assigned\nexactly once, by its complete project-relative path. Each table has at most one\nowner. Data used names a table owned by another declared subsystem. Empty\nsections explicitly say `- Nothing.`; an empty initialized map contains\n`# Subsystems` followed by `- Nothing.`. Data-only and code-only subsystems are\nvalid. No subsystem hierarchy is inferred from paths.\n\nTable references contain three distinct values: declared Stack resource **id**,\nschema, and table. `default` selects that resource's default schema; other schema\nnames are literal. Never put host database names or environment values here.\nGenesis validates declarations and resource references without opening a database.\nHosts resolve table references against their inspected schema and show missing\nreferences and unassigned tables explicitly; the map is not a complete schema\ninventory. Table/column descriptions and relationships remain database metadata.\n\n`inspectSubsystems({ projectRoot })` and `genesis inspect subsystems --json`\nreturn `genesis.subsystems.v0`, normalized entries, status and a deterministic\nidentity. Program inspection additionally validates membership and referenced\nmodules. Context includes the relevant subsystem through its Program Sources;\n`context .` includes all subsystems. Program City uses authored titles and table\nassociations, including data-only districts, and changes its hash when the map\nchanges. Opening context stays concise; detailed associations load on demand.\n\nAdoption, Program refresh, work prompts, session guidance and installed workflow\nskills maintain the map alongside Program in the same turn. Review checks it\nread-only; Blueprint-only work leaves it alone. Ordinary private helper edits\nneed no map change. Existing projects do not need a bulk update: missing or empty maps preserve\nProgram access and instruct the agent to author the map from source before its\nnext implementation task. Until then, operations have no declared subsystem;\nthere is no folder-based compatibility reader or automatic ownership inference. Initialization creates an empty map without replacing one.\n","readmeFilename":"README.md"}