setup-check

Setup Check

Audit Claude Code configuration and report issues, overlaps, update status, and cleanup recommendations.

Arguments

Parse from $ARGUMENTS. Default: all.

Arg	Scope
`all`	Full audit (all categories below, including updates)
`updates`	Claude Code CLI + plugin version/update checks
`skills`	Skills: duplicates, broken symlinks, unused, placeholders
`hooks`	Hooks: conflicts, broken paths, event collisions
`plugins`	Plugins: disabled, stale cache, version tracking
`rules`	Rules: contradictions, overlap with plugin behavior
`settings`	Settings files: duplicates, conflicting keys (health only)
`security`	Security: broad permissions, skipped prompts, orphaned MCP perms
`mcp`	MCP servers: empty configs, duplicate servers
`memory`	Memory: empty dirs, stale entries, index mismatches
`overlaps`	Cross-category overlap detection only

Multiple args supported: /setup-check skills plugins runs both.

Goal Message

In addition to category args, the user can pass a quoted free-text string as a goal message:

/setup-check "ready for production?" /setup-check settings "security hardening"

If an argument is not a recognized category keyword, treat it as a goal message. The goal triggers an additional Goal Assessment section in the output (see below).

Scan Paths (MANDATORY)

You MUST read ALL of these paths for the relevant category. Do not skip any. Missing a path means missing findings.

Updates:

Claude Code CLI binary (run claude --version to get current version)
npm registry (run npm view @anthropic-ai/claude-code version 2>/dev/null for latest published version; requires network)
~/.claude/plugins/installed_plugins.json (plugin versions, gitCommitSha, lastUpdated)
~/.claude/plugins/cache/ (all cached versions; detect stale ones not matching active installPath)
claude plugins update <name>@<marketplace> -s <scope> output (authoritative source for update availability; the scope flag is required and must come from each plugin's scope field in installed_plugins.json)
~/.claude/plugins/known_marketplaces.json (installed marketplaces with per-marketplace lastUpdated timestamps; used to detect which marketplaces changed after a refresh)
claude plugin marketplace list --json output (authoritative current marketplace set; read-only)
~/.claude/skills/setup-check/.last-checked.json (state file: last-briefed CLI version and dismissed config keys; created on first run if absent)

Skills:

~/.claude/skills/ (symlinks; check for broken links with ls -la)
~/.agents/skills/ (source directories; compare against symlinks for orphans)
~/.claude/plugins/cache/<marketplace>/<plugin>/<version>/skills/ and .../agents/ (plugin-provided; the nesting is marketplace/plugin/version, so glob accordingly)

Hooks:

~/.claude/plugins/cache/*/hooks/hooks.json (glob ALL versions, not just active)
Cross-reference against ~/.claude/plugins/installed_plugins.json to identify stale vs active

Plugins:

~/.claude/plugins/installed_plugins.json (installed list with versions)
~/.claude/settings.json > enabledPlugins (enabled/disabled state)
~/.claude/plugins/cache/ (all cached versions; detect stale ones)

Rules:

~/.claude/rules/*.md (read every rule file)

Settings:

~/.claude/settings.json (main; lower precedence)
~/.claude/settings.local.json (local overrides; higher precedence, wins on conflicts)

Security:

~/.claude/settings.json (check skipDangerousModePermissionPrompt, permissions)
~/.claude/settings.local.json (check permissions for broad Bash(<command>:*) patterns)
MCP server sources (for orphaned-permission detection): ~/.claude.json → mcpServers (user-scope, authoritative), project-level .mcp.json, ~/.claude/.mcp.json (if present), claude mcp list stdout (fallback)

MCP:

~/.claude.json → mcpServers key (user-scope servers; authoritative location)
~/.claude/.mcp.json (legacy/optional; often absent)
Project-level .mcp.json files in workspace directories

Memory:

~/.claude/projects/<current-project-path>/memory/ (project memory)
MEMORY.md in that directory (index file)

Checks Per Category

Updates

Execution order within this category: (0) marketplace refresh, (1) CLI version check, (2) CLI version-upgrade brief, (3) plugin version freshness, (4) stale plugin cache. Steps 0 and 2 are new. Never abort the audit on a failure in any step; degrade to an i or ⚠ finding and continue.

Marketplace refresh (mutating, runs first):
- Read ~/.claude/plugins/known_marketplaces.json and record each marketplace's lastUpdated timestamp BEFORE updating (this is the baseline for change detection).
- Run claude plugin marketplace update (no name argument updates all marketplaces). Capture stdout, stderr, and exit code.
- Re-read known_marketplaces.json AFTER and compare each marketplace's lastUpdated:
  - Timestamp advanced: ⬆ <marketplace> refreshed (pulled latest from <repo>)
  - Timestamp unchanged: ✓ <marketplace> already current
- Parse output for per-marketplace failures. Each failure: ⚠ <marketplace> refresh failed (<reason>) -> Run 'claude plugin marketplace update <name>' manually
- If the whole command fails (network down, CLI error): emit a single i Marketplace refresh skipped (<reason>) and continue to the CLI version check. Do NOT abort.
- Compare timestamps rather than trusting stdout for success: the bulk update stdout format is not guaranteed stable across CLI versions; known_marketplaces.json lastUpdated is the durable record of what was actually pulled. Stdout is used only to surface failures.
Claude Code CLI version: Run claude --version to get current version. Then run npm view @anthropic-ai/claude-code version 2>/dev/null to get the latest published version. Compare the two. If npm is unavailable or network fails, report current version as i (INFO) only with message "Could not check for updates".
CLI version-upgrade config brief (interactive, only when version increased):
- Read ~/.claude/skills/setup-check/.last-checked.json. Schema: { "lastBriefedVersion": "<semver>", "lastBriefedAt": "<YYYY-MM-DD>", "dismissedKeys": ["<key>", ...] }.
- If the file is missing or unparseable: treat lastBriefedVersion as the CURRENT version, write a fresh file silently, and do NOT brief (no baseline to diff against on first run). Emit i CLI config baseline initialized at v<current> (no brief on first run).
- Compare CURRENT claude --version to lastBriefedVersion using semantic (numeric major.minor.patch) comparison, not string comparison:
  - current == lastBriefedVersion: skip the brief; emit ✓ CLI config up to date (briefed at v<x>).
  - current < lastBriefedVersion (downgrade): skip the brief; emit i CLI downgraded (v<old> -> v<current>), no new-config brief; rewrite the state file to current.
  - current > lastBriefedVersion: run the brief (continue below).
- Research: Call the gemini_search_grounded MCP tool asking which settings.json keys and environment variables were added to Claude Code between v<lastBriefedVersion> and v<current>, and for each whether it works when Claude Code runs on Amazon Bedrock. Request citations. For each returned option, record: name, type (setting or env), one-line purpose, default if known, Bedrock flag (compatible / not compatible / unknown), and source citation URL.
- Filter: Drop options already present in ~/.claude/settings.json. Drop options listed in dismissedKeys. Only genuinely-new, not-yet-declined options proceed.
- Research failure: If the Gemini call fails (no network / unavailable / error): emit i CLI upgraded v<old> -> v<new>, but config brief unavailable (Gemini/network) -> Re-run /setup-check updates when online. Do NOT advance the state file (retry next run). Continue the audit.
- No new config: If Gemini succeeds but nothing remains after filtering: emit ✓ CLI upgraded v<old> -> v<new>, no new user-facing config; advance the state file to current.
- Present the brief as an interactive block inside the Updates section (format below under Output Format > CLI Config Brief Block).
- Bedrock flag rules: ✓ compatible = sources confirm it works under Bedrock, or it is provider-neutral; ✗ not compatible = explicitly Anthropic-API-only or Vertex-only, or documented as ignored under Bedrock; ? unknown = no authoritative source either way (state this plainly, do not guess).
- Approval: Use a single AskUserQuestion multi-select listing the surfaced options; each label carries its Bedrock badge. Options flagged ✗ not compatible are shown but pre-excluded from the add list with the note "not added, incompatible with your Bedrock setup" (user can override via the "Other" path). ? unknown options are selectable with a label warning they are unverified for Bedrock.
- Write approved options: For each approved option, invoke the update-config skill to add the key to ~/.claude/settings.json with a sensible default (for an env type, add it under the env block). The update-config skill is responsible for preserving the rest of the file and writing valid JSON; if it reports a failure or the resulting file would be invalid JSON, do NOT advance the state file for that option, skip the write, and emit ⚠ Could not add "<key>" to settings.json (<reason>) -> Add it manually. Confirm each successful write: ✓ Added "<key>" to settings.json (<value>).
- Record declines: Append each declined option to dismissedKeys in the state file.
- Advance state: Set lastBriefedVersion to current and lastBriefedAt to today ONLY after the add/decline pass completes. If the user aborts mid-brief, do NOT advance (the brief reappears next run, no silent loss).
Plugin version freshness: For each plugin in installed_plugins.json:
- If version is "unknown", flag as ⚠ (WARN) with recommendation to reinstall for version tracking
- Read the plugin's scope field (values: user, project, local, managed) from its entry in installed_plugins.json. claude plugins update defaults to -s user, so the scope flag MUST be passed explicitly for non-user scopes or the command will fail with "Plugin X is not installed at scope user".
- Run claude plugins update <name>@<marketplace> -s <scope> for each plugin (the plugin key in installed_plugins.json is already in name@marketplace format). Parse the output:
  - If output contains "already at the latest version", mark as ✓ with current version
  - If output indicates an update was applied (version changed), mark as ⬆ with old and new versions
  - If the command fails with "not installed at scope ", retry once with -s project, then -s user as fallbacks before giving up
  - If the command fails for any other reason, fall back to checking lastUpdated: flag plugins not updated in 30+ days as i (INFO, "not updated in N days, possibly stale")
- Important: Do NOT compare gitCommitSha against the marketplace repo HEAD. Marketplace repos contain multiple plugins, so repo HEAD advances when any plugin changes, causing false positives for unrelated plugins.
- Show one finding per plugin, using the full name@marketplace identifier so users can copy-paste directly into commands
Stale plugin cache: Detect version directories in ~/.claude/plugins/cache/<marketplace>/<plugin>/ where more than one version directory exists. The active version is the one matching installPath in installed_plugins.json. Other directories are stale cache. Flag as ⚠ (WARN) with recommendation to clean up.

Skills

Broken symlinks: ls -la ~/.claude/skills/ and verify each target exists
Orphaned sources: Directories in ~/.agents/skills/ with no symlink in ~/.claude/skills/
Semantic duplicates: Skills with overlapping names OR overlapping descriptions (read frontmatter). Common pairs: api-docs-generator/api-documentation-generator, android-design-guidelines/mobile-android-design, kubernetes-specialist/kubernetes-best-practices
Plugin collisions: Standalone skill with same name as a plugin-provided skill (double-loaded). Also check partial overlaps: a standalone skill whose functionality is a subset of a plugin's sub-skills (e.g., standalone slack-messaging vs plugin providing slack:slack-messaging)
Placeholder skills: Skills with unfilled template content in either the description ("Replace with description") OR the body ("Insert instructions below", empty body)
Tech stack mismatch: Skills for technologies not found in any workspace project. Check ~/workspace/ for project indicators (go.mod, build.gradle, package.json, Cargo.toml, etc.). If ~/workspace/ does not exist, skip this check and note it as i

Hooks

Event collisions: Multiple hooks on the same event (e.g., two UserPromptSubmit handlers)
Broken commands: Hook commands referencing non-existent scripts
Stale hooks: Hooks from old plugin versions still in cache (compare installPath in installed_plugins.json)

Plugins

Disabled plugins: enabledPlugins: false entries (candidates for removal)
Version unknown: Plugins with "version": "unknown" (cannot track updates)
Stale cache: Old version directories in cache that are not the active installPath
Enablement mismatch: Plugin in installed_plugins.json but missing from enabledPlugins or vice versa

Rules

Contradictions: Rules that give opposing instructions (read all rule files, compare)
Plugin overlap: Rules that duplicate behavior a plugin already provides (e.g., formatting rules when a formatting plugin is installed)
Outdated references: Rules mentioning tools, commands, or patterns that no longer exist

Settings

Duplicate keys: Same key in both settings.json and settings.local.json with identical values (redundant)
Conflicting keys: Same key with different values (settings.local.json takes precedence over settings.json)

Security

Skipped prompts: skipDangerousModePermissionPrompt set to true in settings
Broad permissions: Bash(<command>:*) patterns that allow arbitrary arguments (especially python3:*, osascript:*, chmod:*, xargs:*)
Orphaned MCP permissions: MCP tool permissions (mcp__<server>__*) for servers not found in any configured source. Important: Claude Code stores user-scope MCP servers in ~/.claude.json under the mcpServers key, NOT in ~/.claude/.mcp.json (which often does not exist). Build the known-server set from multiple sources in this order: (a) mcpServers keys in ~/.claude.json, (b) mcpServers keys in any project-level .mcp.json in the current workspace, (c) mcpServers keys in ~/.claude/.mcp.json if it exists, (d) fallback: parse claude mcp list stdout (lines like ^ <name>: ... - [✓✗] ...). Flag a permission as orphaned only when <server> is absent from ALL sources.
Credential exposure: Credential files with loose filesystem permissions

MCP

Empty configs: All MCP sources empty (no mcpServers in ~/.claude.json, no project .mcp.json, no ~/.claude/.mcp.json)
Duplicate servers: Same server name configured at multiple scopes (e.g., in both ~/.claude.json and a project .mcp.json)

Memory

Empty directory: Memory dir exists but has no files
Missing index: Memory files exist but no MEMORY.md
Index mismatch: MEMORY.md references files that do not exist, or files exist but are not in the index
Stale entries: Memories referencing deleted files or very old dates

Overlaps (Cross-Category)

When running overlaps, you need data from ALL categories. Read all scan paths from every category, then run ONLY the cross-category checks below (not per-category checks like broken symlinks).

Skill vs plugin: Standalone skill duplicates plugin-provided skill or behavior (exact name match or functional subset)
Rule vs plugin/hook: Rule enforces what a plugin or hook already does
Permission vs actual tools: Permissions granted for tools/servers not actually configured
Multi-concern overlap: Multiple components (skill + plugin + rule) all addressing the same concern (e.g., Slack formatting)

Scoring note: Overlap findings are cross-category views of issues already counted in their source categories. Do NOT count overlap findings toward either score. They appear in the report for visibility but have zero weight.

Goal Assessment

This section only appears when the user provides a quoted goal message in the arguments. It is NOT a standard check category; it is generated after all other checks complete.

How it works:

All standard checks run first (whichever categories are selected)
Review all findings through the lens of the user's stated goal
Produce a filtered view: only findings relevant to the goal, plus any concerns that were not flagged by standard checks but matter for the stated goal
End with a one-line "Verdict" summarizing readiness

Output structure:

┌─ GOAL ASSESSMENT ───────────────────────────────────
│
│  Goal: "<user's quoted message>"
│
│  ✓  <relevant positive finding>
│  ⚠  <relevant warning> -> <recommendation>
│  ✗  <relevant error> -> <how to fix>
│
│  Verdict: <one-line readiness assessment>
│
└─────────────────────────────────────────────────────

Examples of how to interpret goal messages:

"ready for production?" - focus on errors, security settings, broken configs, stale versions
"security hardening" - focus on broad permissions, MCP orphaned permissions, security flags, unknown versions
"clean up unused stuff" - focus on disabled plugins, stale cache, placeholder skills, duplicates, orphans
"starting a new React project" - focus on relevant skills available, missing skills for React ecosystem, MCP servers for dev tooling

Verdict tone: Be direct and honest. Examples:

"Ready. No blockers found for your goal."
"Almost ready. Address the 2 warnings above first."
"Not ready. 3 errors must be fixed before proceeding."

Output Format

Use this exact structure. Do not wrap the report in markdown code blocks. Render all box-drawing characters directly as plain text output.

Header

╭─────────────────────────────────────────────────────
│  Claude Code Setup Check
│  YYYY-MM-DD  |  Scope: <scope>
│  Claude Code v<version>
╰─────────────────────────────────────────────────────

Replace YYYY-MM-DD with today's date, <scope> with the selected scope (e.g., "all", "skills, plugins"), and <version> with the output of claude --version.

Scores

Displayed immediately after the header, stacked on two lines:

  Health:   N.N / 10  ████████░░░░  <Label>
  Security: N.N / 10  ████████░░░░  <Label>

Health Score Calculation:

Health measures functional correctness. Only health-classified findings contribute.

Severity	Tier	Weight
ERROR (✗)	Major	-2.0
ERROR (✗)	Minor	-1.0
WARN (⚠)	Major	-0.7
WARN (⚠)	Minor	-0.3
INFO (i)	--	-0.1
OK (✓)	--	0.0
UPDATE (⬆)	--	0.0

Formula: health_score = max(0.0, min(10.0, 10.0 - sum_of_health_penalties))

Health Labels:

9.0 to 10.0: "Excellent"
7.0 to 8.9: "Healthy"
5.0 to 6.9: "Needs Attention"
0.0 to 4.9: "Critical"

Security Score Calculation:

Security measures how locked-down the permission model is. These are intentional preferences, not defects, so no ✗ ERROR is used; all findings are ⚠ WARN with recalibrated weights.

Finding	Indicator	Weight
`skipDangerousModePermissionPrompt` enabled	⚠	-1.0
Broad permission (each `Bash(<command>:*)` pattern)	⚠	-0.5
Orphaned MCP permissions (server not configured)	⚠	-0.5
Credential files with loose permissions	⚠	-0.5

Formula: security_score = max(0.0, min(10.0, 10.0 - sum_of_security_penalties))

Security Labels:

9.0 to 10.0: "Locked Down"
7.0 to 8.9: "Guarded"
5.0 to 6.9: "Relaxed"
0.0 to 4.9: "Permissive"

Progress bar (both scores): 12 characters wide. Calculate filled blocks as round(score / 10 * 12). Use █ for filled and ░ for empty.

Category Sections

Each category renders as a left-bordered section with its name and finding count in the header:

┌─ CATEGORY NAME (N findings) ────────────────────────
│
│  ✓  Finding with no issues
│  i  Informational note (details inline)
│  ⚠  Problem description (specifics) -> Recommendation
│  ✗  Broken config (specifics) -> How to fix
│
└─────────────────────────────────────────────────────

Indicators (use these exact symbols, not text tags):

✓ = OK (check passed, no issues)
⚠ = WARN (actionable recommendation)
✗ = ERROR (broken configuration, must fix)
i = INFO (informational, no action needed)
⬆ = Update available (used only in the Updates section)

Formatting rules:

One finding per line. Each finding MUST fit on a single line: indicator + description + (details) + -> recommendation. Do not wrap findings across multiple lines. Use concise language to keep lines compact.
Examples of single-line findings:
- ✓ 88 symlinks intact, no broken links
- ⚠ 3 plugins "unknown" version (frontend-design, playwright, skill-creator) -> Reinstall for version tracking
- ✗ Broken symlink: my-skill -> missing target -> Remove or recreate symlink
- ⬆ prompt-improver@severity1-marketplace updated (0.5.1 -> 0.6.0) -> Was auto-updated by check
Use parentheses for inline details rather than separate indented lines
Use -> to attach the recommendation directly on the same line
If ALL sub-checks in a category pass, show a single ✓ No issues found
Missing scan paths: show i <path> not found, skipping and continue. Do not error out.
Long findings may extend past the bottom rule width. This is expected behavior; there is no right border to align with. Do not truncate or wrap findings to match the rule length.

Severity rules (applies to health categories):

✗ (ERROR): Broken symlinks, missing scripts, corrupted configs, CLI not found
⚠ (WARN): Duplicates, overlaps, disabled plugins, stale cache, available updates, unknown versions
i (INFO): Version not checked (network unavailable), tech stack mismatch, empty memory, component not updated in 30+ days
✓ (OK): Category or sub-check passed with no issues

Severity rules (Security category):

⚠ (WARN): All security findings (broad permissions, skipped prompts, orphaned MCP perms, credential exposure)
✓ (OK): All security checks passed
No ✗ ERROR in Security; these are intentional preferences, not broken configuration

Tier classification (determines weight, see Scores section above):

Major = impacts runtime correctness. Ask: "Does this cause wrong behavior?"
Minor = housekeeping, cosmetic, or redundant. Ask: "Is this messy but harmless?"
When unsure, default to minor. Promote to major only if the finding can cause incorrect behavior.
Security findings have their own fixed weights (see Security Score Calculation) and do not use tier classification.

Health Tier Assignment Table

Use this table to classify each health finding as major or minor for health score calculation. Security findings are NOT in this table; they use the Security Score weights above.

ERROR Tier Assignments

Check	Tier
Corrupted/unparseable config files	Major
CLI not found / `claude --version` fails	Major
Broken hook commands (script doesn't exist)	Major
Broken skill symlinks	Minor
Missing scan paths for critical configs	Minor

WARN Tier Assignments

Check	Tier
Contradicting rules	Major
Conflicting settings keys (different values)	Major
Stale plugin cache (old versions in cache/)	Minor
Disabled plugins still installed	Minor
Unknown plugin versions	Minor
Semantic duplicate skills	Minor
Plugin collisions (standalone + plugin-provided)	Minor
Duplicate settings keys (identical values)	Minor
Orphaned skill sources (no symlink)	Minor
Placeholder skills	Minor
Stale hooks from old plugin versions	Minor
Event collisions (multiple hooks on same event)	Minor
Rule overlaps with plugin behavior	Minor
Empty MCP configs	Minor
Duplicate MCP servers across scopes	Minor
Memory index mismatches	Minor
Marketplace refresh failed (single marketplace)	Minor

INFO (all single-tier, -0.1)

No tier distinction. All INFO findings use the flat -0.1 weight. New Updates INFO findings: marketplace refresh skipped (whole command failed), CLI config brief unavailable (Gemini/network), CLI downgraded, CLI config baseline initialized on first run.

Zero-weight Updates findings (0.0, no penalty)

These render in the Updates section but contribute nothing to the health score, matching the existing treatment of plugin updates:

Check	Indicator
Marketplace refreshed	`⬆`
Marketplace already current	`✓`
CLI config up to date	`✓`
CLI upgraded, no new config	`✓`
Config option added to settings.json	`✓`

CLI Config Brief Block

When the CLI version-upgrade brief (Updates step 2) surfaces new options, render this interactive block inside the Updates section before continuing. It is not a scored finding line; only the resulting ✓/i outcome lines are scored.

┌─ CLI CONFIG BRIEF ──────────────────────────────────
│
│  Claude Code upgraded: v<old> -> v<new>
│  <N> new config options found. Each is flagged for Amazon Bedrock.
│
│  1. settings.json: "<key>"  [Bedrock: ✓ compatible]
│     <one-line purpose>. Default: <default>.
│     Source: <citation url>
│
│  2. env: <VAR_NAME>  [Bedrock: ✗ not compatible]
│     <one-line purpose>. (Vertex/Anthropic-API only.)
│     Source: <citation url>
│
│  3. settings.json: "<key>"  [Bedrock: ? unknown]
│     <one-line purpose>. Bedrock support not documented.
│     Source: <citation url>
│
└─────────────────────────────────────────────────────

After rendering, present the AskUserQuestion multi-select described in Updates step 2, write approved options, and emit the per-option ✓ Added ... confirmations as normal findings within the Updates section.

Section Ordering

When all is selected, render sections in this order:

Updates
Skills
Hooks
Plugins
Rules
Settings
Security
MCP
Memory
Overlaps
Goal Assessment (only if a goal message was provided)

When a single category is selected, show only that category section plus the summary.

Summary

╭─────────────────────────────────────────────────────
│  Summary
├─────────────────────────────────────────────────────
│
│  Health:   ✓ OK: N   ✗ ERROR: N major, N minor   ⚠ WARN: N major, N minor   i INFO: N
│  Security: ✓ OK: N   ⚠ WARN: N
│
│  Top Recommendations:
│
│  1. Most impactful recommendation
│  2. Second most impactful
│  3. Third
│  4. Fourth
│  5. Fifth
│
╰─────────────────────────────────────────────────────

Summary counts formatting:

Health line: show tier breakdown for ERROR and WARN: ✗ ERROR: 1 major, 2 minor
Health line: when a severity has zero findings for a tier, omit that tier: ⚠ WARN: 3 minor
Health line: when a severity has zero findings entirely, show 0: ✗ ERROR: 0
Security line: show total WARN count only (no tier breakdown): ⚠ WARN: 3
Security line: when no warnings, show: ✓ OK: all clear

Rank recommendations across both dimensions by severity (health ERROR first, then health WARN, then security WARN), and within the same severity by impact. Show up to 5 recommendations.

Execution Order

Parse arguments to determine scope. Separate category keywords from a quoted goal message (if any).
Read ALL mandatory scan paths for selected categories (use parallel tool calls where possible).
Run update checks first (if all or updates is selected) in this sub-order: (0) claude plugin marketplace update to refresh all marketplaces, comparing known_marketplaces.json lastUpdated before/after; (1) claude --version and npm view for the CLI version check; (2) the CLI version-upgrade config brief: read ~/.claude/skills/setup-check/.last-checked.json, and if the current version is higher, call gemini_search_grounded for new Bedrock-flagged settings/env options, present the brief, write approved options via the update-config skill, and advance the state file; (3) read installed_plugins.json and run claude plugins update <name>@<marketplace> -s <scope> for each plugin (scope read from the plugin's entry); (4) detect stale plugin cache.
Run checks for each remaining selected category (including the Security category).
Run overlap checks (if all or overlaps is selected).
Calculate dual scores:
- Health score: start at 10.0, classify each health finding by tier (see Health Tier Assignment Table), subtract the corresponding weight. Floor at 0.0, cap at 10.0.
- Security score: start at 10.0, subtract each security finding's fixed weight (see Security Score Calculation). Floor at 0.0, cap at 10.0.
Generate goal assessment (if a goal message was provided): review all findings against the stated goal, filter to relevant findings, write verdict.
Render the full report: header, dual score lines, category boxes (including Security), goal assessment (if any), summary.
End with the summary box containing per-dimension counts and top 3-5 recommendations sorted by impact across both dimensions.