CLI Reference

Complete command reference for the cora CLI.

Global Flags

Flag	Description
--config <path>	Override config file path (default: .cora.yaml)
--format <fmt>	Output format: pretty, json, compact, sarif
--no-color	Disable colored output
--provider <name>	Override provider
--model <name>	Override model
--base-url <url>	Override API base URL
--api-key <key>	Override API key
--verbose	Enable debug logging

Commands

Setup & Config

Command	Description
cora init	Create .cora.yaml config file and install pre-commit hook
cora init --force	Overwrite existing config file
cora init --no-hook	Skip pre-commit hook installation
cora config show	Show resolved configuration
cora config show --global	Show global config (~/.cora/config.yaml)
cora config show --project	Show project config (.cora.yaml)
cora config set <key> <value>	Set a config value
cora config set <key> <value> --global	Write to global config instead of project
cora config validate	Validate configuration and report status
cora auth login	Save API key interactively
cora auth login --provider <name> --api-key <key>	Non-interactive login
cora auth login --model <model>	Set model with provider
cora auth login --base-url <url>	Custom API endpoint
cora auth login --force	Overwrite existing key without confirmation
cora auth status	Check current auth status
cora auth remove	Remove stored API key
cora providers	List detected AI providers
cora install	Auto-detect and configure AI coding agents for Cora MCP
cora install --list	List detected agents without installing
cora install --agents "cline,cursor"	Install specific agents
cora install --dry-run	Show what would be changed
cora install --force	Overwrite existing cora entry
cora install --yes	Install ALL detected agents (non-interactive)
cora hook install	Install pre-commit hook
cora hook uninstall	Remove pre-commit hook
cora completion <shell>	Generate shell completions (bash/zsh/fish/powershell)

Review & Scan

Command	Description
cora review	Review code changes (default: tries staged, then unpushed)
cora review --staged	Review staged git changes
cora review --unstaged	Review unstaged working changes
cora review --unpushed	Review unpushed commits
cora review --base <branch>	Compare current branch against target
cora review --commit <ref>	Review specific commit or range
cora review --diff-file <path>	Review from a diff file
cora review --upload	Review and upload SARIF to GitHub Code Scanning
cora review --no-auto-chunk	Disable auto-chunking for large diffs
cora review --progress	Output NDJSON progress events to stderr
cora review --quiet	Suppress all output except result
cora review --output-file <path>	Write output to file instead of stdout
cora review --severity <level>	Filter by min severity (info/minor/major/critical)
cora review --no-cache	Disable review caching
cora review --ci	CI mode: skip diff size limit, exit 2 if any findings
cora review --max-diff-size <chars>	Override max diff size
cora review --memory	Recall project patterns from Uteke before review
cora review --learn	Save findings to Uteke after review (implies --memory)
cora commit	Review staged + generate commit message + commit (HITL prompt)
cora commit --yolo	Auto-commit without prompts
cora commit --force	Commit even if quality gate fails
cora commit --no-review	Skip review, only generate commit message
cora commit --edit	Always open $EDITOR to edit message
cora commit --stream	Stream LLM response in real-time
cora commit --quiet	Suppress all output except result
cora scan [--path <dir>]	Scan files for issues (default: current directory)
cora scan --include "src/**/*.rs"	Include glob patterns
cora scan --exclude "vendor/**"	Exclude glob patterns
cora scan --extensions "ts,js"	Additional file extensions to scan
cora scan --incremental	Scan only files changed since last scan
cora scan --focus security	Override focus areas
cora scan --batch-files N	Max files per LLM batch (default: 20)
cora scan --no-continue-on-batch-error	Abort on batch failure (default: skip and continue)

Code Intelligence

See Code Intelligence for detailed usage.

Command	Description
cora index	Index project symbols into SQLite + usearch
cora index --rebuild	Rebuild index from scratch
cora index --watch	Auto-sync file watcher (2s poll interval)
cora index --stats	Show index statistics (symbol count, languages, DB size)
cora index --prune	Remove stale entries for deleted files
cora explore <query>	Keyword search (FTS5) over symbol names
cora explore --kind function	Filter by symbol kind
cora explore --file "src/"	Filter by file path prefix
cora explore --language rust	Filter by language
cora explore --limit N	Max results (default: 50)
cora brain <query>	Hybrid search: FTS5 + vector + graph → RRF fusion
cora brain --limit N	Max results (default: 20)
cora callers <symbol>	Find all callers of a symbol (reverse call graph)
cora callers --limit N	Max callers to return (default: 50)
cora impact <symbol>	Analyze blast radius of changing a symbol
cora impact --depth N	Traversal depth (default: 3)
cora trace <symbol>	Trace call chains (depth-limited BFS)
cora trace --direction incoming	Trace callers instead of callees
cora trace --depth N	Max hops (default: 3)
cora arch	Architecture overview — modules, edge types, top connectors
cora affected <files...>	Find test files affected by source changes
cora affected --stdin	Read changed files from stdin (pipe from git diff --name-only)
cora affected --filter "*test*"	Custom test file glob pattern
cora dead-code	Detect dead code — functions/methods with zero callers
cora dead-code --include-tests	Include test functions in results
cora dead-code --min-lines N	Filter out tiny functions
cora query "main -> *"	Query the code graph with simple patterns
cora query --limit N	Max results (default: 50)
cora routes	List detected HTTP routes (Axum, Actix, Express, FastAPI, Flask, Go)
cora routes --method GET	Filter by HTTP method
cora routes --prefix /api	Filter by path prefix

Quality Profiles

Command	Description
cora profile list	List available quality profiles
cora profile show <name>	Show details of a specific profile
cora profile validate <path>	Validate a custom profile YAML file

Findings & Debt

Command	Description
cora findings list	Show open findings
cora findings list --all	Show all findings including resolved
cora findings list --severity major	Filter by severity
cora findings list --file "src/main.rs"	Filter by file
cora findings list --json	JSON output
cora findings stats	Summary counts with resolution rate
cora findings dismiss <id>	Mark finding as won't-fix
cora findings dismiss <id> --reason "..."	Dismiss with reason
cora findings reopen <id>	Reopen a dismissed/resolved finding
cora debt	Show tech debt report from review history
cora debt --json	Debt report as JSON (for CI/dashboards)
cora debt --trend	Quality score trend graph
cora debt --badge	Shields.io badge JSON endpoint
cora debt --estimate	Show estimated fix time
cora debt --since v0.4.5	Filter by git tag or date
cora debt --branch main	Filter by branch
cora upload-sarif <file>	Upload SARIF to GitHub Code Scanning

MCP Server

Command	Description
cora mcp	Start MCP server for AI coding agents (Claude Code, Cursor, Windsurf)
cora serve	Start MCP server with auto-reindex on startup

Quick Examples

# Review staged changes (what's about to be committed)
$ cora review --staged

# Compare your feature branch against main
$ cora review --base main

# Full project scan with incremental caching
$ cora scan --incremental

# Install pre-commit hook
$ cora hook install

# Review + auto-generate commit message + commit
$ cora commit

# YOLO mode — auto-commit, no prompts
$ cora commit --yolo

# Index your project and search with Brain Mode
$ cora index
$ cora brain "error handling"
$ cora brain "TokenEmbedding" --json --limit 5

# Trace call chains and view architecture
$ cora trace main
$ cora arch

# Find callers and analyze impact
$ cora callers handle_request
$ cora impact process_order --depth 5
$ cora affected src/order.rs src/payment.rs