### Quick Start

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

A quick guide to get started with verilib-cli for repository and verification workflows.

```APIDOC
## Quick Start

### Repository Workflow

```bash
# 1. Authenticate
verilib-cli auth

# 2. Initialize repository
verilib-cli init --id <repo-id>    # From existing ID
verilib-cli init                    # Create new (auto-detects git URL)

# 3. Work with repository
verilib-cli pull      # Pull latest changes
verilib-cli deploy    # Deploy changes
verilib-cli reclone   # Trigger server reclone
```

### Verification Workflow

```bash
# 1. Create structure files
verilib-cli create

# 2. Enrich with atom metadata
verilib-cli atomize --update-stubs

# 3. Manage specifications
verilib-cli specify

# 4. Run verification
verilib-cli verify
```

### Auto-Validation for Trusted Specs

For high-trust projects where all specifications are considered valid by default (e.g., in CI environments), you can enable auto-validation.

Add the following to your `.verilib/config.json`:
```json
{
  "auto-validate-specs": true
}
```

When enabled, `verilib-cli specify` will automatically generate specification certificates for all uncertified specifications instead of prompting interactively. This is ideal for CI workflows.
```

--------------------------------

### Installation

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Instructions for installing the verilib-cli tool using various methods.

```APIDOC
## Installation

### One-Line Installers (Recommended)

**Linux & macOS:**
```bash
curl -sSL https://github.com/Beneficial-AI-Foundation/verilib-cli/releases/latest/download/verilib-cli-installer.sh | sh
```

**Windows (PowerShell):**
```powershell
irm https://github.com/Beneficial-AI-Foundation/verilib-cli/releases/latest/download/verilib-cli-installer.ps1 | iex
```

**NPM (Cross-platform):**
```bash
npm install -g verilib-cli
```

### Package Managers

**Homebrew (macOS):**
```bash
brew tap Beneficial-AI-Foundation/verilib-cli
brew install verilib-cli
```

**Windows MSI Installer:**
Download the latest `.msi` installer from the [releases page](https://github.com/Beneficial-AI-Foundation/verilib-cli/releases/latest).

### Manual Installation

Download the appropriate binary from the [releases page](https://github.com/Beneficial-AI-Foundation/verilib-cli/releases/latest):

| Platform | File |
|----------|------|
| macOS (Apple Silicon) | `verilib-cli-aarch64-apple-darwin.tar.xz` |
| macOS (Intel) | `verilib-cli-x86_64-apple-darwin.tar.xz` |
| Linux (x86_64) | `verilib-cli-x86_64-unknown-linux-gnu.tar.xz` |
| Linux (ARM64) | `verilib-cli-aarch64-unknown-linux-gnu.tar.xz` |
| Windows | `verilib-cli-x86_64-pc-windows-msvc.zip` |

Extract the archive and place the binary in your PATH.
```

--------------------------------

### User Workflow: Initialize and Setup

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Steps for cloning a project, setting up Verilib authentication, and initializing the Verilib environment.

```bash
git clone git@github.com:Beneficial-AI-Foundation/dalek-lite.git
cd dalek-lite
git checkout -b sl/structure

# Step 1: Initialize with Verilib (one-time setup)
verilib-cli auth
verilib-cli init
```

--------------------------------

### Install Proof Tools

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Installs necessary proof tools including Verus, Verus Analyzer, and SCIP. Ensure you are in the cloned directory before running.

```bash
git clone https://github.com/Beneficial-AI-Foundation/installers_for_various_tools
cd installers_for_various_tools
python3 verus_installer_from_release.py --version "0.2025.08.25.63ab0cb"
python3 verus_analyzer_installer.py
python3 scip_installer.py
```

--------------------------------

### User Workflow: Clone and Setup

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Initial steps for a user workflow, involving cloning a repository and checking out a specific branch.

```bash
git clone git@github.com:Beneficial-AI-Foundation/dalek-lite.git
cd dalek-lite
git checkout -b sl/structure
```

--------------------------------

### Install probe-verus

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Installs the probe-verus tool. This command should be run after cloning the repository and navigating into its directory.

```bash
git clone https://github.com/Beneficial-AI-Foundation/probe-verus
cd probe-verus
cargo install --path .
```

--------------------------------

### Install verilib-cli via NPM

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Install the verilib-cli globally using npm for cross-platform compatibility.

```bash
npm install -g verilib-cli
```

--------------------------------

### Install verilib-cli on Windows (PowerShell)

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Use this PowerShell command to install the verilib-cli on Windows.

```powershell
irm https://github.com/Beneficial-AI-Foundation/verilib-cli/releases/latest/download/verilib-cli-installer.ps1 | iex
```

--------------------------------

### Building Verilib CLI from Source

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Steps to clone the Verilib CLI repository, build the release version, run tests, and install it locally.

```bash
git clone https://github.com/Beneficial-AI-Foundation/verilib-cli.git
cd verilib-cli
cargo build --release
cargo test
cargo install --path .
```

--------------------------------

### Install verilib-cli with Homebrew

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Install the verilib-cli on macOS using the Homebrew package manager.

```bash
brew tap Beneficial-AI-Foundation/verilib-cli
brew install verilib-cli
```

--------------------------------

### Install Verilib CLI

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Installs the Verilib CLI on Linux and macOS using a one-line curl command.

```bash
curl -sSL https://github.com/Beneficial-AI-Foundation/verilib-cli/releases/latest/download/verilib-cli-installer.sh | sh
```

--------------------------------

### Verilib Project Configuration

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Example of the .verilib/config.json file, defining repository details, structure root, execution mode, Docker image, and auto-validation settings.

```json
{
  "repo": {
    "id": "abc123",
    "url": "https://verilib.org",
    "is_admin": false
  },
  "structure-root": ".verilib/structure",
  "execution-mode": "local",
  "docker-image": "ghcr.io/beneficial-ai-foundation/verilib-cli:latest",
  "auto-validate-specs": false
}
```

--------------------------------

### User Workflow

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Step-by-step guide for the interactive user workflow to set up and manage verification on a Verus project.

```APIDOC
## User Workflow

### Description
Complete interactive workflow for setting up and managing verification on a Verus project.

### Steps

1.  **Clone and Setup**
    ```bash
    git clone git@github.com:Beneficial-AI-Foundation/dalek-lite.git
    cd dalek-lite
    git checkout -b sl/structure
    ```
2.  **Initialize Verilib** (one-time setup)
    ```bash
    verilib-cli auth
    verilib-cli init
    ```
3.  **Create Structure Files**
    *Auto-discovers exec functions with Verus specs via probe-verus.*
    ```bash
    verilib-cli create
    ```
4.  **Run Atomization**
    *Generates stubs.json with atom dependencies from SCIP analysis. Updates .md files with code-name, code-path, and code-line.*
    ```bash
    verilib-cli atomize --update-stubs
    ```
5.  **Manage Specifications**
    *Prompts user to certify functions with changed specs. Updates stubs.json with specification statuses.*
    ```bash
    verilib-cli specify
    ```
6.  **Run Verification**
    *Runs Verus verification and updates stubs.json with proof statuses.*
    ```bash
    verilib-cli verify
    ```
7.  **Deploy to Server**
    ```bash
    verilib-cli deploy
    ```
```

--------------------------------

### API Get File Metadata

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Retrieves metadata for a specific file using the Verilib CLI API.

```bash
verilib-cli api get --file example
```

--------------------------------

### Get File Metadata

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Retrieves metadata for a specific file using the Verilib API.

```bash
verilib-cli api get --file path/to/function
```

--------------------------------

### API Set File Metadata

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Sets metadata fields for a specified file. For example, setting the 'specified' status to true.

```bash
verilib-cli api set --file example --specified true
```

--------------------------------

### User Workflow: Deploy to Server

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Deploys the verified project changes to the Verilib server.

```bash
# Step 6: Deploy to server
verilib-cli deploy
```

--------------------------------

### Create Structure Files

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Initializes structure files from source analysis using probe-verus. Use the --root option to specify a custom directory.

```bash
verilib-cli create                  # Default structure root
```

```bash
verilib-cli create --root custom/path
```

--------------------------------

### Initialize Verilib Repository

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Initialize a Verilib repository either from an existing repository ID or by creating a new one, which auto-detects the git URL.

```bash
verilib-cli init --id <repository-id>   # From existing ID
verilib-cli init                         # Create new repository
```

--------------------------------

### List All Files

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Lists all files managed by Verilib.

```bash
verilib-cli api list
```

--------------------------------

### Local Files Structure

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Illustrates the typical file structure within a Verilib project's .verilib directory.

```bash
# Local files structure:
# .verilib/
#   config.json         - Repository and structure configuration
#   stubs.json          - Enriched stub data with dependencies
#   atoms.json          - Atom metadata from probe-verus
#   specs.json          - Specification info
#   proofs.json         - Verification results
#   tracked_functions.csv
#   structure/          - Structure files (.md with YAML frontmatter)
#   certs/specs/        - Specification certificates
```

--------------------------------

### Configuration

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Details on the `.verilib/config.json` file and environment variable overrides for customizing Verilib CLI behavior.

```APIDOC
## Configuration

### Description
Project configuration is stored in `.verilib/config.json`. You can customize execution mode, Docker image, and auto-validation settings. Environment variables can override these settings.

### Configuration File (`.verilib/config.json`)

```json
{
  "repo": {
    "id": "abc123",
    "url": "https://verilib.org",
    "is_admin": false
  },
  "structure-root": ".verilib/structure",
  "execution-mode": "local",
  "docker-image": "ghcr.io/beneficial-ai-foundation/verilib-cli:latest",
  "auto-validate-specs": false
}
```

### Environment Variable Overrides

- `export VERILIB_EXECUTION_MODE=<docker|local>`: Overrides the `execution-mode` setting.
- `export VERILIB_DOCKER_IMAGE=<my-custom-image:tag>`: Overrides the `docker-image` setting.
- `export VERILIB_STORAGE=<file>`: Forces file-based credential storage.

### Local Files Structure

- `.verilib/config.json`: Repository and structure configuration.
- `.verilib/stubs.json`: Enriched stub data with dependencies.
- `.verilib/atoms.json`: Atom metadata from probe-verus.
- `.verilib/specs.json`: Specification info.
- `.verilib/proofs.json`: Verification results.
- `.verilib/tracked_functions.csv`
- `.verilib/structure/`: Directory for structure files (.md with YAML frontmatter).
- `.verilib/certs/specs/`: Directory for specification certificates.
```

--------------------------------

### Build and Run Verilib CLI

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/CLAUDE.md

Standard Cargo commands for building, testing, formatting, linting, and running the Verilib CLI locally.

```bash
cargo build              # Debug build
```

```bash
cargo build --release    # Release build
```

```bash
cargo test               # Run tests
```

```bash
cargo fmt                # Format code
```

```bash
cargo clippy             # Lint check
```

```bash
cargo run -- <args>      # Run locally
```

--------------------------------

### User Workflow: Create Structure Files

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Generates structure files from source analysis, automatically discovering functions with Verus specs via probe-verus.

```bash
# Step 2: Create structure files from source analysis
# Auto-discovers exec functions with Verus specs via probe-verus
verilib-cli create
```

--------------------------------

### Server Workflow Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Commands for server environments using Verilib CLI with --no-probe and --check-only flags, reading from pre-generated JSON files.

```bash
# probe-verus commands run separately in Docker containers:
#   probe-verus atomize ... -o .verilib/atoms.json
#   probe-verus specify ... -o .verilib/specs.json
#   probe-verus verify ... -o .verilib/proofs.json

# Step 1: Verify structure files match atoms.json
verilib-cli atomize --no-probe --check-only
```

```bash
# Step 2: Verify all specs are certified from specs.json
verilib-cli specify --no-probe --check-only
```

```bash
# Step 3: Verify no failures from proofs.json
verilib-cli verify --no-probe --check-only
```

--------------------------------

### Create File with Content

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Creates a new file with specified content, either directly, from another file, or via piped input.

```bash
verilib-cli api create-file --path ./config.json --content '{"key": "value"}'
verilib-cli api create-file --path ./dest.txt --from-file ./source.txt
echo "content" | verilib-cli api create-file --path ./piped.txt
```

--------------------------------

### Initialize Verilib Repository

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Initializes a new Verilib repository or from an existing repository ID. The CLI auto-detects git remote URL and branch. Prompts for execution mode (Local or Docker).

```bash
verilib-cli init --id abc123
```

```bash
verilib-cli init
```

```bash
verilib-cli init --id abc123 --url https://custom.verilib.org
```

--------------------------------

### Server Workflow Script for Verilib CLI

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

This bash script demonstrates a server workflow for Verilib CLI. It assumes probe-verus commands are run separately in Docker containers and uses --no-probe with verilib-cli to read pre-generated JSON files for verification steps.

```bash
#!/bin/bash
# Server workflow - probe-verus runs in separate Docker containers

# probe-verus commands run separately in Docker containers:
# probe-verus atomize ... -o .verilib/atoms.json
# probe-verus specify ... -o .verilib/specs.json
# probe-verus verify ... -o .verilib/proofs.json

# verilib-cli reads from pre-generated JSON files with --no-probe

# Step 1: Verify structure files match atoms.json
verilib-cli atomize --no-probe --check-only

# Step 2: Verify all specs are certified from specs.json
verilib-cli specify --no-probe --check-only

# Step 3: Verify no failures from proofs.json
verilib-cli verify --no-probe --check-only

```

--------------------------------

### Authenticate with Verilib API

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Authenticates with the Verilib API by storing the API key securely in the system keyring. Use `export VERILIB_STORAGE=file` to force file-based storage if keyring fails.

```bash
verilib-cli auth
```

```bash
verilib-cli status
```

```bash
export VERILIB_STORAGE=file
verilib-cli auth
```

--------------------------------

### User Workflow: Run Atomization

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Generates stubs.json with atom dependencies from SCIP analysis and updates .md files with code information.

```bash
# Step 3: Run atomization
# Generates stubs.json with atom dependencies from SCIP analysis
# Updates .md files with code-name, code-path, and code-line
verilib-cli atomize --update-stubs
```

--------------------------------

### Deploy Local Changes

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Deploys local changes to the Verilib server. Can specify a custom API URL.

```bash
verilib-cli deploy
verilib-cli deploy --url https://custom.verilib.org
```

--------------------------------

### Create Verification Structure Files

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Generates verification structure files (e.g., `.md` stubs with YAML frontmatter) from source analysis using `probe-verus tracked-csv`. Can specify a custom root directory.

```bash
verilib-cli create
```

```bash
verilib-cli create --root custom/path
```

--------------------------------

### Basic Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Commands for pulling repository structure and triggering reclone operations.

```APIDOC
## `pull`

### Description
Pull the latest repository structure from the server.

### Method
CLI Command

### Endpoint
N/A

### Request Example
```bash
verilib-cli pull
```

### Response
N/A
```

```APIDOC
## `reclone`

### Description
Trigger a reclone operation on the server. Includes safety checks for uncommitted changes.

### Method
CLI Command

### Endpoint
N/A

### Request Example
```bash
verilib-cli reclone
```

### Response
N/A
```

--------------------------------

### Deploy Repository Changes

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Command to deploy local repository changes to the Verilib server. A custom API base URL can be specified.

```bash
verilib-cli deploy

# Options:
# | Option | Description |
# |--------|-------------|
# | --url <url> | Custom API base URL |
```

--------------------------------

### Deploy and Pull Commands

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Commands to synchronize local repository changes with the Verilib server.

```APIDOC
## Deploy and Pull Commands

### Description
Synchronize repository changes with the Verilib server. Deploy pushes local changes, pull fetches the latest structure from the server.

### Commands

- `verilib-cli deploy`: Deploy local changes to the server.
- `verilib-cli deploy --url <https://custom.verilib.org>`: Deploy with a custom API URL.
- `verilib-cli pull`: Pull the latest repository structure from the server.
- `verilib-cli reclone`: Trigger a server-side reclone, including safety checks for uncommitted changes.
- `verilib-cli --debug deploy`: Enable debug output for the deploy command.
- `verilib-cli --debug pull`: Enable debug output for the pull command.
```

--------------------------------

### Environment Variable Overrides for API Key Storage

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Demonstrates how to override the default API key storage method using environment variables.

```bash
export VERILIB_STORAGE=file    # Force file storage
export VERILIB_STORAGE=keyring # Use system keyring
```

--------------------------------

### Global Options

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Global options applicable to most Verilib CLI commands.

```APIDOC
## Global Options

### Description
Options that can be applied to various Verilib CLI commands.

### Parameters
#### Query Parameters
- **--debug** (boolean) - Enable debug output.
- **--json** (boolean) - Output in JSON format (API commands).
- **--dry-run** (boolean) - Show changes without applying (API commands).

### Request Example
```bash
verilib-cli --debug deploy
```
```

--------------------------------

### Tagging for Release

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/CLAUDE.md

Commands to tag a release using semantic versioning and push tags to trigger GitHub Actions for deployment.

```bash
git tag 0.1.7
```

```bash
git push --tags
```

--------------------------------

### User Workflow: Manage Specifications

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Prompts the user to certify functions with changed specifications and updates stubs.json with specification statuses.

```bash
# Step 4: Manage specifications
# Prompts user to certify functions with changed specs
# Updates stubs.json with specification statuses
verilib-cli specify
```

--------------------------------

### Repository Workflow Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Sequence of commands for managing a Verilib repository, including authentication, initialization, pulling, deploying, and recloning.

```bash
# 1. Authenticate
verilib-cli auth

# 2. Initialize repository
verilib-cli init --id <repo-id>    # From existing ID
verilib-cli init                    # Create new (auto-detects git URL)

# 3. Work with repository
verilib-cli pull      # Pull latest changes
verilib-cli deploy    # Deploy changes
verilib-cli reclone   # Trigger server reclone
```

--------------------------------

### API Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Programmatic interface for managing `.verilib` files, useful for scripting and automation.

```APIDOC
## `api get`

### Description
Get metadata for a specific file.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **--file** (string) - Required - The name of the file to get metadata for.

### Request Example
```bash
verilib-cli api get --file example
```

### Response
N/A
```

```APIDOC
## `api list`

### Description
List all files, optionally filtered by status.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **--filter** (string) - Optional - Filter the list by status (e.g., `specified`).

### Request Example
```bash
verilib-cli api list
verilib-cli api list --filter specified
```

### Response
N/A
```

```APIDOC
## `api set`

### Description
Set metadata fields for a file.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **--file** (string) - Required - The name of the file to set metadata for.
- **--specified** (boolean) - Required - The value to set for the specified field (e.g., `true`).

### Request Example
```bash
verilib-cli api set --file example --specified true
```

### Response
N/A
```

```APIDOC
## `api batch`

### Description
Batch update multiple files from JSON input.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **--input** (string) - Required - Path to the JSON file containing updates.

### Request Example
```bash
verilib-cli api batch --input updates.json
```

### Response
N/A
```

```APIDOC
## `api create-file`

### Description
Create a new file with content from string, file, or stdin.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **--path** (string) - Required - The path for the new file.
- **--content** (string) - Optional - The content of the file as a string.
- **--from-file** (string) - Optional - Path to a file to copy content from.

### Request Example
```bash
verilib-cli api create-file --path ./config.json --content '{"key": "value"}'
verilib-cli api create-file --path ./dest.txt --from-file ./source.txt
echo "content" | verilib-cli api create-file --path ./piped.txt
```

### Response
N/A
```

--------------------------------

### Authenticate with Verilib API

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Command to authenticate with the Verilib API. Your API key is securely stored in your system's keyring.

```bash
verilib-cli auth
```

--------------------------------

### User Workflow: Run Verification

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Executes Verus verification and updates stubs.json with the resulting proof statuses.

```bash
# Step 5: Run verification
# Runs Verus verification and updates stubs.json with proof statuses
verilib-cli verify
```

--------------------------------

### API Commands

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Programmatic interface for managing `.verilib` metadata files, useful for scripting and automation.

```APIDOC
## API Commands

### Description
Programmatic interface for managing `.verilib` metadata files. Useful for scripting, automation, and CI integration.

### Commands

- `verilib-cli api get --file <path/to/function>`: Get metadata for a specific file.
- `verilib-cli api list`: List all files.
- `verilib-cli api list --filter <specified|ignored|verified>`: List files filtered by status.
- `verilib-cli api set --file <path/to/function> --specified <true|false>`: Set the 'specified' metadata field for a file.
- `verilib-cli api set --file <path/to/function> --ignored <true|false>`: Set the 'ignored' metadata field for a file.
- `verilib-cli api set --file <path/to/function> --verified <true|false>`: Set the 'verified' metadata field for a file (Admin only).
- `verilib-cli api batch --input <updates.json>`: Batch update multiple files from a JSON input file. The `updates.json` should have the format:
  ```json
  {
    "operations": [
      {"file": "path/to/func1", "specified": true},
      {"file": "path/to/func2", "ignored": false}
    ]
  }
  ```
- `verilib-cli api create-file --path <path> --content <content>`: Create a new file with specified content.
- `verilib-cli api create-file --path <path> --from-file <source_path>`: Create a new file from an existing file.
- `echo "content" | verilib-cli api create-file --path <piped_path>`: Create a new file from piped content.

### Global Options

- `verilib-cli --json api list`: Output API list results in JSON format.
- `verilib-cli --dry-run api set --file f --specified true`: Preview changes without applying them.
```

--------------------------------

### Repository Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Documentation for commands related to managing Verilib repositories.

```APIDOC
## Repository Commands

### `auth`
Authenticate with the Verilib API. Your API key is stored securely in your system's keyring.

```bash
verilib-cli auth
```

### `status`
Display current authentication status.

```bash
verilib-cli status
```

### `init`
Initialize a repository from an existing ID or create a new one from a git URL.

```bash
verilib-cli init --id <repository-id>   # From existing ID
verilib-cli init                         # Create new repository
```

**Options:**
| Option | Description |
|--------|-------------|
| `--id <id>` | Initialize from existing repository ID |
| `--url <url>` | Custom API base URL |

When creating a new repository (no `--id`), the CLI will:
1. Auto-detect git URL from current directory
2. Prompt for repository URL (supports branches and subfolders)
3. Collect metadata (language, proof language, summary)
4. Create repository and save ID locally

### `deploy`
Deploy repository changes to the server.

```bash
verilib-cli deploy
```

**Options:**
| Option | Description |
|--------|-------------|
| `--url <url>` | Custom API base URL |
```

--------------------------------

### API Command Global Options

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Applies global options like JSON output or dry-run preview to API commands.

```bash
verilib-cli --json api list              # Output in JSON format
verilib-cli --dry-run api set --file f --specified true  # Preview changes
```

--------------------------------

### API List Files

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Lists all files managed by Verilib, with an option to filter by status.

```bash
verilib-cli api list
```

```bash
verilib-cli api list --filter specified
```

--------------------------------

### Pull Repository Structure

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Fetches the latest repository structure from the Verilib server.

```bash
verilib-cli pull
```

--------------------------------

### CI Workflow: Verify Specifications

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Checks if all stubs with specifications have a valid certificate. Fails if any are missing.

```bash
# Step 2: Verify all specs are certified
# Fails if any stub with specs is missing a cert
verilib-cli specify --check-only
```

--------------------------------

### Structure Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Commands for managing verification structure files, integrating with probe-verus for static analysis.

```APIDOC
## `create`

### Description
Initialize structure files from source analysis. Uses `probe-verus tracked-csv` to auto-discover exec functions with Verus specs and generate `.md` stub files.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **--root** (string) - Optional - Custom structure root (default: `.verilib/structure`)

### Request Example
```bash
verilib-cli create
verilib-cli create --root custom/path
```

### Response
N/A

### Requirements
- `probe-verus` installed and in PATH
```

```APIDOC
## `atomize`

### Description
Enrich structure files with metadata from SCIP atoms.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **-s, --update-stubs** (boolean) - Optional - Update .md files with code-name
- **-n, --no-probe** (boolean) - Optional - Skip running probe-verus atomize and read existing atoms.json
- **-c, --check-only** (boolean) - Optional - Check if .md stub files match enriched stubs.json without writing
- **--atoms-only** (boolean) - Optional - Only generate atoms.json, skip stubs enrichment (no `create` needed)
- **--rust-analyzer** (boolean) - Optional - Use rust-analyzer instead of verus-analyzer for SCIP generation

### Request Example
```bash
verilib-cli atomize
verilib-cli atomize -s
verilib-cli atomize --atoms-only
```

### Response
N/A

### Auto-detection
When no `.verilib/config.json` exists and the project's `Cargo.toml` has no Verus dependencies (`vstd`, `verus_builtin`, `verus_builtin_macros`, or `[package.metadata.verus]`), atoms-only mode is enabled automatically. This lets `verilib-cli atomize` work on pure Rust projects without running `create` first.
```

```APIDOC
## `specify`

### Description
Check specification status and manage spec certificates.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **-n, --no-probe** (boolean) - Optional - Skip running probe-verus specify and read existing specs.json
- **-c, --check-only** (boolean) - Optional - Check if all stubs with specs have certs, error if any are missing

### Request Example
```bash
verilib-cli specify
```

### Response
N/A

### Functionality
1. Runs `probe-verus specify` to get spec info
2. Shows interactive menu for uncertified functions
3. Creates cert files for selected functions
4. Updates `specified` status in stubs
```

```APIDOC
## `verify`

### Description
Run verification and update stubs with verification status.

### Method
CLI Command

### Endpoint
N/A

### Parameters
#### Query Parameters
- **--verify-only-module** (string) - Optional - Only verify functions in this module
- **-n, --no-probe** (boolean) - Optional - Skip running probe-verus verify and read existing proofs.json
- **-c, --check-only** (boolean) - Optional - Check if any stub has status "failure", error if any are found

### Request Example
```bash
verilib-cli verify
verilib-cli verify --verify-only-module my_module
```

### Response
N/A
```

--------------------------------

### Set File Metadata

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Sets metadata fields (specified, ignored, verified) for a specific file. 'verified' is admin-only.

```bash
verilib-cli api set --file path/to/function --specified true
verilib-cli api set --file path/to/function --ignored false
verilib-cli api set --file path/to/function --verified true  # Admin only
```

--------------------------------

### Verify and Update Stubs

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Runs verification and updates stubs with the verification status. Can be used to verify only a specific module.

```bash
verilib-cli verify
```

```bash
verilib-cli verify --verify-only-module my_module
```

--------------------------------

### Force File Storage for Verilib CLI Authentication

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Command to force Verilib CLI to use file storage for authentication, useful when keyring storage fails.

```bash
export VERILIB_STORAGE=file
verilib-cli auth
```

--------------------------------

### Verilib CLI Authentication and Status Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Commands to check the status of Verilib CLI and re-authenticate if necessary.

```bash
verilib-cli status    # Check status
verilib-cli auth      # Re-authenticate
```

--------------------------------

### Verification Workflow Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Sequence of commands for managing the verification process, including creating structure files, atomizing, specifying, and verifying.

```bash
# 1. Create structure files
verilib-cli create

# 2. Enrich with atom metadata
verilib-cli atomize --update-stubs

# 3. Manage specifications
verilib-cli specify

# 4. Run verification
verilib-cli verify
```

--------------------------------

### Interactive Workflow Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Commands for interactive use of Verilib CLI, including discovery, atomization, specification, and verification.

```bash
verilib-cli create
```

```bash
verilib-cli atomize --update-stubs
```

```bash
verilib-cli specify
```

```bash
verilib-cli verify
```

--------------------------------

### CI Workflow: Verify Structure Files

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Checks if .md stub files match the enriched stubs.json. Fails if they do not.

```bash
# Step 1: Verify structure files are up to date
# Fails if .md stub files don't match enriched stubs.json
verilib-cli atomize --check-only
```

--------------------------------

### Enable Debug Output

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Enables debug output for troubleshooting deployment and pull commands.

```bash
verilib-cli --debug deploy
verilib-cli --debug pull
```

--------------------------------

### Skip Probe Verification

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Use existing proofs.json to skip the probe-verus step during verification.

```bash
verilib-cli verify --no-probe
verilib-cli verify -n
```

--------------------------------

### CI Workflow: Verify No Verification Failures

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Ensures no stub has a 'failure' status. Fails the build if any verification failures are found.

```bash
# Step 3: Verify no verification failures
# Fails if any stub has status "failure"
verilib-cli verify --check-only
```

--------------------------------

### Display Authentication Status

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Command to check the current authentication status with the Verilib API.

```bash
verilib-cli status
```

--------------------------------

### Atomize Structure Files

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Enriches structure files with metadata from SCIP atoms by running static analysis. Options include updating `.md` files, generating only `atoms.json`, using `rust-analyzer`, skipping `probe-verus`, or running in CI check-only mode.

```bash
verilib-cli atomize
```

```bash
verilib-cli atomize --update-stubs
```

```bash
verilib-cli atomize -s
```

```bash
verilib-cli atomize --atoms-only
```

```bash
verilib-cli atomize --rust-analyzer
```

```bash
verilib-cli atomize --no-probe
```

```bash
verilib-cli atomize -n
```

```bash
verilib-cli atomize --check-only
```

```bash
verilib-cli atomize -c
```

--------------------------------

### API Batch Update Files

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Performs batch updates on multiple files using JSON input. The input file should contain the update instructions.

```bash
verilib-cli api batch --input updates.json
```

--------------------------------

### CI Workflow Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Commands for continuous integration using Verilib CLI with the --check-only flag to validate without modifications.

```bash
# Step 1: Verify structure files are up to date
# Fails if .md stub files don't match enriched stubs.json
verilib-cli atomize --check-only
```

```bash
# Step 2: Verify all specs are certified
# Fails if any stub with specs is missing a cert
verilib-cli specify --check-only
```

```bash
# Step 3: Verify no failures
# Fails if any stub has status "failure"
verilib-cli verify --check-only
```

--------------------------------

### Enable Debug Mode for Verilib CLI Commands

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Commands to run Verilib CLI in debug mode for enhanced logging during initialization and deployment.

```bash
verilib-cli --debug init
verilib-cli --debug deploy
```

--------------------------------

### Batch Update Files

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Performs batch updates on multiple files using a JSON input file. The JSON should contain an 'operations' array with file paths and their desired states.

```json
{
  "operations": [
    {"file": "path/to/func1", "specified": true},
    {"file": "path/to/func2", "ignored": false}
  ]
}
```

```bash
verilib-cli api batch --input updates.json
```

--------------------------------

### Verification Commands

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Commands for verifying Verus code, with options to skip probing, use existing proofs, or perform checks only.

```APIDOC
## Verification Commands

### Description
Commands for verifying Verus code, with options to skip probing, use existing proofs, or perform checks only.

### Commands

- `verilib-cli verify --no-probe` or `verilib-cli verify -n`: Skip running probe-verus and use existing proofs.json.
- `verilib-cli verify --check-only` or `verilib-cli verify -c`: CI mode; checks if any stub has status "failure" and fails if any are found.
```

--------------------------------

### Configure Auto-Validation for Specs

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Enables automatic specification validation in CI environments by setting `auto-validate-specs` to `true` in `.verilib/config.json`.

```json
{
  "auto-validate-specs": true
}
```

--------------------------------

### Atomize Structure Files

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Enriches structure files with metadata from SCIP atoms. Use flags like -s to update .md files or --atoms-only to only generate atoms.json.

```bash
verilib-cli atomize                 # Generate stubs.json (full pipeline)
```

```bash
verilib-cli atomize -s              # Also update .md files with code-name
```

```bash
verilib-cli atomize --atoms-only    # Only generate atoms.json (no stubs needed)
```

--------------------------------

### Enable Debug Output

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Enables debug output for Verilib CLI commands. This can be combined with other commands to troubleshoot.

```bash
verilib-cli --debug deploy
```

--------------------------------

### CI Mode Verification Check

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

In CI mode, this command checks if any stub has a status of 'failure' and fails the build if any are found.

```bash
verilib-cli verify --check-only
verilib-cli verify -c
```

--------------------------------

### Run Verus Verification

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Executes Verus verification on the codebase and updates stubs with verification status. Allows specifying a module or package to verify.

```bash
verilib-cli verify
```

```bash
verilib-cli verify --verify-only-module my_module
```

```bash
verilib-cli verify --package my-crate
```

--------------------------------

### Specify Command for Verus Specifications

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Checks specification status and manages certification files. Supports interactive mode, skipping `probe-verus`, and CI check-only mode. Can enable auto-validation via `.verilib/config.json`.

```bash
verilib-cli specify
```

```bash
verilib-cli specify --no-probe
```

```bash
verilib-cli specify -n
```

```bash
verilib-cli specify --check-only
```

```bash
verilib-cli specify -c
```

--------------------------------

### List Files Filtered by Status

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Lists files filtered by their status (specified, ignored, or verified).

```bash
verilib-cli api list --filter specified
verilib-cli api list --filter ignored
verilib-cli api list --filter verified
```

--------------------------------

### Specify Verification Status

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Checks specification status and manages spec certificates by running probe-verus specify, showing an interactive menu, creating cert files, and updating status.

```bash
verilib-cli specify
```

--------------------------------

### Environment Variable Overrides

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Overrides for Verilib configuration using environment variables, such as execution mode, Docker image, and storage type.

```bash
export VERILIB_EXECUTION_MODE=docker  # or "local"
export VERILIB_DOCKER_IMAGE=my-custom-image:tag
export VERILIB_STORAGE=file  # Force file-based credential storage
```

--------------------------------

### CI Workflow

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Non-interactive workflow for continuous integration, utilizing check-only modes that fail on mismatches.

```APIDOC
## CI Workflow

### Description
Non-interactive workflow for continuous integration with check-only validation modes that fail on mismatches.

### Script

```bash
#!/bin/bash
set -e

# CI Workflow - fails fast on any validation error

# Step 1: Verify structure files are up to date
# Fails if .md stub files don't match enriched stubs.json
verilib-cli atomize --check-only

# Step 2: Verify all specs are certified
# Fails if any stub with specs is missing a cert
verilib-cli specify --check-only

# Step 3: Verify no verification failures
# Fails if any stub has status "failure"
verilib-cli verify --check-only

echo "All checks passed!"
```
```

--------------------------------

### CI Workflow Success Message

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Indicates that all CI checks have passed successfully.

```bash
echo "All checks passed!"
```

--------------------------------

### Trigger Server Reclone

Source: https://context7.com/beneficial-ai-foundation/verilib-cli/llms.txt

Triggers a server-side reclone, including safety checks for uncommitted changes.

```bash
verilib-cli reclone
```

--------------------------------

### Remove Quarantine Attribute on macOS

Source: https://github.com/beneficial-ai-foundation/verilib-cli/blob/master/README.md

Command to remove the quarantine attribute from the Verilib CLI executable on macOS, often required to bypass security warnings.

```bash
xattr -d com.apple.quarantine /path/to/verilib-cli
```

=== COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.