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change evidence, impact review, and verification receipts for developers, CI, and coding agents.","maintainers":[{"name":"mirnoorata","email":"mirnoorata@gmail.com"}],"readme":"# Codexa\n\n[![Check](https://github.com/mirnoorata/codexa/actions/workflows/check.yml/badge.svg)](https://github.com/mirnoorata/codexa/actions/workflows/check.yml)\n[![npm](https://img.shields.io/npm/v/%40mirnoorata%2Fcodexa)](https://www.npmjs.com/package/@mirnoorata/codexa)\n\n**Understand the code. See what a change could affect. Check the evidence.**\n\nCodexa helps developers and AI coding assistants work on a repository with\nmore context and fewer guesses. It builds a local map of your code, connects\nfiles to their dependencies and tests, and produces readable reports about\nproposed and completed changes.\n\nThink of it as a map and a change checklist for your project. The person—or\ncoding assistant—still drives. Codexa points out the bridge you might want to\ncheck before taking the truck across it.\n\nUse it from a terminal, with **Codex**, **Claude Code**, or another compatible\ncoding assistant, or in **GitHub Actions** to help review pull requests. The\ncore needs **no API key, hosted account, or database**. Codexa is free and\nMIT-licensed; your AI assistant and any optional hosted services have their\nown requirements and costs.\n\n[Get started](#quick-start) · [Connect an assistant](#connect-your-coding-assistant) ·\n[Everyday use](#the-everyday-workflow) · [GitHub reviews](#review-pull-requests) ·\n[Troubleshooting](#troubleshooting) · [Full reference](docs/reference.md)\n\n> **Maintainer expectations:** Codexa is a focused project maintained by one\n> person in spare time. Expect replies in days to weeks. Please discuss larger\n> changes before opening a PR; see [Contributing](CONTRIBUTING.md).\n\n## What does it actually do?\n\n| Your question | What Codexa gives you |\n| --- | --- |\n| “Where does this behavior live?” | Relevant files, functions, and exact text matches, with related code when useful. |\n| “What might break if we change this?” | A map of connected code and tests that may be affected. |\n| “What should we test?” | Suggested checks tied to the changed files and known relationships. |\n| “Did the work stay within the plan?” | A comparison between a saved plan and the actual edits, including unexpected changes. |\n| “What evidence supports this handoff?” | A **proof card**: a summary of the plan, verification evidence, and remaining gaps. |\n| “What is this pull request changing?” | A **change receipt**: a report covering committed changes, possible impact, and review guidance. |\n\nFor example, changing a login timeout can affect more than one number. Codexa\ncan help locate the setting, identify code that uses it, suggest related tests,\nand flag edits outside the agreed scope. Its findings depend on what it can\nread and connect in your repository; it cannot predict every runtime behavior.\n\nCodexa supplies context and checks. Your editor or assistant makes the edits,\nand your project's tests establish whether the behavior works. A green-looking\nreport is useful evidence, not a force field.\n\n## Quick start\n\nYou need **Node.js 22 or newer**, **npm** (included with Node.js), **Git**, and a\nlocal Git repository—the project folder you want to inspect. You do not need\nto clone Codexa itself or install an AI assistant to use the terminal commands.\n\n### 1. Install\n\nRun these commands in a terminal:\n\n```bash\nnode --version\ngit --version\nnpm install -g @mirnoorata/codexa\ncodexa --version\n```\n\n### 2. Try it on your project\n\nReplace `/path/to/project` with your repository's actual folder path. Quote the\npath if it contains spaces. In the examples below, `.` means “this folder.”\n\n```bash\ncd /path/to/project\ncodexa index .\ncodexa repo-map .\n```\n\n`index` reads the repository and creates the local map. `repo-map` shows the\nranked files and modules. This terminal-only path needs no assistant setup.\n\nAsk a question relevant to your project:\n\n```bash\ncodexa search . --query \"login timeout\"\n```\n\nThis is an example query, not a built-in demo: results depend on your code.\nFor ongoing use, follow the [generated-files guidance](#what-gets-written-to-your-repository)\nand choose your assistant setup below.\n\n**No global install?** Prefix commands with `npx -y @mirnoorata/codexa`, for\nexample `npx -y @mirnoorata/codexa index /path/to/project`. npm may download the\npackage; the default indexing itself runs locally.\n\n## Connect your coding assistant\n\nCodexa uses **MCP (Model Context Protocol)**, the connection that lets an AI\nassistant ask external tools for information. The assistant runs the model;\nCodexa provides repository context. Install and sign in to your chosen\nassistant separately.\n\n### Codex\n\nFrom your project folder:\n\n```bash\ncodexa init . --agents-md\ncodexa session-start .\n```\n\nThis creates the index, adds the Codexa server to `.codex/config.toml`, installs\nCodex startup/edit hooks, and adds a small managed workflow block to `AGENTS.md`.\nOmit `--agents-md` if you want to manage your own agent instructions. If a\nCodexa plugin already supplies your MCP connection, avoid registering a second\nserver for the same repository.\n\nOpen or reload that same project in Codex and trust it when prompted.\nProject-scoped MCP configuration is loaded only for trusted projects. In\nCodex CLI, `/mcp` shows active connections; see the\n[official MCP setup guide](https://learn.chatgpt.com/docs/extend/mcp).\n\nA successful `session-start` check confirms observable setup and index state;\nit cannot prove that an already-running assistant has loaded the server.\n\n**Windows:** use `codexa init . --agents-md --no-hooks` for native Windows\nMCP-only setup. The generated shell hooks require a POSIX environment such as\nWSL. macOS and Linux can use the standard command above.\n\n### Claude Code\n\nFor the simplest connection:\n\n```bash\ncodexa init . --claude --claude-md --no-hooks\ncodexa session-start .\n```\n\nThis also writes the server entry to `.mcp.json` and workflow guidance to\n`CLAUDE.md`. Restart Claude Code in that repository and approve the project MCP\nserver if prompted. `--no-hooks` disables Codexa's Codex hooks; this setup gives\nClaude tools and instructions, without Claude hooks or slash commands.\n\nWant automatic startup guidance, a review hook, and commands such as\n`/codexa-plan` and `/codexa-review`? Use the bundled\n[Claude Code plugin](integrations/claude-code/README.md#install). Choose either\nthe plugin or the `.mcp.json` connection above to avoid duplicate servers.\n\n### Other MCP clients\n\nConfigure a local command server in your client's MCP settings:\n\n```json\n{\n  \"mcpServers\": {\n    \"codexa\": {\n      \"command\": \"codexa\",\n      \"args\": [\"serve\", \"/path/to/project\", \"--auto-refresh\"]\n    }\n  }\n}\n```\n\nReplace the path and adapt the outer configuration format to your client.\nThe client must be able to find `codexa` and access the repository. It launches\nthe server; `serve` is not an interactive chat command.\n\nFresh installs expose three tools: `search`, `change_plan`, and `capabilities`.\nThat small menu is intentional: `capabilities` provides access to the remaining\noperations. Use `--tools full` with `init` or `serve` if your client needs every\noperation listed directly.\n\nThe default connection uses a local process. Optional HTTP transport binds\nonly to the local machine; Codexa does not ship a public remote server.\n\n## The everyday workflow\n\n**Use Codexa when it resolves uncertainty.** A small fix in a known file may\nneed only direct inspection and the project's normal tests. No ceremony is\nrequired for changing a comma. A change spanning several files benefits more\nfrom planning and review.\n\nFor a coding assistant, a useful request is:\n\n> Find where login timeouts are handled. Use Codexa if the target or impact is\n> unclear. Before a substantial edit, save a change plan. Make the change, run\n> the relevant checks, and review the result against the plan. Tell me what\n> remains unverified.\n\nYou can also run that workflow yourself. This example assumes your repository\nhas `src/auth.ts`; substitute a real file and task:\n\n```bash\ncodexa change-plan . --task \"Adjust the login timeout\" --file src/auth.ts --task-id login-timeout --save-snapshot\n```\n\nRead the plan, make the edits, and run the checks appropriate to your project.\nThen review the work **before committing**, while the edits are still visible\nas local changes:\n\n```bash\ncodexa post-edit-review . --task-id login-timeout\n```\n\nReport checks you actually ran with `--ran-command`. For example, **only if\n`npm test` is a real check in your project and you ran it**:\n\n```bash\ncodexa post-edit-review . --task-id login-timeout --ran-command \"npm test\"\n```\n\nThat flag records a claim; it does not execute the command. Codexa checks\nwhether the reported command could cover the relevant work. A command that\nhides failures, such as `npm test || true`, does not earn credit. Codexa cannot\ndetect a completely fabricated report.\n\nFor a formal handoff, `codexa prove . --task-id login-timeout` summarizes the\nsaved plan, available evidence, and unresolved gaps. Supply actual command\nreports or selected verification artifacts when the handoff needs them.\n\nStartup and edit hooks reduce manual steps, but their reviews do not replace\none final review with the actual test evidence. Detailed workflow, invariants,\nand repeat-attempt controls are in the [reference](docs/reference.md#the-everyday-workflow).\n\n### A few useful commands\n\nRun these from the project root, using your own file names and questions:\n\n| Command | Purpose |\n| --- | --- |\n| `codexa search . --query \"password reset\"` | Find a starting point. |\n| `codexa explain . --file src/auth.ts` | Inspect a file and its relationships. |\n| `codexa impact . --file src/auth.ts` | See what a change could affect. |\n| `codexa diff-impact .` | Inspect the impact of uncommitted changes. |\n| `codexa test-plan . --diff` | Get test suggestions for current edits. |\n| `codexa status .` | Check freshness and parser errors without refreshing. |\n| `codexa watch .` | Keep the index updated during a session; stop with Ctrl+C. |\n| `codexa doctor .` | Diagnose local setup problems. |\n\nMost context commands refresh an outdated index automatically. Use\n`codexa --help`, `codexa <command> --help`, or the\n[command reference](docs/reference.md#main-commands) for more options.\n\n## Review pull requests\n\nCodexa can generate a report for a committed branch without an AI assistant.\nFrom a **clean checkout of that branch**, with `origin/main` available locally:\n\n```bash\ngit fetch origin\ncodexa review . --base origin/main --head HEAD\ncodexa review . --base origin/main --head HEAD --format json\n```\n\nReplace `origin/main` if your repository uses a different base branch. Codexa\ncompares changes since the branches' common ancestor. `HEAD` must match the\nchecked-out commit, and the index must represent that clean checkout.\n\nTo add the same review to GitHub Actions:\n\n```bash\ncodexa init . --ci\n```\n\nReview and commit the generated `.github/workflows/codexa-review.yml` with your\nnormal PR process. It checks out the PR's exact head, uses read-only repository\npermissions, and writes results to the Actions summary and annotations. It\ndoes not post PR comments or run your project's tests. Keep your existing CI.\n\nThe default `observe` mode reports findings without blocking on them. `warn`\nadds warning annotations. Explicit `fail` mode can block on local plan drift,\nan unavailable requested local plan, or reported command failures. Suggested\nbut unrun tests alone do not fail the review. Invalid inputs and setup errors\ncan fail in any mode.\n\nSee [committed change receipts](docs/reference.md#committed-change-receipts)\nfor plan comparison, trust limits, and CI options.\n\n## What gets written to your repository?\n\n| Location | Contents | Usual Git treatment |\n| --- | --- | --- |\n| `.codex/codebase/` | Generated maps, relationships, and index. | Ignore; regenerate per checkout. |\n| `.codex/cache/` | Saved plans, session notes, review state, and optional caches. | Ignore; keep local evidence private. |\n| `.codex/static-analysis/` | Imported or explicitly generated scanner reports. | Ignore. |\n| `.codex/config.toml`, `.codex/hooks.json` | Codex connection and hooks from `init`. | Usually local; share deliberately. |\n| `.mcp.json` | Claude connection, when requested. | Inspect paths and existing servers before sharing. |\n| `AGENTS.md`, `CLAUDE.md` | Managed workflow block, only with the corresponding flag. | Share if useful to your team. |\n| `.codex/policies/` | Optional JSON policies for proof cards. | Share if they express team policy. |\n| `.github/workflows/codexa-review.yml` | Optional GitHub Actions review. | Commit to enable it. |\n\nAdd these generated paths to your project's `.gitignore` (Codexa does not add\nthem for you):\n\n```gitignore\n.codex/codebase/\n.codex/cache/\n.codex/static-analysis/\n```\n\nIf your MCP config and hooks are local to your machine, ignore those files too.\nAvoid ignoring the entire `.codex/` directory if your team tracks policies or\nsetup scripts there. Inspect generated launch paths before committing wiring;\n`init` supports portable wiring for already-tracked files. Each teammate and\nfresh checkout still needs its own install and index.\n\nRe-running `init` refreshes Codexa's managed configuration and preserves other\nMCP server entries. Optional instruction blocks replace only the region between\nCodexa's markers. `--policy-pack` creates local proof policies without\nreplacing existing policy files. See the\n[setup reference](docs/reference.md#codex-project-worktrees-and-local-setup)\nfor portability and managed-file behavior.\n\n## Support, privacy, and limits\n\n- **Language support:** TypeScript, JavaScript, and Python get the deepest\n  parsing. Rust, Go, and Java get shallower declarations and relationships.\n  Other recognized files receive lighter facts. External symbol reports can\n  extend coverage; this is not full compiler-level understanding of every language.\n- **Coverage:** Codexa reads supported Git-visible files, including unignored\n  new files. It skips common generated/dependency directories and source files\n  larger than 2 MiB. Impact analysis follows at most three relationship steps;\n  dynamic behavior and large repositories can need additional investigation.\n- **Privacy:** Default indexing and queries run locally without model calls.\n  Context returned to an AI assistant is handled under that assistant's data\n  policy. Optional OpenAI embeddings send selected source text and queries to\n  OpenAI; optional TypeSafe reranking sends queries and candidate source snippets\n  to TypeSafe. Both are off by default.\n- **Execution:** MCP tools can update Codexa's generated state, but do not edit\n  your source files or run verification commands. Optional **AutoVerify** lets\n  edit hooks run selected local checks after explicit user-owned configuration.\n  It is off by default and is not a sandbox.\n- **Evidence:** Directly observed facts, inferred relationships, and guesses\n  carry different confidence labels. Reported verification is distinguished\n  from AutoVerify execution. A proof card records evidence and gaps; it does\n  not certify that your code is correct or secure.\n\nThere is no web dashboard or hosted indexing service to operate. Optional\nembeddings, TypeSafe, language-server assistance, scanner imports, session\nmemory, and AutoVerify are documented in the\n[reference](docs/reference.md#optional-lanes).\n\n## Troubleshooting\n\n| Symptom | What to check |\n| --- | --- |\n| `codexa` is not found | Reopen your terminal, check npm's global executable directory is on `PATH`, or use the `npx` alternative. |\n| Installation fails building a native dependency | Check Node.js is 22+; Tree-sitter dependencies may need your platform's native build tools when a prebuilt binary is unavailable. |\n| The assistant cannot see Codexa | Run `codexa doctor .`, confirm the repository path, then reload that project in the assistant. In Codex, check project trust and `/mcp`. |\n| “Current-thread MCP: unverified” | The CLI cannot inspect your assistant's live connection. Check the assistant's active server list; this alone is not an installation failure. |\n| Missing, stale, or mismatched index | Run `codexa index .` in the actual checkout. Never copy an index from another worktree. |\n| Parser errors or missing relationships | Check `codexa status .`, language support, ignored files, and source-size limits. A degraded result is incomplete evidence. |\n| Committed review refuses to run | Resolve local changes, check out the requested head, and rebuild the index. Use `post-edit-review` for uncommitted edits. |\n| Hooks fail on native Windows | Re-run `init` with `--no-hooks` for MCP-only use, or use WSL for shell hooks. |\n\n### Updating or removing Codexa\n\nUpdate with `npm install -g @mirnoorata/codexa@latest`, re-run your chosen `init`\ncommand in each repository, and reload the assistant connection. Reuse optional\nflags such as `--claude` or `--agents-md` to refresh those integrations. Plain\n`init` preserves the existing tool profile; use `--tools core` to switch it.\n\nTo remove Codexa, first disable its server/plugin and remove only its managed\nconfig entries, hooks, and instruction blocks. Preserve other tools' settings.\nThen run `npm uninstall -g @mirnoorata/codexa`. Generated indexes can be removed;\nexport any plans or evidence you want to keep before deleting `.codex/cache/`.\nRemove its CI workflow too if you enabled one. There is no all-in-one uninstall\ncommand.\n\n## Codex Project Worktrees And Local Setup\n\nA Git worktree is another checkout of the same repository. Run `codexa init`\ninside each one so its configuration and index match its own code. Automate\nthat step in your project's setup if you create worktrees frequently.\n\nWhen **developing Codexa itself**, this repository includes a Codex local\nenvironment and bootstrap scripts that install locked dependencies, build the\npackage, and verify worktree setup. Those scripts are for this repository;\nordinary users do not need to copy them. See the\n[worktree and recovery guide](docs/reference.md#codex-project-worktrees-and-local-setup).\n\n## For contributors and curious readers\n\nCodexa's engine is TypeScript. Its main path is:\n\n```text\nRepository → local index → relevant context and change analysis → evidence report\n```\n\n| Area | Where to look |\n| --- | --- |\n| Installation and commands | [`src/init.ts`](src/init.ts), [`src/cli.ts`](src/cli.ts) |\n| File discovery, parsing, and relationships | [`src/indexer/`](src/indexer/), [`src/parser/`](src/parser/), [`src/resolver.ts`](src/resolver.ts), [`src/graph.ts`](src/graph.ts) |\n| Search, plans, review, and test evidence | [`src/query/`](src/query/), [`src/prove.ts`](src/prove.ts) |\n| Assistant tools and local session state | [`src/mcp/`](src/mcp/), [`src/session-memory/`](src/session-memory/) |\n| Host integrations and CI | [`plugins/codexa/`](plugins/codexa/), [`integrations/claude-code/`](integrations/claude-code/), [`action.yml`](action.yml) |\n| Verification and packaging | [`tests/`](tests/), [`scripts/`](scripts/) |\n\nTo build from source:\n\n```bash\ngit clone https://github.com/mirnoorata/codexa.git\ncd codexa\nnpm ci\nnpm run build\nnpm link\nnpm run check\n```\n\n`npm link` makes this checkout's `codexa` command available locally; skip it if\nyou prefer `node dist/cli.js`. The full gate builds and type-checks the package,\nchecks hygiene and public paths, runs tests, and checks the startup context\nbudget. See [Contributing](CONTRIBUTING.md) and the\n[architecture reference](docs/reference.md#architecture-for-engineers).\n\n### Public Proof\n\nThe repository includes reproducible retrieval evaluations and an agent A/B\nharness. These measure different things: finding useful context does not by\nitself prove that an assistant finishes tasks faster or better. An archived\nsmall agent pilot showed extra overhead without a completion benefit; it is\nnot evidence of universal savings. Results, dates, caveats, and reproduction\ncommands are kept in [Public Proof](docs/reference.md#public-proof).\n\n## GitHub Release Timeline\n\nGitHub Releases are the visible source timeline for the current project.\nMaintainers normally use [Release Automation](#release-automation). An explicitly\nrequested manual `npm run release:github` generates a changelog-style summary,\nchanged-area summary, restore instructions, and forward-only PR rollback commands.\nSee the [manual release reference](docs/reference.md#github-release-timeline).\n\n## Release Automation\n\nRelease Please prepares version/changelog PRs and GitHub Releases using the\nrepository's `GITHUB_TOKEN`. This does not publish npm on every main merge:\nordinary changes land first, and npm publishing follows a published release.\nSee [release automation](docs/reference.md#release-automation) and the\n[public release checklist](docs/PUBLIC_RELEASE_CHECKLIST.md).\n\n## npm Package Publishing\n\nThe maintainer workflow publishes through GitHub Actions and npm trusted\npublishing. It runs after an explicit Release Please dispatch or a manually\npublished GitHub Release (`release: published`), not a tag push alone.\nAfter its release and security checks, the workflow runs:\n\n```bash\nnpm publish --registry https://registry.npmjs.org --access public --tag latest --provenance --ignore-scripts\n```\n\nPackage users only need the installation instructions above. Maintainers can\nfind authentication and recovery procedures in the\n[publishing reference](docs/reference.md#npm-package-publishing).\n\n## Help and license\n\nUse [Discussions](https://github.com/mirnoorata/codexa/discussions) for questions\nand [Issues](https://github.com/mirnoorata/codexa/issues) for reproducible bugs.\nReport vulnerabilities through\n[private security advisories](https://github.com/mirnoorata/codexa/security/advisories/new);\nsee [SECURITY.md](SECURITY.md).\n\nCodexa is licensed under [MIT](LICENSE).\n","readmeFilename":"README.md"}