anchors doctor

X-ray of the ecosystem: systemic loose ends, health and maturity.

The ecosystem's health validator (QUALITY §5.2) — the GLOBAL view.
Unlike check (node against gate, incremental), doctor sweeps the map + the
Structure + the disk and hunts the SYSTEMIC loose ends no local gate sees:
map integrity (dead edges, phantom nodes), orphans (code without spec,
missing identity), loose layers, and gate coverage holes.

It PRESENTS and RECORDS, but does NOT block — it is diagnosis, run on demand.

With --fix, it creates what is missing: pipelines, git hooks, state labels and the
protection of the integration branch. It is IDEMPOTENT — in an already assembled
repository it changes nothing, and each repair checks before acting. Run it without asking
for authorization: it is the environment preparation step, not a project
change.

Usage

anchors doctor [flags]

Flags

Flag	Default	What it does
--check-pipelines		exits with 1 if any Anchors pipeline is out of date (so CI can self-verify)
--fix		creates what is missing in the github mode environment (pipelines, labels, branch protection). IDEMPOTENT: in an already set-up repository it changes nothing, and it is safe to always run
--map		path to the map
--root	.	project root

Project health — family

Commands of the same family — what tells each apart:

Command	What it does
anchors doctor	X-ray of the ecosystem: systemic loose ends, health and maturity
anchors audit	Dossier of one file’s pending items (gates + doctor), for batch fixing
anchors status	Where the project stands in the cycle, and what the next step is
anchors task-status	The round’s report: what is delivered, what remains, and what comes next
anchors compliance	The state of each regulatory duty: how many nodes subject, how many comply
anchors governs	Show who each guide governs (and how many) — sizes the audit per guide

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While check evaluates local gate rules, anchors doctor provides a global, holistic X-ray of your entire ecosystem.

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1. Running anchors doctor

# Run standard health diagnosis
anchors doctor

# Run with verbose diagnostic breakdown
anchors doctor --verbose

What doctor Detects:

1. Orphaned Artifacts: Specs without implementation code, or test files that verify deleted rules.
2. Identity Code Collisions: Duplicated codes like AUTH-B01 declared in two separate files.
3. Architectural Drift: Discrepancies between declared layer boundaries in anchors.yaml and real-world imports.
4. Coverage Voids: Governed layers that have fallen below required maturity levels.

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2. File Audit with anchors audit

When a specific file or module fails multiple checks, use audit to generate an actionable punch list:

anchors audit src/services/billing/invoice.spec.md

This outputs a unified dossier of every missing scenario, failed assertion, stale dependency, and layer violation associated with that unit.