harness-doctor

name	harness-doctor
description	On-demand harness health diagnostic. Checks manifest presence, version drift, file integrity, cross-reference validity, MCP tool availability, and template variable residue. Produces a per-category graded health report.
argument-hint	[mode:report|mode:fix]

Harness Doctor

Diagnose the health of an installed autoharness harness. Produces a graded per-category health report covering manifest integrity, version drift, file completeness, cross-reference validity, MCP tool availability, and template variable residue.

When to Use

Invoke when:

• Something in the harness appears broken or out of sync
• Preparing to run tune-harness and you want a baseline health snapshot first
• After a manual edit to harness artifacts to confirm consistency
• At the start of an agent session when MCP tool availability is uncertain (pre-flight mode)

Invocation

Invoke harness-doctor [mode:report|mode:fix]

Default: mode:report

mode:report — Diagnose and report only. Never modify files. mode:fix — Apply deterministic low-risk repairs (Phase 7 describes eligible repairs). Never modify application or template source.

Subagent Depth Constraint

This is a leaf executor. No subagent spawning. Maximum depth: 0.

Variables

Variable	Purpose
.autoharness/harness-manifest.yaml	Path to the installed harness manifest (default: .autoharness/harness-manifest.yaml)
1.4.6	Expected autoharness version string from autoharness_home metadata

Workflow

Phase 1: Install Scope Detection

Determine what is installed before running any checks.

1. Check for the harness manifest at .autoharness/harness-manifest.yaml.
   • If absent: record MISSING MANIFEST — set scope-detection grade to F and skip Phases 2 and 3. Phases 4–6 proceed using directory heuristics.
2. If the manifest is present, load it and extract:
   • schema_version
   • autoharness_version (the version that performed the install)
   • installed_at timestamp
   • artifacts — the array of installed artifact objects; each has a path (workspace-relative), checksum, primitive, template, and optional artifact_type
3. Enumerate artifact directories on disk: .github/agents, .github/skills, .github/instructions, .github/prompts, .github/policies.
4. Derive the expected directory set from artifacts[*].path (extract the top-level .github/<dir> prefix from each path). Flag any derived directories absent from disk.

Phase 1 health signal:

• All declared artifact dirs present → PASS
• One or more missing → WARN (directories listed in findings)
• Manifest absent → FAIL

---

Phase 2: Version Check

Skip condition: Skip if Phase 1 found no manifest.

Compare the installed version with the current autoharness_home version.

1. Read autoharness_version from the manifest.
2. Compare against 1.4.6 (the version of the autoharness installation that would perform upgrades).
3. Classify the drift:

Condition	Signal
Versions match	PASS
Patch-level difference	WARN — minor drift, tune-harness recommended
Minor-version difference	WARN — drift, tune-harness required
Major-version difference	FAIL — breaking drift, reinstall recommended
Manifest version field absent	WARN — legacy install, version unknown

Phase 2 health signal: Highest severity condition found above.

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Phase 3: File Integrity

Skip condition: Skip if Phase 1 found no manifest.

Verify that each artifact listed in the manifest's artifacts array still exists on disk.

1. For each entry in artifacts:
   • Resolve entry.path as a workspace-relative path.
   • Check existence on disk.
2. Compute a presence rate: (found / total) * 100.

Presence Rate	Signal
100%	PASS
90–99%	WARN — some artifacts missing
75–89%	FAIL — significant artifact loss
< 75%	FAIL — critical artifact loss, reinstall recommended

Phase 3 health signal: Signal from the table above.

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Phase 4: Cross-Reference Validation

Verify that internal cross-references within harness artifacts resolve correctly.

1. Scan all Markdown files under .github/agents/, .github/skills/, and .github/instructions/.
2. For each file, extract:
   • Markdown links with relative paths (e.g., [text](../instructions/foo.md))
   • Explicit skill invocation references (e.g., Invoke skill-name)
   • Agent references (e.g., spawns sub-agent: foo.agent.md)
3. For each relative path reference, resolve it relative to the directory of the file that contains the link (not relative to the workspace root), then normalize the result to a workspace-absolute path for existence checking. Flag any normalized path that does not exist on disk.
4. For skill invocations: check that a corresponding skill directory exists under .github/skills/.
5. For agent references: check that the corresponding .agent.md file exists under .github/agents/.

Phase 4 health signal:

• Zero broken references → PASS
• 1–3 broken references → WARN
• 4+ broken references → FAIL

---

Phase 5: MCP Prerequisite Check

Verify that the MCP tools the harness declares as required are currently available.

This phase doubles as a pre-flight gate. Running harness-doctor at session start is a reliable way to confirm tool availability before agents attempt to use them.

1. Read the list of required MCP tool names from the installed harness. Sources (in order):
   • .github/instructions/ files that list tool names in their frontmatter or body
   • AGENTS.md if it enumerates required tools
   • Known harness defaults: backlogit (when backlogit capability pack is installed)
2. For each declared tool name, attempt a lightweight connectivity check:
   • Invoke a read-only operation (e.g., list or status) using the tool.
   • Record: tool name, reachable (yes/no), response latency (if measurable).
3. Classify availability:

Condition	Signal
All declared tools reachable	PASS
1 tool unreachable	WARN — degraded capability, list affected workflows
2+ tools unreachable	FAIL — agents will fall back to grep/file operations; operator action needed
No tools declared (no capability packs requiring MCP)	PASS (N/A)

4. For each unreachable tool, list the harness skills and agents that depend on it, so the operator knows which workflows are degraded.

Phase 5 health signal: Signal from the table above.

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Phase 6: Template Variable Residue

Detect unresolved double-brace placeholders (the pattern \{\{NAME\}\}) in installed harness artifacts. Their presence indicates an incomplete or failed installation.

1. Scan all files under .github/ for patterns matching \{\{[A-Z_]+\}\}.
2. Exclude known legitimate uses:
   • Files that are themselves templates (.tmpl extension) — skip entirely.
   • Variables inside fenced code blocks that serve as documentation examples only (heuristic: block is illustrative if the surrounding context is a "Variable" table or "Example" section).
3. For each match outside the exclusions: record file, line number, variable name.

Phase 6 health signal:

• Zero residue matches → PASS
• 1–5 residue matches → WARN — partial installation
• 6+ residue matches → FAIL — incomplete installation, re-run install-harness

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Phase 7: Graded Report

Compute a per-category health grade and produce the consolidated report.

Grade Computation

Each phase produces one of: PASS, WARN, FAIL, SKIP, or N/A.

Phase Signal	Grade
PASS	A
WARN	B
FAIL	F
SKIP (due to upstream failure)	— (noted as dependent on upstream phase)
N/A	— (not applicable to this workspace)

Overall harness health grade = lowest individual phase grade (F overrides B overrides A).

Report Structure

Produce the health report with these sections:

1. Summary — Overall grade, phase-by-phase grade table, diagnosis date and time, manifest path, installed version, current version.
2. Phase Results — One subsection per phase (1–6): signal, findings list (if any), and recommended action.
3. Findings List — All WARN and FAIL findings consolidated, ordered by severity (FAIL first), each with: phase, location (file:line if applicable), description, and recommended fix.
4. Repair Actions (mode:fix only) — List of repairs applied with before/after description.
5. Pre-Flight Summary — Boolean checklist for quick session readiness confirmation:
   • [ ] Manifest present
   • [ ] Version current
   • [ ] Artifacts complete
   • [ ] Cross-references valid
   • [ ] MCP tools reachable
   • [ ] No variable residue

mode:fix Eligible Repairs

In mode:fix, apply only these deterministic, low-risk repairs:

• Phase 1: Create missing artifact directories derived from artifacts[*].path if the parent path exists (empty directory creation only — never generate content).
• Phase 6: Quarantine clearly orphaned .tmpl extension files accidentally copied to .github/ by moving them to .autoharness/quarantine/ (never delete). Record the source path, destination path, and reason. Prompt the operator to review quarantined files before permanent removal.

All other findings are report-only. Source files, agent definitions, and skill content are never auto-modified by harness-doctor.

After applying repairs, re-run the affected phase to confirm the finding is resolved and update the phase grade accordingly.

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Quality Criteria

• All six phases must run (or be explicitly skipped with documented reason) before the report is complete.
• Every finding includes a specific location (file path and line number where applicable).
• The Pre-Flight Summary section is always present and reflects the final phase states.
• In mode:fix, the repair list is populated even when no repairs were applied (record "No eligible repairs found").
• The overall grade must be derivable from the phase grades — no subjective inflation.

Model Routing

This skill operates at Tier 1 (Fast/Cheap). All checks are deterministic pattern-matching and file system inspection. No complex reasoning is required.

Generated by autoharness | Template: harness-doctor/SKILL.md.tmpl