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One command. They'll think they thought of it themselves.\n\nToday, inception-engine works as a cross-agent deployer for skills on all listed agents, plus single-file writes and JSON config patches. It also supports MCP server registration and global rules-file deployment for the subset of agents whose config surfaces are implemented and validated today.\n\nGitHub Copilot is no longer treated as a separate instruction or skill target in the product direction when it can consume Claude-native artifacts directly. If Copilot uses `CLAUDE.md` or Claude-style skill layouts without translation, inception-engine should rely on the Claude deployment path instead of maintaining duplicate Copilot-specific surfaces. Dedicated Copilot customization remains justified only where Copilot exposes a materially different interface, such as MCP-related configuration.\n\nThe broader portability layer is the roadmap direction, but this README focuses on what is working now.\n\n`init` is available as a bootstrap command. It scans for directories containing `SKILL.md`, discovers agent-rules Markdown files using the Claude-first portability conventions, and reads `mcp-servers.json` from the repo root to populate `mcpServers`. Shared surfaces now default to the primary deploy target in generated manifests: for example, `init` emits `claude-code` rather than `github-copilot` for shared Claude-native skills and rules, and emits `gemini-cli` rather than `antigravity` for shared `GEMINI.md` rules surfaces. `files` and `configs` remain empty — `init` emits guidance when it detects a `files/` or `configs/` directory.\n\n## SBOM\n\nThis repo can generate an SPDX SBOM without adding any new runtime dependency by using npm's built-in `sbom` command:\n\n```bash\nnpm ci\nnpm sbom --sbom-format spdx --omit dev > sbom.spdx.json\n```\n\n`--omit dev` keeps the SBOM focused on the published CLI's runtime dependency graph.\n\nFor GitHub Actions, the repository includes [`.github/workflows/sbom.yml`](.github/workflows/sbom.yml). It:\n\n- installs dependencies and runs the normal release checks\n- creates the npm package tarball with `npm pack`\n- generates `dist-artifacts/sbom.spdx.json` via `npm sbom`\n- uploads both the tarball and SBOM as workflow artifacts\n- creates a GitHub artifact attestation that binds the SBOM to the packaged tarball\n\nRun it manually with `workflow_dispatch`, or let it run automatically when a GitHub Release is published.\n\n## Quick Start\n\n```bash\nnpx @kuznai/inception-engine <directory>\n```\n\nWhere `<directory>` is a repo (or subdirectory) containing an `inception.json` manifest and skill files.\n\n## How It Works\n\ninception-engine reads a manifest file (`inception.json`) from the target directory, detects which AI coding agents are installed on the system, and deploys skills to each agent's expected location.\n\n- **POSIX (macOS, Linux)**: creates symlinks from the source skill directory to each agent's skill path\n- **Windows**: copies skill directories to each agent's skill path\n\nManaged skills overwrite their previous version. If a target exists but was not created by inception-engine, deployment refuses to replace it. On POSIX systems, symlinks mean updates to the source repo are reflected immediately.\n\nBefore executing, the deploy command runs preflight analysis on instruction files and capability planning inputs. It validates that `agentRules` and `agentDefinitions` for targets requiring specific structure (like `github-copilot` and `antigravity`) include valid YAML frontmatter with `name` and `description` fields. For `github-copilot`, it further ensures either `tools` or `instructions` are defined; for `antigravity`, it validates the shape of any `mcp-servers` or `mcpServers` defined in the frontmatter. It also warns when a manifest targets a surface that is implementation-only, planned, unsupported, or shared through another agent, when the same agent will have multiple `agentRules` scopes active simultaneously, when the same source file is deployed to multiple scopes (duplicate-content risk), when `agentRules` or `agentDefinitions` source files exceed 50 KB (context-budget risk), and when GitHub Copilot appears to be running under enterprise-managed policy that may override local configuration. Warnings are printed but do not block deployment; structural validation failures block deployment for the affected targets.\nAgent-specific preflight reads and deploy actions targeting distinct files now run with bounded concurrency, while warning order, dry-run output, and deploy result ordering remain deterministic.\n\n## Agent Compatibility Matrix\n\n| Agent | ID | Skills | macOS | Linux | Windows |\n|---|---|---|---|---|---|\n| Claude Code | `claude-code` | `~/.claude/skills/` | Yes | Yes | Yes |\n| OpenAI Codex | `codex` | `~/.codex/skills/` | Yes | Yes | Yes |\n| Gemini CLI | `gemini-cli` | `~/.gemini/skills/` | Yes | Yes | Yes |\n| Antigravity | `antigravity` | `~/.gemini/antigravity/skills/` | Yes* | Yes* | Yes* |\n| OpenCode | `opencode` | `~/.config/opencode/skills/` | Yes | Yes | Yes* |\n\n\\* Antigravity support is currently based on the implementation's registry path assumptions and local validation, not a strong official doc set equivalent to the other agents.\n\n\\* OpenCode on Windows uses `%APPDATA%\\opencode\\skills\\`.\n\n### Feature Support\n\n| Feature | Deploy | Revert |\n|---|---|---|\n| Skills (SKILL.md) | All agents via manifest and CLI | All agents |\n| File write | All agents via manifest and CLI | All agents |\n| Config patch (JSON merge) | All agents via manifest and CLI | All agents |\n| MCP Servers | claude-code (`scope: \"global\"` → `~/.claude.json`; `scope: \"repo\"` → `{repo}/.claude/mcp.json`; `scope: \"workspace\"` → `{workspace}/.claude/mcp.json`), gemini-cli, codex, antigravity (`scope: \"global\"` → `~/.gemini/antigravity/mcp_config.json`; `scope: \"repo\"` → `{repo}/.agents/rules/{name}.md`), opencode; github-copilot with `scope: \"repo\"` deploys to `{repo}/.vscode/mcp.json` and `scope: \"workspace\"` deploys to `{workspace}/.vscode/mcp.json`; github-copilot with `scope: \"global\"` (default) is unsupported and warns | claude-code, gemini-cli, codex, antigravity, opencode, github-copilot |\n| Global/Repo/Workspace Rules Files | `scope: \"global\"` and `scope: \"repo\"` are supported on the implemented agent surfaces; `scope: \"workspace\"` is supported for `claude-code`, `codex`, and `gemini-cli`; `github-copilot` reads Claude-native rules via `claude-code` (shared-via) and also supports native `scope: \"copilot-repo\"` (`{repo}/.github/copilot-instructions.md`) and `scope: \"copilot-scoped\"` (`{repo}/.github/instructions/{name}.instructions.md`) | All supported agents |\n| Permissions / Approval Config | claude-code (`~/.claude/settings.json`), codex (`~/.codex/config.toml`), opencode (`~/.config/opencode/opencode.json` on POSIX, `%APPDATA%\\\\opencode\\\\opencode.json` on Windows); other agents are warned and skipped | claude-code, codex, opencode |\n| Execution Hooks | claude-code (`~/.claude/settings.json`), github-copilot (`planned`); other agents are warned and skipped | claude-code |\n| Execution / Safety Config | gemini-cli (`~/.gemini/settings.json`); other agents are warned and skipped | gemini-cli |\n| Agent Definitions | claude-code (`{repo}/.claude/agents/{name}.md`), gemini-cli (`{repo}/.gemini/agents/{name}.md` or `.toml`, plus `scope: \"global\"` to `~/.gemini/agents/{name}.md` or `.toml`), antigravity (`{repo}/.agents/rules/{name}.md`), opencode (`{repo}/.opencode/agents/{name}.md`, plus `scope: \"global\"` to the user config dir), github-copilot (`{repo}/.github/copilot/agents/{name}.md`, with migration from legacy `.github/agents/{name}.agent.md`); codex is warned and skipped | All supported agents |\n| `init` manifest generation | Scans `SKILL.md` directories (`skills`), `.md` files with Claude-first agent mapping (`agentRules`), `mcp-servers.json` (`mcpServers`), and agent-definition Markdown files (`agentDefinitions`); shared surfaces default to the primary deploy target instead of shared riders; emits hints for `files/` and `configs/` directories | N/A |\n| Instruction preflight analysis | Emits capability warnings for implementation-only, planned, unsupported, and shared-through surfaces used by the manifest; emits `precedence` warnings when an agent has multiple `agentRules` scopes active simultaneously or the same source file is deployed to multiple scopes; emits `budget` warnings when `agentRules` or `agentDefinitions` source files exceed 50 KB; emits GitHub Copilot enterprise-policy warnings when local configuration may be overridden; emits a `config-authority` warning when Gemini CLI's `settings.json` contains an `instructionFilename` override that differs from the deploy target | N/A |\n\nFeatures that depend on agent-specific config surfaces are intentionally conservative: deploy and preflight now classify each surface through the same planner. If a target path or schema is implementation-only, planned, unsupported, or only shared through another agent, inception-engine warns and either routes through the primary surface or skips it rather than guessing.\n\nFor GitHub Copilot specifically, the portability rule is Claude-first: if Copilot accepts the same Claude-native instruction or skill artifact, inception-engine should not add a separate Copilot deployment feature for it.\n\n## Manifest Format\n\nCreate an `inception.json` file at the root of your skills directory:\n\n```json\n{\n  \"skills\": [\n    {\n      \"name\": \"my-skill\",\n      \"path\": \"skills/my-skill\",\n      \"agents\": [\"claude-code\", \"codex\", \"gemini-cli\", \"antigravity\", \"opencode\"]\n    }\n  ],\n  \"files\": [\n    {\n      \"name\": \"my-settings\",\n      \"path\": \"files/settings.json\",\n      \"target\": \"{home}/.claude/settings.json\",\n      \"agents\": [\"claude-code\"]\n    }\n  ],\n  \"configs\": [\n    {\n      \"name\": \"enable-feature\",\n      \"target\": \"{home}/.claude/settings.json\",\n      \"patch\": { \"someFeature\": true },\n      \"agents\": [\"claude-code\"]\n    }\n  ],\n  \"mcpServers\": [\n    {\n      \"name\": \"my-server\",\n      \"agents\": [\"claude-code\", \"gemini-cli\"],\n      \"config\": { \"command\": \"npx\", \"args\": [\"-y\", \"my-mcp-server\"] }\n    },\n    {\n      \"name\": \"my-server\",\n      \"agents\": [\"github-copilot\"],\n      \"scope\": \"repo\",\n      \"config\": { \"type\": \"stdio\", \"command\": \"npx\", \"args\": [\"-y\", \"my-mcp-server\"] }\n    }\n  ],\n  \"agentRules\": [\n    {\n      \"name\": \"my-rules\",\n      \"path\": \"rules/CLAUDE.md\",\n      \"agents\": [\"claude-code\"],\n      \"scope\": \"global\"\n    },\n    {\n      \"name\": \"project-rules\",\n      \"path\": \"rules/CLAUDE.md\",\n      \"agents\": [\"claude-code\", \"codex\", \"gemini-cli\", \"opencode\"],\n      \"scope\": \"repo\"\n    }\n  ],\n  \"permissions\": [\n    {\n      \"name\": \"safety-defaults\",\n      \"agents\": [\"claude-code\"],\n      \"config\": {\n        \"permissions\": {\n          \"allow\": [\"Read\", \"Glob\"],\n          \"deny\": [\"Bash(rm:*)\"]\n        }\n      }\n    }\n  ],\n  \"agentDefinitions\": [\n    {\n      \"name\": \"code-reviewer\",\n      \"path\": \"agents/code-reviewer.md\",\n      \"agents\": [\"claude-code\", \"opencode\", \"github-copilot\"]\n    }\n  ],\n  \"hooks\": [\n    {\n      \"name\": \"pre-exec-check\",\n      \"agents\": [\"claude-code\"],\n      \"config\": {\n        \"hooks\": {\n          \"PreToolUse\": [\n            {\n              \"matcher\": \"Bash\",\n              \"hooks\": [{ \"type\": \"command\", \"command\": \"scripts/check-env.sh\" }]\n            }\n          ],\n          \"Stop\": [\n            {\n              \"hooks\": [{ \"type\": \"command\", \"command\": \"scripts/notify.sh\" }]\n            }\n          ]\n        }\n      }\n    }\n  ],\n  \"executionConfigs\": [\n    {\n      \"name\": \"gemini-safety\",\n      \"agents\": [\"gemini-cli\"],\n      \"config\": {\n        \"safeMode\": true\n      }\n    }\n  ]\n}\n```\n\n`files` and `configs` are intentionally narrower than the raw target-template syntax might suggest. Arbitrary project-local targets under `{repo}` and `{workspace}` are allowed, but user-profile targets under `{home}`, `{appdata}`, and `{xdg_config}` must resolve to documented agent-owned global surfaces such as `~/.claude/settings.json` or `~/.codex/AGENTS.md`. Manifests cannot target inception-engine's own `~/.inception-engine/` state directory.\n\nEach **skill** entry has:\n\n- **name** - Unique identifier using letters, digits, dots, underscores, or hyphens; must not start with a dot\n- **path** - Relative path to the skill directory within the repo\n- **agents** - Array of agent IDs to deploy this skill to. If an agent isn't installed, it's skipped.\n\nEach **file** entry deploys a single file to an agent's configuration location:\n\n- **name** - Unique identifier (same format as skill names)\n- **path** - Relative path to the source file within the repo\n- **target** - Destination path using a placeholder prefix: `{home}`, `{appdata}`, `{xdg_config}`, `{repo}`, or `{workspace}`. For example: `{home}/.claude/settings.json`\n- **agents** - Array of agent IDs to deploy this file to\n\nEach **config** entry applies a [JSON merge patch (RFC 7386)](https://datatracker.ietf.org/doc/html/rfc7386) to an existing agent config file:\n\n- **name** - Unique identifier (same format as skill names)\n- **target** - Config file to patch, using the same placeholder prefix as file entries\n- **patch** - JSON object of keys to set. A `null` value removes the key from the target file. Nested object values are merged recursively; non-object values replace the existing value directly.\n- **agents** - Array of agent IDs to apply this patch to\n\nThe engine records an undo-patch for each config-patch deployment so that `revert` can restore the original values.\n\nEach **mcpServer** entry registers an MCP server into the agent's config file by applying a JSON merge patch under the `mcpServers` key:\n\n- **name** - Unique identifier (same format as skill names); used as the server's key in the config\n- **agents** - Array of agent IDs to register this server with\n- **config** - Raw server descriptor object. For the currently supported JSON-backed adapters, inception-engine requires at least one non-empty `command` or `url` field, validates `args` as an array of strings when present, and validates `env` as a string-to-string object when present. Additional keys are passed through verbatim.\n- **scope** - `\"global\"` (default), `\"repo\"`, `\"workspace\"`, or `\"devcontainer\"`. For most agents this field is ignored (they have only a single user-level config path). For `github-copilot`, `scope` selects the target file:\n  - `\"global\"` — unsupported; emits a warning and is skipped\n  - `\"repo\"` — deploys to `{repo}/.vscode/mcp.json` under the `servers` key\n  - `\"workspace\"` — deploys to `{workspace}/.vscode/mcp.json` under the `servers` key\n  - `\"devcontainer\"` — deploys to `{repo}/.devcontainer/devcontainer.json` under the `customizations.vscode.mcp.servers` key\n\n  GitHub Copilot's `.vscode/mcp.json` uses `servers` (not `mcpServers`) as the top-level key and optionally accepts a `type` field (`\"stdio\"` | `\"sse\"` | `\"http\"`) in the server descriptor, which is passed through verbatim.\n\nMCP server registration is supported for all agents. Inception-engine automatically uses the correct adapter for each agent's configuration schema:\n- **JSON (Merge Patch)**: `claude-code` (`~/.claude.json` for `scope: \"global\"`; `{repo}/.claude/mcp.json` for `scope: \"repo\"`; `{workspace}/.claude/mcp.json` for `scope: \"workspace\"`), `gemini-cli` (`~/.gemini/settings.json`), `antigravity` (`~/.gemini/antigravity/mcp_config.json` for `scope: \"global\"`), `opencode` (`~/.config/opencode/opencode.json` using the custom `\"mcp\"` key), and `github-copilot` (`{repo}/.vscode/mcp.json`, `{workspace}/.vscode/mcp.json`, or `{repo}/.devcontainer/devcontainer.json`).\n- **TOML (Patch)**: `codex` (`~/.codex/config.toml`).\n- **Markdown Frontmatter (Emit)**: `antigravity` (`{repo}/.agents/rules/{name}.md` for `scope: \"repo\"`).\n\nFor Markdown frontmatter targets, inception-engine now records patch-level provenance for the emitted frontmatter block. Deploy merges only the owned frontmatter keys, preserves unrelated frontmatter and Markdown body content, and `revert` removes only the engine-owned keys instead of deleting the whole file unless inception-engine originally created an otherwise-empty file.\n\nBecause Antigravity currently reuses `.agents/rules/{name}.md` for both MCP frontmatter emit and agent-definition files, planning now rejects a manifest when an `mcpServers` entry and an `agentDefinitions` entry would resolve to the same Antigravity target.\n\nRevert removes the registered server entry from the respective configuration file or frontmatter block.\n\nEach **agentRules** entry deploys a Markdown instruction file to an agent's supported instruction file location:\n\n- **name** - Unique identifier (same format as skill names)\n- **path** - Relative path to the source Markdown file within the repo; supported rules adapters require a `.md` or `.markdown` source path\n- **agents** - Array of agent IDs to deploy this file to\n- **scope** - `\"global\"` (default), `\"repo\"`, `\"workspace\"`, `\"copilot-repo\"`, or `\"copilot-scoped\"`. Controls which instruction surface is targeted:\n  - `\"global\"` — deploys to the agent's home-directory instruction file when that surface is supported (e.g., `~/.claude/CLAUDE.md` for `claude-code`)\n  - `\"repo\"` — deploys to the project-root instruction file inside the deployed repository when that surface is supported (e.g., `{repo}/CLAUDE.md` for `claude-code`)\n  - `\"workspace\"` — deploys to the workspace-root instruction file when an agent exposes one (e.g., `{workspace}/CLAUDE.md` for `claude-code`); when unsupported, deployment is skipped with a warning\n  - `\"copilot-repo\"` — deploys to GitHub Copilot's native repo-level instruction file at `{repo}/.github/copilot-instructions.md` (`github-copilot` only; other agents are warned and skipped)\n  - `\"copilot-scoped\"` — deploys to `{repo}/.github/instructions/{name}.instructions.md` where `{name}` is the manifest entry name (`github-copilot` only; other agents are warned and skipped)\n- **targetDir** - Optional relative subdirectory under the selected `{repo}` or `{workspace}` root. Only valid with `scope: \"repo\"` or `scope: \"workspace\"`. This lets one manifest entry target nested workspaces such as `apps/frontend/CLAUDE.md` without changing the source file path.\n\nInstruction rule deployment is supported for implemented global, repo, and workspace surfaces. The target path depends on the agent and the `scope`:\n\n| Agent | `scope: \"global\"` | `scope: \"repo\"` | `scope: \"workspace\"` |\n|---|---|---|---|\n| `claude-code` | `~/.claude/CLAUDE.md` | `{repo}/CLAUDE.md` | `{workspace}/CLAUDE.md` |\n| `codex` | `~/.codex/AGENTS.md` | `{repo}/AGENTS.md` | `{workspace}/AGENTS.md` |\n| `gemini-cli` | `~/.gemini/GEMINI.md` | `{repo}/GEMINI.md` | `{workspace}/GEMINI.md` |\n| `antigravity` | `~/.gemini/GEMINI.md` | `{repo}/GEMINI.md` | unsupported; warns and skips |\n| `opencode` | `~/.config/opencode/AGENTS.md` | `{repo}/AGENTS.md` | unsupported; warns and skips |\n| `github-copilot` | unsupported / Claude-first | deploy via `claude-code` | unsupported; deploy via `claude-code` with `scope: \"workspace\"` |\n\nGitHub Copilot also exposes two native instruction surfaces via dedicated scope values:\n\n| Agent | `scope: \"copilot-repo\"` | `scope: \"copilot-scoped\"` |\n|---|---|---|\n| `github-copilot` | `{repo}/.github/copilot-instructions.md` | `{repo}/.github/instructions/{name}.instructions.md` |\n\nFor `antigravity`, `agentRules` now targets the shared GEMINI.md surface (`~/.gemini/GEMINI.md` for `global`, `{repo}/GEMINI.md` for `repo`) — the same paths used by `gemini-cli`. When both agents appear in the same entry, deduplication ensures only one write action is emitted. `workspace` scope is not supported and is skipped with a warning. For `github-copilot`, the Claude-first path (targeting via `claude-code` agentRules) remains the recommended approach for shared rules; the `copilot-repo` and `copilot-scoped` scopes are for Copilot-specific instructions that should not be shared with other agents. When both are present, preflight emits a precedence warning. Revert removes the deployed rules file.\n\nEach **permissions** entry deploys execution and safety-oriented configuration to an agent's permission or approval surface:\n\n- **name** - Unique identifier (same format as skill names)\n- **agents** - Array of agent IDs to deploy this entry to\n- **config** - Permission config payload; shape is validated per agent (see below)\n\nPermission deployment is currently supported for `claude-code`, `codex`, and `opencode`. Other agents emit a warning and are skipped.\n\nFor `claude-code`, the config is merged into `~/.claude/settings.json`. Only the `permissions` key is accepted:\n\n```json\n{\n  \"name\": \"safety-defaults\",\n  \"agents\": [\"claude-code\"],\n  \"config\": {\n    \"permissions\": {\n      \"allow\": [\"Read\", \"Glob\", \"Bash(git:*)\"],\n      \"deny\": [\"Bash(rm:*)\"]\n    }\n  }\n}\n```\n\nBoth `allow` and `deny` are optional string arrays. Tool patterns follow Claude Code's permission glob syntax (e.g., `Bash(git:*)` to allow all git commands).\n\nFor `codex`, the config is merged into `~/.codex/config.toml`. Only the `approval_policy` key is accepted:\n\n```json\n{\n  \"name\": \"codex-approval\",\n  \"agents\": [\"codex\"],\n  \"config\": {\n    \"approval_policy\": \"suggest\"\n  }\n}\n```\n\nValid `approval_policy` values are `\"auto\"`, `\"manual\"`, `\"suggest\"`, and `\"on-failure\"`.\n\nFor `opencode`, the config is merged into `~/.config/opencode/opencode.json` on POSIX or `%APPDATA%\\\\opencode\\\\opencode.json` on Windows. Only the `permissions` key is accepted:\n\n```json\n{\n  \"name\": \"opencode-permissions\",\n  \"agents\": [\"opencode\"],\n  \"config\": {\n    \"permissions\": {\n      \"allow\": [\"Read\", \"Glob\"],\n      \"ask\": [\"Bash(git push:*)\"],\n      \"deny\": [\"Bash(rm:*)\"]\n    }\n  }\n}\n```\n\n`allow`, `ask`, and `deny` are optional string arrays.\n\nRevert restores the previous config values using the undo patch recorded at deploy time.\n\nEach **hooks** entry deploys lifecycle-binding configurations to an agent's execution hook surface:\n\n- **name** - Unique identifier (same format as skill names)\n- **agents** - Array of agent IDs to deploy this entry to\n- **config** - Hook configuration payload; shape is validated per agent (see below)\n\nHook deployment is currently supported for `claude-code`. For `github-copilot`, it is marked as `planned`. Other agents emit a warning and are skipped.\n\nFor `claude-code`, the config is merged into `~/.claude/settings.json`. Only the `hooks` key is accepted. Event names follow Claude Code's settings.json hooks surface (e.g. `PreToolUse`, `PostToolUse`, `Notification`, `Stop`, `SubagentStop`). Each event maps to an array of hook matchers; each matcher has an optional `matcher` string and a required `hooks` array of `{ type: \"command\", command: string }` objects:\n\n```json\n{\n  \"name\": \"pre-exec-check\",\n  \"agents\": [\"claude-code\"],\n  \"config\": {\n    \"hooks\": {\n      \"PreToolUse\": [\n        {\n          \"matcher\": \"Bash\",\n          \"hooks\": [{ \"type\": \"command\", \"command\": \"scripts/check-env.sh\" }]\n        }\n      ],\n      \"Stop\": [\n        {\n          \"hooks\": [{ \"type\": \"command\", \"command\": \"scripts/notify.sh\" }]\n        }\n      ]\n    }\n  }\n}\n```\n\nRevert restores the previous config values using the undo patch recorded at deploy time.\n\nEach **executionConfigs** entry deploys agent execution or safety settings to an agent's modeled runtime config surface:\n\n- **name** - Unique identifier (same format as skill names)\n- **agents** - Array of agent IDs to deploy this entry to\n- **config** - Raw execution-config payload; today this is modeled for `gemini-cli` and patched into its settings file\n\nExecution-config deployment is currently supported for `gemini-cli`. Other agents emit a warning and are skipped. Because this surface is still treated as provisional, preflight emits a config-authority warning when you target it so you can sanity-check the current upstream behavior.\n\nFor `gemini-cli`, the config is merged into `~/.gemini/settings.json`:\n\n```json\n{\n  \"name\": \"gemini-safety\",\n  \"agents\": [\"gemini-cli\"],\n  \"config\": {\n    \"safeMode\": true,\n    \"sandbox\": \"workspace-write\"\n  }\n}\n```\n\nValues are passed through as a JSON merge patch so the tool can model emerging Gemini CLI execution settings without inventing a separate schema for each key. Revert restores the previous config values using the undo patch recorded at deploy time.\n\nEach **agentDefinitions** entry deploys an agent-definition file to the agent-definition directory of each targeted agent. `scope: \"repo\"` is the default, and some agents also support `scope: \"global\"`:\n\n- **name** - Unique identifier (same format as skill names); used as the definition filename\n- **path** - Relative path to the source file within the repo; `.md` or `.markdown` for Markdown definitions, `.toml` for Gemini CLI TOML subagent definitions\n- **agents** - Array of agent IDs to deploy this definition to\n\nAgent-definition deployment is supported for `claude-code`, `gemini-cli`, `antigravity`, `opencode`, and `github-copilot`. For `codex`, inception-engine emits a warning and skips the entry. Gemini CLI and OpenCode also support `scope: \"global\"` definitions; other supported agents are repo-local only.\n\nGemini CLI supports two definition formats: Markdown (`.md`) files deploy to `{scope}/.gemini/agents/{name}.md`, and TOML (`.toml`) subagent configuration files deploy to `{scope}/.gemini/agents/{name}.toml`. TOML files are deployed verbatim without frontmatter validation. Agents other than `gemini-cli` that do not have a TOML definition surface silently produce no action when a `.toml` source is specified.\n\nRepo-local targets:\n- **claude-code**: `{repo}/.claude/agents/{name}.md`\n- **gemini-cli**: `{repo}/.gemini/agents/{name}.md` (Markdown) or `{repo}/.gemini/agents/{name}.toml` (TOML)\n- **antigravity**: `{repo}/.agents/rules/{name}.md`\n- **opencode**: `{repo}/.opencode/agents/{name}.md`\n- **github-copilot**: `{repo}/.github/copilot/agents/{name}.md`\n\nGlobal targets where supported:\n- **gemini-cli**: `~/.gemini/agents/{name}.md` or `~/.gemini/agents/{name}.toml`\n- **opencode**: `~/.config/opencode/agents/{name}.md` on POSIX, `%APPDATA%\\\\opencode\\\\agents\\\\{name}.md` on Windows\n\nFor GitHub Copilot, deploy also records migration from the legacy `{repo}/.github/agents/{name}.agent.md` path so older installs can be cleaned up safely.\n\nFor GitHub Copilot, the `tools` YAML frontmatter field in agent definition files declares which MCP tools and built-in Copilot tools the agent has access to (agent-level tool mapping). Inception-engine validates that `tools`, when present, is an array of strings. Deploy agent-level tool mappings through `agentDefinitions` by including the `tools` field in your source file's frontmatter - no separate manifest section is needed.\n\nRevert removes the deployed agent-definition file.\n\n## Creating Skills\n\nEach skill is a directory containing at minimum a `SKILL.md` file with YAML frontmatter:\n\n```markdown\n---\nname: my-skill\ndescription: What this skill does and when to use it\n---\n\n# My Skill\n\nInstructions for the AI agent...\n```\n\nThe `name` and `description` fields in the frontmatter are used by most agents. The description determines when the agent activates the skill. inception-engine now validates this minimum contract during deploy: `SKILL.md` must start with YAML frontmatter and include non-empty single-line `name` and `description` fields. It still does not attempt full YAML/schema validation beyond that targeted check.\n\n## `init` Command\n\n`init` is meant to bootstrap a repository that already has skills and related manifest assets. It recursively scans the target directory, treats any directory containing `SKILL.md` as a skill, discovers supported instruction and MCP conventions, and writes a starter `inception.json`. The scan uses a bounded-concurrency streaming directory walk so large repositories scale more predictably without changing discovery behavior.\n\nCurrent `init` behavior:\n\n- Generates `skills` entries using the discovered relative paths\n- Uses the directory name as the manifest skill name\n- Applies either the `--agents` list or all currently known agent IDs\n- Refuses to overwrite an existing `inception.json` unless `--force` is provided\n- Supports `--plan` so you can inspect the generated manifest before writing it\n- Discovers agent-rules Markdown files in the root and conventional subdirectories (`rules/`, `instructions/`, `.github/`), mapping them to agents using Claude-first portability conventions: `copilot-instructions.md` found outside `.github/` maps to `claude-code` (Copilot reads `CLAUDE.md` natively), `.github/copilot-instructions.md` maps to `github-copilot` with `scope: \"copilot-repo\"`, and `*.instructions.md` files in `.github/instructions/` map to `github-copilot` with `scope: \"copilot-scoped\"`; the fallback for unrecognized files excludes unsupported agents plus shared-surface riders that should default to their primary deploy target\n- Reads `mcp-servers.json` from the repo root (if present) and generates `mcpServers` entries; invalid entries are warned and skipped\n- Reads `files-manifest.json` from the repo root (if present) and generates `files` entries; invalid entries are warned and skipped\n- Reads `configs-manifest.json` from the repo root (if present) and generates `configs` entries; invalid entries are warned and skipped\n- Reads `agent-definitions-manifest.json` from the repo root (if present) and generates `agentDefinitions` entries; if absent, auto-discovers agent-definition Markdown files from `.claude/agents/`, `.gemini/agents/`, `.agents/rules/`, `.opencode/agents/`, `.github/copilot/agents/`, and legacy `.github/agents/`; invalid entries are warned and skipped\n- Emits guidance to create a sidecar manifest when a `files/` or `configs/` directory is detected but the corresponding sidecar file is absent\n\nCurrent `init` limitations:\n\n- It does not reconcile generated manifest entries against `SKILL.md` frontmatter values\n- `files` and `configs` target paths are deployment-system-specific and cannot be inferred; they must be provided explicitly in `files-manifest.json` and `configs-manifest.json`\n\n### Repo Conventions Recognized by `init`\n\nPlace a `mcp-servers.json` file at the repo root to have `init` populate the `mcpServers` section automatically. The file must be a JSON array of MCP server entries using the same schema as the `mcpServers` field in `inception.json`:\n\n```json\n[\n  {\n    \"name\": \"my-server\",\n    \"agents\": [\"claude-code\", \"gemini-cli\"],\n    \"config\": { \"command\": \"npx\", \"args\": [\"-y\", \"my-mcp-server\"] }\n  }\n]\n```\n\nPlace a `files-manifest.json` file at the repo root to have `init` populate the `files` section automatically. The file must be a JSON array of file entries using the same schema as the `files` field in `inception.json`:\n\n```json\n[\n  {\n    \"name\": \"my-settings\",\n    \"path\": \"files/settings.json\",\n    \"target\": \"{home}/.claude/settings.json\",\n    \"agents\": [\"claude-code\"]\n  }\n]\n```\n\nPlace a `configs-manifest.json` file at the repo root to have `init` populate the `configs` section automatically. The file must be a JSON array of config entries using the same schema as the `configs` field in `inception.json`:\n\n```json\n[\n  {\n    \"name\": \"enable-feature\",\n    \"target\": \"{home}/.claude/settings.json\",\n    \"patch\": { \"someFeature\": true },\n    \"agents\": [\"claude-code\"]\n  }\n]\n```\n\nInvalid entries are warned and skipped; the rest are written into the generated manifest verbatim.\n\nPlace an `agent-definitions-manifest.json` file at the repo root to have `init` populate the `agentDefinitions` section automatically. The file must be a JSON array of agent-definition entries using the same schema as the `agentDefinitions` field in `inception.json`:\n\n```json\n[\n  {\n    \"name\": \"code-reviewer\",\n    \"path\": \"agents/code-reviewer.md\",\n    \"agents\": [\"claude-code\", \"opencode\", \"github-copilot\"]\n  }\n]\n```\n\nIf no `agent-definitions-manifest.json` is present, `init` auto-discovers agent-definition Markdown files from six conventional subdirectories: `.claude/agents/`, `.gemini/agents/`, `.agents/rules/`, `.opencode/agents/`, `.github/copilot/agents/`, and legacy `.github/agents/`. Each discovered file is mapped to the owning agent(s). GitHub Copilot files named `{name}.agent.md` in the legacy directory have the `.agent` infix stripped to derive the manifest name (e.g., `foo.agent.md` -> name `foo`).\n\nInvalid entries are warned and skipped; the rest are written into the generated manifest verbatim.\n\nFor shared surfaces, `init` prefers the primary deploy target instead of emitting both agents. That means generated `skills` entries exclude `github-copilot` in favor of `claude-code`, and generated shared `GEMINI.md` `agentRules` entries exclude `antigravity` in favor of `gemini-cli`. This keeps starter manifests minimal while preserving deploy behavior for explicitly authored shared-rider entries.\n\n## CLI Reference\n\n```\ninception-engine <directory> [options]\ninception-engine revert <directory> [options]\ninception-engine init <directory> [options]\n```\n\n### Commands\n\n| Command | Description |\n|---|---|\n| `<directory>` | Deploy skills from the manifest in the given directory |\n| `revert <directory>` | Remove previously deployed skills declared in the manifest |\n| `init <directory>` | Scan a directory for skill folders and generate `inception.json` |\n\n### Options\n\n| Option | Description |\n|---|---|\n| `--plan` | Show what would be done without making changes |\n| `--agents <list>` | Comma-separated list of agent IDs to target (overrides deploy detection; restricts revert) |\n| `--force` | `init` only; overwrite an existing `inception.json` |\n| `--verbose` | Show detailed output including file paths |\n| `--debug` | Show full error stack traces |\n| `--help` | Show help message |\n\nWith `--plan`, deploy and revert print a grouped action preview by agent. Each planned change includes the action verb, the source path when applicable, the resolved target path, and action-specific details such as indented JSON/TOML patch payload blocks or emitted frontmatter content.\n\n### Examples\n\n```bash\n# Deploy all skills to all detected agents\nnpx @kuznai/inception-engine ./my-skills-repo\n\n# Preview what would be deployed\nnpx @kuznai/inception-engine ./my-skills-repo --plan\n\n# Deploy only to Claude Code and Codex\nnpx @kuznai/inception-engine ./my-skills-repo --agents claude-code,codex\n\n# Remove deployed skills\nnpx @kuznai/inception-engine revert ./my-skills-repo\n\n# Preview what would be removed\nnpx @kuznai/inception-engine revert ./my-skills-repo --plan\n\n# Generate a starter manifest from discovered skill folders\nnpx @kuznai/inception-engine init ./my-skills-repo\n\n# Preview the generated manifest without writing it\nnpx @kuznai/inception-engine init ./my-skills-repo --plan\n```\n\n## Sample Skills\n\nThe `limbo/` directory contains exceptional sample skills for testing purposes only.\n\nTry them out:\n\n```bash\nnpx @kuznai/inception-engine init limbo --plan\nnpx @kuznai/inception-engine limbo --plan\n```\n\n## Agent Detection\n\ninception-engine automatically detects which agents are installed by checking:\n\n1. Whether the agent's config directory exists (e.g., `~/.claude/` for Claude Code)\n2. Whether the agent's binary is in your PATH (e.g., `claude`, `codex`, `gemini`)\n\nIf an agent isn't detected, its skills are skipped during deploy. Use `--agents` to override detection.\n\nRevert targets all agents listed in the manifest by default (regardless of detection) so that previously deployed skills are cleaned up even if the agent has since been uninstalled. Use `--agents` to restrict revert to specific agents.\n\n## Cross-Platform Behavior\n\n| Platform | Deploy Method | Behavior |\n|---|---|---|\n| macOS | Symlink | Source changes are reflected immediately |\n| Linux | Symlink | Source changes are reflected immediately |\n| Windows | Copy | Source must be re-deployed after changes |\n\n### Ownership Tracking and Safe Revert\n\ninception-engine maintains a centralized deployment registry at `~/.inception-engine/registry.json`. Each deploy records the target path, skill name, agent ID, action-specific provenance (`source`/`method` for skill-dir, `source` for file-write, `patch`/`undoPatch` for config-patch, `patch`/`undoPatch` plus frontmatter-shape metadata for frontmatter-emit), and timestamp. Registry entries also carry a stable surface ID so future surface migrations can preserve ownership continuity. No files are written to the source repository.\n\n- **Registry-based ownership**: On revert, the registry is checked before removing any target. Only targets with a valid registry entry are removed. On redeploy, unmanaged targets are never replaced.\n\n- **Strong binding**: Each registry entry binds a specific target path to its skill, agent, and action kind. For `skill-dir` and `file-write`, ownership checks also require the recorded `source` to match before an existing target is treated as managed. For `config-patch` and `frontmatter-emit`, overwrite protection is keyed by target path, kind, skill, and agent; the stored `patch` and `undoPatch` are used for patch-level revert bookkeeping rather than deploy-time identity checks.\n\n- **Reserved state**: Manifest-driven deploy and revert actions are not allowed to touch `~/.inception-engine/`, and the registry loader refuses symlinked registry files or directories.\n\n- **Atomic redeploy**: When overwriting an existing managed `skill-dir` target, the engine renames the old target to a backup, creates the new deployment, and only removes the backup on success. If the new deployment fails, the backup is restored. `file-write` and `config-patch` deployments write directly to the target without this backup/rollback model.\n\n- **Cross-platform**: The registry uses the same resolved home directory as the rest of the tool, including sudo scenarios on POSIX and elevated PowerShell on Windows. On POSIX, inception-engine keeps the state directory at `0700` and the registry file at `0600`.\n\n## Running with Privilege Escalation\n\nThe tool works without elevated privileges. If run with `sudo` on POSIX systems, it looks up the real user's home directory from the OS directory services (`getent passwd` on Linux, `dscl` on macOS, `/etc/passwd` as a universal fallback) so skills are deployed to the correct location regardless of where home directories are stored — standard `/home/<user>`, LDAP/NIS paths, enterprise layouts, or otherwise.\n\nIf the real home cannot be determined, the tool exits with an error rather than silently deploying to a guessed path.\n\nOn Windows, `os.homedir()` correctly resolves even in elevated PowerShell or cmd.\n\n## Security & Compatibility Notes\n\n### SUDO_USER handling\n\nWhen run under `sudo` on POSIX, `SUDO_USER` is read as an advisory signal to identify the real user. The username is validated through OS directory services (`getent passwd` on Linux, `dscl` on macOS, `/etc/passwd` as a fallback) — it is never used as a raw path. This is standard practice for sudo-aware CLI tools.\n\n`SUDO_USER` is only consulted when the process is actually running as root (UID 0). If `SUDO_USER` is present in the environment but the process is not root — for example, as a stale shell variable from a prior `sudo` session or an externally injected value in automation — it is ignored and the standard home directory is used instead.\n\n### XDG_CONFIG_HOME support\n\nOn POSIX, agents whose config lives under `~/.config/` (currently OpenCode) honor `$XDG_CONFIG_HOME` when it is set to an absolute path. If the variable is unset or contains a relative path (which the XDG Base Directory Specification disallows), the tool falls back to the standard `~/.config` default. This has no effect on Windows.\n\n### Windows %APPDATA% fallback\n\nOn Windows, `%APPDATA%` is used to locate agent config directories (currently only OpenCode). When `%APPDATA%` is unset — which can happen in some service or minimal sandbox contexts — the tool falls back to `AppData\\Roaming` under the resolved home directory. This fallback is intentional and correct for interactive user sessions and elevated PowerShell. Running as a Windows service account is outside the supported use case for this tool.\n\n### Future: mixed asset layouts on Windows\n\nWindows deployment currently uses directory-level copy (one `cp -r` per skill). This works correctly for the present skill model where each skill is a single directory. If file-based assets or mixed (file + directory) skill layouts are added in the future, the copy strategy in `src/core/deploy.ts` will need revisiting.\n\n## Requirements\n\n- Published CLI runtime: Node.js >= 22.3.0\n- Direct TypeScript execution in this repo (`npm run dev`, `npm test`): Node.js >= 22.18.0\n\n`inception-engine` publishes compiled JavaScript from `dist/`, so end users do not need the newer Node version required for this repository's direct `.ts` workflows. The higher contributor floor exists only because this repo intentionally runs TypeScript straight through `node` for local development and tests, with no `tsx`, `ts-node`, or experimental TypeScript flags.\n\n## License\n\nMIT\n","readmeFilename":"README.md"}