CLI commands
Every command in the ana CLI, grouped by category. Run ana --help or ana <command> --help for flags and usage.
Getting Started
ana scan [path]Detect stack, conventions, and patterns
--json--save-q--quickana initScan project and generate agent context
-f-y--platforms <platforms>ana setupEnrich context with team knowledge
ana setup completeValidate context files and finalize setup
--forceana setup check [filename]Validate context files for quality gates
--jsonana setup indexBuild symbol index for citation verification
ana doctorCheck project health and configuration
--jsonPipeline
ana workStart, track, and complete development tasks
ana work statusShow pipeline state for all active work items
--json--sessionana work start <slug>Start a new work item
--force--req <id>ana work complete <slug>Archive completed work after PR merge, optionally merging the PR first
--json--mergeana run [agent]Run an Anatomia agent
--platform <platform>--slug <slug>ana artifactSave pipeline outputs with hash verification
ana artifact save <type> <slug>Commit a pipeline artifact to the correct branch
ana artifact save-all <slug>Commit all artifacts in a plan directory atomically
ana verifyVerify contract assertions before code review
ana verify pre-check <slug>Run contract seal verification
ana planPlan-time helpers for writing contracts
ana plan coverage <slug>Preview the AC → assertion coverage map (read-only, never gates)
ana testRun tests with engine-captured, seal-gated evidence
--stage <stage>--slug <slug>--surface <name>--jsonana prCreate pull request from verified build
ana pr create <slug>Create GitHub PR from pipeline artifacts
Configuration
ana configRead and write ana.json settings
ana config showShow all settings
--jsonana config get <field>Get a config field value
--jsonana config set <field> <value>Set a config field value
ana config delete <field>Delete a config field
ana config schemaList the configurable surface — every key, its shape, and an example
Intelligence
ana proof [slug]View proof chain entries, health, and findings
--json--latest--whyana proof context <files>Query proof chain for context about specific files
--jsonana proof close <ids>Close active findings with a reason
--reason <reason>--dry-run--jsonana proof promote <ids>Promote findings to a skill rule
--skill <skill>--text <text>--section <section>--force--jsonana proof strengthen <ids>Commit a skill file edit and mark findings as promoted
--skill <skill>--reason <reason>--force--jsonana proof auditList active findings grouped by file
--json--full--severity <values>--entry <slug>--matrix--surface <name>--new--since <date>ana proof healthDisplay proof chain health dashboard
--json--surface <name>ana proof staleShow findings with staleness signals from subsequent pipeline runs
--after <slug>--min-confidence <level>--jsonana learnManage learn sessions
ana learn endEnd learn session — mark timestamp for next session
--jsonana agentsAgent dashboard — list agents, manage models & projected skills
ana agents model [agent] [model]Show or set agent model overrides
--default--allana agents skills <agent> [list]Set, append, or clear an agent\'s projected skills (writes ana.json + projects into Claude & Codex now)
--add--clear