Claude Health Check

Trigger

• Keywords: health check, .claude check, config audit, lint .claude, claude health, plugin sync, version drift, upgrade check, doctor

When NOT to Use

• Code review (use /codex-review-fast)
• Doc review (use /codex-review-doc)
• Security review (use /codex-security)

Scope

Argument	Description
--scope hygiene	Only run C1-C7 hygiene checks
--scope sync	Only run S1-S3 sync checks
--scope all	Run both modules (default)

Workflow

[--scope] → Select modules → Scan → Classify → Report → Fix suggestions
               │                                  │
       ┌───────┴───────┐                     P0/P1/P2
       ▼               ▼                    + fix commands
  Hygiene (C1-C7)  Sync (S1-S3)

Hygiene Module — Checks (7 items)

#	Check	Method	Criteria
1	Junk files	find .claude/ -name ".DS_Store" -o -name "*.zip" -o -name ".tmp*"	Any exists → P1
2	.gitignore exists	ls .claude/.gitignore	Missing → P1
3	.gitignore completeness	Read .claude/.gitignore, compare required items	Missing required → P2
4	Naming consistency	Scan all skills/*/ for reference vs references	Inconsistent → P2
5	README count sync	Count actual vs README description	Mismatch → P2
6	Command-Skill pairing	Each core skill should have corresponding command	Missing → P1
7	Cache size	du -sh .claude/cache/	> 50M → P2

Check 1: Junk Files

find .claude/ -name ".DS_Store" -o -name "*.zip" -o -name ".tmp*" 2>/dev/null

• Has results → P1: List files, suggest deletion
• No results → ✅

Check 2-3: .gitignore

ls .claude/.gitignore 2>/dev/null || echo "MISSING"

Missing → P1. If exists, read content and compare required items:

Required Item	Reason
.DS_Store	macOS generates continuously
settings.local.json	Personal config
cache/	Runtime cache
.tmp*	Temp files
*.tmp	Temp files (suffix variant)
*.zip	Backup archives

Missing any → P2

Check 4: Naming Consistency

# Scan all skill subdirectories
for dir in .claude/skills/*/; do
  if [ -d "${dir}reference" ]; then echo "INCONSISTENT: ${dir}reference"; fi
done

Has reference/ (singular) → P2, suggest renaming to references/

Check 5: README Count Sync

# Count actual items
ls .claude/commands/ 2>/dev/null | wc -l
ls .claude/skills/ 2>/dev/null | wc -l
ls .claude/agents/ 2>/dev/null | wc -l
ls .claude/rules/ 2>/dev/null | wc -l
ls .claude/hooks/*.sh 2>/dev/null | wc -l

Extract counts from README.md, compare. Mismatch → P2

Check 6: Command-Skill Pairing

Scan all skills/*/SKILL.md, exclude these types, then check for corresponding command:

Exclude Type	Examples	Reason
Domain KB	portfolio, aum	Referenced by other skills, no standalone entry
External	agent-browser	Not maintained by this project

Remaining skills without command → P1

Check 7: Cache Size

du -sh .claude/cache/ 2>/dev/null

• > 50M → P2, suggest cleanup
• ≤ 50M → ✅

Sync Module — Checks (S1-S3)

Only runs when --scope sync or --scope all (default).

S1: Version Check

#	Check	Method	Criteria
S1.1	Manifest exists	Read .sd0x/install-state.json	Missing → P1
S1.2	Manifest parseable	JSON.parse	Parse error → P1
S1.3	schema_version current	== 1	Mismatch → P2
S1.4	plugin_version matches	manifest vs .claude-plugin/plugin.json or package.json	Mismatch → P1
S1.5	Manifest completeness	Has rules + hook_scripts + scripts keys	Missing key → P2 (MANIFEST_GAP)

Plugin version resolution (priority order):

.claude-plugin/plugin.json → package.json → "unknown"

Plugin source location (same as /install-rules Phase 1):

Glob: ~/.claude/plugins/**/sd0x-dev-flow/rules/auto-loop.md
Glob: ${REPO_ROOT}/node_modules/sd0x-dev-flow/rules/auto-loop.md
Fallback: @rules/auto-loop.md (plugin-relative)

S2: Component Classification

For each managed component (rules, hooks, scripts), compute 3 hashes and classify:

manifest_hash  = manifest[category][filename].hash    # null if missing
local_hash     = git hash-object --no-filters <local-path>  # null if file missing
plugin_hash    = git hash-object --no-filters <plugin-path>  # source of truth

Classification table (read-only diagnostic; maps to install-rules states for delegation):

Doctor State	Condition	Severity	install-rules Equivalent
OK	local == manifest == plugin	✅	SKIP
MISSING	local_hash is null, plugin exists	P1	FRESH_INSTALL
OUTDATED	local == manifest, plugin != manifest	P1	AUTO_UPDATE
LOCAL_MODIFIED	local != manifest, plugin == manifest	✅	KEEP_LOCAL
CONFLICT	local != manifest, plugin != manifest	P2	CONFLICT
LEGACY	manifest_hash is null, local exists	P2	LEGACY
MANIFEST_GAP	manifest category key missing	P2	N/A
TOMBSTONED	manifest deleted: true, local missing	✅	SKIP_DELETED

Managed inventory (hardcoded):

Category	Local Path	Plugin Source	Files
Rules	.claude/rules/*.md	rules/*.md	auto-loop.md, codex-invocation.md, fix-all-issues.md, framework.md, testing.md, security.md, git-workflow.md, logging.md, docs-writing.md, docs-numbering.md, self-improvement.md, context-management.md
Hooks	.claude/hooks/*.sh	hooks/*.sh	pre-edit-guard.sh, post-edit-format.sh, post-skill-auto-loop.sh, post-compact-auto-loop.sh, stop-guard.sh, user-prompt-review-guard.sh
Scripts	.claude/scripts/	scripts/	precommit-runner.js, verify-runner.js, review-state.js, dep-audit.sh, commit-msg-guard.sh, pre-push-gate.sh, lib/utils.js, lib/tree-digest.js

S2.5: Override Safeguard Checks

6 checks for project override files (e.g., auto-loop-project.md):

#	Check	Severity	Detection	Recommendation
1	Override drift	P2	based_on hash comment in project file vs the hash of the base file that comment names (derived, never hard-coded — both auto-loop-project.md and testing-project.md ship) — only when the override file has active content; a scaffold with every section still commented out has no overrides to review, so drift is not reported	"Base <rule> updated since override authored; review your overrides"
2	Policy contradiction	P1	An overridden section omits a required check command that the same section of the base rule contains	"Override drops a required check command its base section carries"
3	Missing reference or base	P1	For each shipped override file (auto-loop-project.md, testing-project.md): .claude/CLAUDE.md has @rules/<file> but the file is missing, OR the file exists but is not referenced, OR the file exists but the base rule its Based on: comment names is missing from .claude/rules/	/install-rules to recreate the missing file or base, or add the reference
4	Wrong-layer edit	P2	Base auto-loop.md has LOCAL_MODIFIED, CONFLICT, or LEGACY state while project override exists	"Move customization to auto-loop-project.md"
5	Duplicate heading	P2	Override file has multiple active ## <heading> with same text	"Keep one, remove duplicates. Last occurrence takes effect."
6	Legacy precedence header	P2	Precedence declaration exists only inside an HTML comment (<!-- Precedence: present, no live Precedence: line before the first ##) — HTML comments are stripped from model context (R8), so the declaration never reaches its only reader	"Header predates the live-precedence contract; migrate the precedence line to live text by hand or regenerate via /install-rules --customize <rule> --reset. This check is read-only — it never edits the user-owned file"

Policy contradiction detection: For each ## <heading> section the override restates, extract the backticked check commands (/codex-review-fast, /codex-review-doc, /precommit) from the same-heading section of the base auto-loop.md and require the restated section to keep every one of them. A verbatim copy therefore never flags; only a restatement that drops a command its base section carries is P1. (The base's Auto-Trigger table was retired by R3 — code/doc routing now lives in the unheaded terminal-invariant paragraph, which the exact-##-heading override mechanism cannot restate, so routing itself is not overridable and is out of this check's scope.) No restated section → check passes vacuously.

Override drift detection: First check whether the project file has active content. Two forms count, and the distinction matters because the scaffold ships its ## headings live: a non-empty, non-comment body line under any heading, or a heading that carries its own value (## Plan Review: enabled, ## Git Memory: enabled — for these settings the heading is the value, so there is no body to look for). A bare scaffold heading with nothing but comments beneath it is an empty slot, not an override. The live Precedence: header is preamble material and never activation. A scaffold whose sections are all still commented out is skipped: drift means "the base changed since you wrote your overrides", and there are none, so reporting it on a fresh install is a false positive rather than a finding. Otherwise read the <!-- Based on: <base>.md @ <hash> --> comment and derive the base file from the comment's own filename — git hash-object --no-filters .claude/rules/<base>.md | cut -c1-7. The base must not be hard-coded: R8 distributes testing-project.md alongside auto-loop-project.md, so a fixed auto-loop.md comparand would check a testing override's hash against the wrong rule and report drift that does not exist. If the derived base file is missing, drift is undefined rather than zero — report it through check #3's missing base branch (P1) and do not emit a drift finding. Both checks must cover every shipped override file, not just auto-loop-project.md: an active testing-project.md whose testing.md has been deleted would otherwise fall through both. If the hashes differ, the base has been updated since the override was authored. Uses blob hash for content-level comparison; accepts legacy commit-style hashes (any 7+ hex chars) during backward-compat transition.

S3: Settings Compatibility

Check both settings.json and settings.local.json (precedence: settings.local.json > settings.json). A hook entry in either file satisfies the integrity check.

#	Check	Method	Criteria
S3.1	Legacy hook paths	Grep both settings files for bare .claude/hooks/ without $CLAUDE_PROJECT_DIR	Found → P2
S3.2	Retired guard-mode setting	Read env.STOP_GUARD_MODE (and legacy hooks_config.stop_guard_mode) from either settings file	Found in either → P2 (retired: the Stop hook is reminder-only since hook-lightweighting — the setting is dead config, recommend removing it). Absent → ✅
S3.3	Hook entry integrity	Each installed hook script has matching entry in either settings file	Missing from both → P1
S3.4	Orphan hook entries	Either settings file references script that doesn't exist on disk	Orphan → P2

Settings file precedence: settings.local.json overrides settings.json at runtime. When delegating S3 fixes, use /install-hooks --local if the issue is in settings.local.json.

Legacy path detection:

Grep for: "\.claude/hooks/[^"]+\.sh"  (without leading "$CLAUDE_PROJECT_DIR")
Applied to both: settings.json and settings.local.json

Fix Tiers

Only applies when --fix-safe or --fix is specified alongside sync scope.

Tier	Flag	Description
Report	(default)	Diagnosis only — output actionable recommendations
Safe	--fix-safe	Auto-fix P1 hygiene + safe sync fixes
Guided	--fix	Auto-fix P1 hygiene + guided sync remediation (interactive)

Category-specific safe fix delegation:

Category	MISSING	OUTDATED	CONFLICT/LEGACY
Rules	/install-rules <names>	/install-rules <names> (smart merge AUTO_UPDATE)	Skip (report only)
Hooks	/install-hooks <names>	Report only + suggest /install-hooks <names> --force	Skip (report only)
Scripts	/install-scripts <names>	Report only + suggest /install-scripts <names> --force	Skip (report only)

Why hooks/scripts OUTDATED is report-only in safe tier: /install-hooks and /install-scripts use skip/force semantics (no manifest-aware smart merge). Only /install-rules has 7-state classification for safe auto-update.

S3 settings fix delegation: All settings mutations delegate to /install-hooks (sync module never writes JSON directly).

--fix tier: Delegates all actionable states (including CONFLICT, LEGACY) to /install-* commands which handle interactive resolution.

Argument conflict: --fix and --fix-safe are mutually exclusive. If both specified, error.

Output

# .claude/ Health Check Report

## Hygiene Summary (C1-C7)

| Item | Status | Notes |
|------|--------|-------|
| Junk files | ✅/⛔ | ... |
| .gitignore | ✅/⛔ | ... |
| Naming consistency | ✅/⛔ | ... |
| README count | ✅/⛔ | ... |
| Command-Skill | ✅/⛔ | ... |
| Cache size | ✅/⛔ | ... |

## Sync Summary (S1-S3)

### S1: Version
| Check | Status | Detail |
|-------|--------|--------|
| Manifest | ✅/⛔ | Found / Missing |
| Plugin version | ✅/⛔ | 2.0.3 == 2.0.3 / 1.8.12 → 2.0.3 |
| Manifest keys | ✅/⛔ | Complete / Missing: hook_scripts, scripts |

### S2: Component Status
| File | Category | Status | Action |
|------|----------|--------|--------|
| auto-loop.md | Rules | OUTDATED | `/install-rules auto-loop` |
| security.md | Rules | OK | — |
| stop-guard.sh | Hooks | MISSING | `/install-hooks stop-guard` |
| ... | ... | ... | ... |

### S3: Settings Compatibility
| Check | Status | Detail |
|-------|--------|--------|
| Hook paths | ✅/⛔ | Modern / Legacy found |
| Retired guard mode | ✅/⚠️ | absent / STOP_GUARD_MODE found (dead config) |
| Entry integrity | ✅/⛔ | All matched / N missing |
| Orphan entries | ✅/⛔ | None / N orphans |

## Statistics

| Category | Count |
|----------|-------|
| Commands | N |
| Skills | N |
| Rules | N (installed) / N (managed) |
| Hooks | N |

## Issues

### P1
- [Issue] → [Fix recommendation / command]

### P2
- [Issue] → [Fix recommendation]

## Gate
✅ All Pass / ⛔ N issues need fixing

Verification

• Hygiene: All 7 checks executed (when scope includes hygiene)
• Sync: S1-S3 checks executed (when scope includes sync)
• Each check has clear ✅/⛔ status
• P1 issues have specific fix commands
• S2 classification covers all 23 managed files
• Fix delegation uses targeted file names (not --all)

References

• references/best-practices.md — Best practices for .claude/ directory structure

Examples

Input: /claude-health
Action: Scan hygiene (7 items) + sync (S1-S3) → Generate consolidated report

Input: /claude-health --scope sync
Action: Scan S1-S3 only → Report version drift + component status

Input: /claude-health --fix-safe
Action: Scan all → Auto-fix safe items → Delegate to /install-* → Report

Input: Is my plugin up to date?
Action: Trigger sync check → Report version + component drift