CLI Reference

rnex is a zero-dependency CLI written entirely in pure POSIX /bin/sh. It orchestrates Virtual Meta Repository (meta repo) and Nexus Repository (nexus repo) workspaces, single-repository management under rnex repo, batch operations across <repos_dir>/ (default ./repos/), and extensible plugin commands.

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Global Options

rnex [global-options] <command> [command-options] [arguments]

Flag	Shorthand	Type	Description
--config <file>	-c <file>	string	Path to custom workspace configuration file (e.g. /path/to/rnex.yaml). Executes as if running from that file's directory.
--help	-h	boolean	Display command usage and help summary.
--version	-v	boolean	Output CLI version.

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Workspace Commands

rnex init

Initializes a new Repo Nexus Virtual Meta-Repo workspace.

rnex init [options] [directory]

• -y, --yes: Non-interactive mode; accepts all defaults automatically.
• --repos-dir <dir>: Set custom directory for member repositories (default: repos).
• --code-workspace: Enable VS Code multi-root workspace file (pass string for custom file name).
• --hooks: Force-enable automated Git hooks setup during initialization.
• --no-hooks: Skip Git hooks configuration during initialization.
• --copilot: Enable GitHub Copilot plugin (.github/copilot-instructions.md, .github/skills/).
• --claude: Enable Claude Code plugin (CLAUDE.md, .claude/skills/).
• --cursor: Enable Cursor plugin (.cursorrules, .cursor/rules/).
• --codex: Enable OpenAI Codex plugin (CODEX.md, .codex/skills/).
• --gemini: Enable Google Gemini plugin (GEMINI.md, .agents/skills/).
• --windsurf: Enable Windsurf plugin (.windsurfrules, .windsurf/rules/).
• --karpathy: Enable Karpathy LLM Wiki plugin (wiki/, docs/).
• --plugin <name>: Enable any specified plugin during initialization (repeatable).

rnex sync

Single reconciliation command: syncs skills, plugins, Git hooks & ignore rules, compiles .rnex/ai-instructions.md, and prunes unlisted/deleted member repositories from <repos_dir> so the directory strictly matches configuration.

rnex sync [options]

• -y, --yes: Automatically confirm non-destructive schema upgrades if prompted.
• --upgrade: Explicitly trigger non-destructive configuration and schema upgrade checks.
• -q, --quiet: Quiet mode; suppresses non-error informational messages (ideal for hooks).

rnex status

Strictly read-only diagnostic report: inspects workspace health, active repos, loaded config, hooks, and plugins.

rnex status

rnex clone

Clones all enabled member repositories declared in configuration that are missing from <repos_dir>/ (default: ./repos/).

rnex clone

rnex list

Prints a formatted table of all registered repositories with state, clone status, branch, and readonly flag.

rnex list

rnex exec

Runs an arbitrary shell command sequentially across all enabled member repositories.

rnex exec <command...>

• Preserves and returns exact non-zero exit codes upon command failure.
• Exports RNEX_REPO_NAME, RNEX_REPO_PATH, RNEX_REPO_BRANCH.

rnex install

Installs and symlinks rnex and repo-nexus to ~/.local/bin (or custom directory).

rnex install [bin-dir]

rnex completion

Generates shell auto-completion scripts.

rnex completion <bash|zsh|fish>

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Single-Repository Commands (rnex repo)

Manage individual member repositories without affecting the entire workspace.

rnex repo add

Registers a repository in configuration and clones it into <repos_dir>/<name> (default: ./repos/<name>).

rnex repo add <url> [--name <name>] [--branch <branch>] [--local] [--disabled] [--readonly]

• <url>: Git repository URL or local repository path.
• --name <name>: Custom repository name (inferred from URL basename if omitted).
• --branch <branch>: Initial Git branch to checkout.
• --local: Register in .local.rnex.yaml instead of rnex.yaml.
• --disabled: Register with enabled: false.
• --readonly: Register with readonly: true.

rnex repo remove

Unregisters a repository from configuration and deletes its directory from disk.

rnex repo remove <name> [--purge] [-y|--yes]

• --purge: Deletes the repository directory from disk (<repos_dir>/<name>). (Retained for backward compatibility; repo directory is deleted upon removal).
• -y, --yes: Skip confirmation prompt.

rnex repo set

Updates repository state and flags.

rnex repo set <name> [--enable|--disable] [--readonly|--readwrite] [--global|--local]

• --enable / --disable: Toggle active state.
• --readonly / --readwrite: Toggle read-only flag.
• --local / --global: Write to .local.rnex.yaml (default) or rnex.yaml.

rnex repo clone

Clones a single registered member repository into <repos_dir>/<name> (default: ./repos/<name>).

rnex repo clone <name>

rnex repo status

Inspects configuration, branch, and Git working tree status for a specific repository.

rnex repo status <name>

rnex repo exec

Executes an arbitrary shell command targeting an individual repository.

rnex repo exec <name> <command...>

rnex repo list

Alias for rnex list.

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Plugin Commands (rnex plugin)

Manage plugins and execute plugin-provided CLI commands.

rnex plugin list

Lists all available, enabled, and disabled plugins (from built-in plugins or configured external plugin paths via plugins.<name>.path) along with their declared CLI commands.

rnex plugin list

rnex plugin info

Displays detailed metadata, options, and commands for a plugin.

rnex plugin info <name>

rnex plugin enable

Enables a plugin in configuration and copies assets to .rnex/plugins/<name>/.

rnex plugin enable [--local] <name>

rnex plugin disable

Disables a plugin, executes its cleanup hook, and prunes scoped assets.

rnex plugin disable [--local] <name>

rnex plugin update

Re-synchronizes and updates enabled plugins from plugin sources.

rnex plugin update [<name>]

rnex plugin <name> <command>

Executes a subcommand exposed by an enabled plugin:

rnex plugin <name> <command> [options...]

• Example: rnex plugin karpathy-llm ingest docs/notes.md
• Example: rnex plugin karpathy-llm ingest --source docs/notes.md
• Example: rnex plugin karpathy-llm lint --strict
• Shorthand execution: rnex plugin <command> [options...] when <command> is unique across enabled plugins.