Site Audit Pro — Sequential Wave Multi-MCP Audit

Flagship audit combining Ahrefs and GSC data across 3 sequential waves with checkpoint saves to disk. Designed to be resilient to rate-limit errors — each tool call is independent, skipped tools are logged, and the audit always completes.

LOCKED DECISION (GitHub Issue #6594): Sequential wave execution only. Do NOT parallelize tool calls. Do NOT spawn subagents. All tool calls are inline.

References

@skills/seo/references/mcp-degradation.md @skills/seo/references/ahrefs-api-reference.md @skills/seo/references/gsc-api-reference.md

Inputs

• domain

  : Bare domain to audit (required). Example:

  example.com

  . Strip

  https://

  ,

  http://

  , and trailing slashes before use.

• site

  (optional): GSC property URL to include GSC data in the audit. Example:

  https://example.com

  or

  sc-domain:example.com

  . If not provided, audit runs Ahrefs-only.

Important: API Usage Warning

Before starting execution, display this notice to the user:

API Usage Notice: This command calls approximately 10–12 Ahrefs API tools sequentially. Each call consumes API units from your Ahrefs account. You can stop after any wave if budget is a concern. Estimated time: 3 waves × 1–2 minutes each = 3–6 minutes total. Wave breakdown:

• Wave 1: Domain Authority and Backlink Health (4 tool calls)
• Wave 2: Keyword and Competitive Position (3–4 tool calls)
• Wave 3: Content and Technical Insights (3–4 tool calls)

MCP Check

Before proceeding, verify MCP availability:

Ahrefs (required):

1. Use ToolSearch with query

   +ahrefs

2. If tools returned → Ahrefs MCP available, proceed
3. If no tools returned → display the Ahrefs error template (see Error section below) and stop

GSC (optional — only relevant if

site

param was provided):

1. Use ToolSearch with query

   +google-search-console

2. If tools returned → note "GSC MCP available — will include GSC overlay in Waves 2 and 3"
3. If no tools returned AND

   site

   param was provided → note "GSC MCP unavailable — audit will use Ahrefs data only, GSC overlay skipped" and continue
4. If

   site

   param was NOT provided → skip GSC check entirely

Architecture

This command uses SEQUENTIAL wave execution with checkpoint saves between waves.

Critical design rules:

• Each tool call runs ONE AT A TIME — never in parallel
• Results from each tool are stored before proceeding to the next
• After each wave completes, all results are written to a checkpoint file on disk
• If a tool returns a rate-limit error or any error: log as

  SKIPPED: {tool-name} — {reason}

  and continue to the next tool immediately
• A failed tool call NEVER stops the wave or the audit
• The final report lists all skipped data sources so the user knows what's missing

This pattern prevents cascade failures from shared AbortController state (GitHub Issue #6594).

Execution

Step 0 — Initialize Checkpoint File

Use Bash to resolve the absolute path for the checkpoint file:

echo "$(pwd)/seo-audit-pro-checkpoint-{domain}.md"

Use the Write tool to create the initial checkpoint file at that path:

# Site Audit Pro: {domain}
**Started:** {current date and time}
**Status:** In progress
**Waves:** 0 of 3 complete

---

Tell the user: "Checkpoint file created. Starting Wave 1..."

---

Wave 1 — Domain Authority and Backlink Health

Run each tool call sequentially. For each: if success → store result. If error of any kind → log

SKIPPED: {tool-name} — {error reason}

and immediately move to the next tool. NEVER stop the wave because one tool failed.

Tool call 1a — Site Metrics: Call

mcp__claude_ai_ahrefs__site-explorer-metrics

with:

• target

  : {domain}

Returns:

organic_traffic

,

traffic_cost

(CENTS — divide by 100 for USD),

organic_keywords

,

backlinks

,

referring_domains

Store result as Wave1_Metrics. If error: log

SKIPPED: site-explorer-metrics — {reason}

Tool call 1b — Domain Rating: Call

mcp__claude_ai_ahrefs__site-explorer-domain-rating

with:

• target

  : {domain}

Returns:

domain_rating

(0–100),

ahrefs_rank

Store result as Wave1_DR. If error: log

SKIPPED: site-explorer-domain-rating — {reason}

Tool call 1c — All Backlinks (top 20): Call

mcp__claude_ai_ahrefs__site-explorer-all-backlinks

with:

• target

  : {domain}
• Limit/top results to 20

Returns: list of backlinks with source domain, anchor text, DR, link type

Store result as Wave1_Backlinks. If error: log

SKIPPED: site-explorer-all-backlinks — {reason}

Tool call 1d — Broken Backlinks: Call

mcp__claude_ai_ahrefs__site-explorer-broken-backlinks

with:

• target

  : {domain}

Returns: backlinks pointing to 404/broken pages on the domain

Store result as Wave1_BrokenLinks. If error: log

SKIPPED: site-explorer-broken-backlinks — {reason}

Wave 1 Checkpoint Save: Use the Write tool to APPEND Wave 1 results to the checkpoint file:

## Wave 1 Results — Domain Authority and Backlink Health
**Completed:** {timestamp}

### Metrics
{Wave1_Metrics data or "SKIPPED: {reason}"}

### Domain Rating
{Wave1_DR data or "SKIPPED: {reason}"}

### Top Backlinks (up to 20)
{Wave1_Backlinks data or "SKIPPED: {reason}"}

### Broken Backlinks
{Wave1_BrokenLinks data or "SKIPPED: {reason}"}

---

Tell the user: "Wave 1 complete (Domain Authority & Backlinks). Checkpoint saved. Starting Wave 2..."

---

Wave 2 — Keyword and Competitive Position

Tool call 2a — Organic Keywords (top 20): Call

mcp__claude_ai_ahrefs__site-explorer-organic-keywords

with:

• target

  : {domain}
• Limit to top 20 results

Returns: list of keywords with position, volume, traffic, difficulty

Store result as Wave2_Keywords. If error: log

SKIPPED: site-explorer-organic-keywords — {reason}

Tool call 2b — Organic Competitors: Call

mcp__claude_ai_ahrefs__site-explorer-organic-competitors

with:

• target

  : {domain}

Returns: list of competing domains with overlap score, common keywords, their traffic

Store result as Wave2_Competitors. If error: log

SKIPPED: site-explorer-organic-competitors — {reason}

Tool call 2c — Content Gap via Keywords Explorer: Using the top competitor identified from Wave2_Competitors (or skip if Wave2_Competitors was skipped):

First, use ToolSearch with query

keywords-explorer-matching-terms

to discover the exact parameter schema for this tool. Do NOT assume parameter names.

Then call

mcp__claude_ai_ahrefs__keywords-explorer-matching-terms

using the competitor domain as the seed to find content gap keywords.

Store result as Wave2_ContentGap. If error: log

SKIPPED: keywords-explorer-matching-terms — {reason}

Tool call 2d — GSC Query Analytics (only if

site

param provided AND GSC MCP available): If GSC is available and

site

param was given: Call the GSC

query_search_analytics

tool (use ToolSearch "+google-search-console" to find the exact tool name first) with:

• Site/property: {site}
• Row limit: 20
• Dimensions: query
• Sort by: clicks descending

Returns: top queries by clicks with impressions, CTR, average position

Note: CTR is returned as a decimal (e.g., 0.0523). Multiply by 100 for display (5.23%).

Store result as Wave2_GSC. If error or GSC unavailable: log

SKIPPED: GSC query_search_analytics — {reason}

Wave 2 Checkpoint Save: Use the Write tool to APPEND Wave 2 results to the checkpoint file:

## Wave 2 Results — Keyword and Competitive Position
**Completed:** {timestamp}

### Organic Keywords (top 20)
{Wave2_Keywords data or "SKIPPED: {reason}"}

### Organic Competitors
{Wave2_Competitors data or "SKIPPED: {reason}"}

### Content Gap (keywords competitor ranks for, you don't)
{Wave2_ContentGap data or "SKIPPED: {reason}"}

### GSC Query Analytics (top queries by clicks)
{Wave2_GSC data or "SKIPPED: not requested or GSC unavailable"}

---

Tell the user: "Wave 2 complete (Keywords & Competition). Checkpoint saved. Starting Wave 3..."

---

Wave 3 — Content and Technical Insights

Tool call 3a — GSC Opportunities (only if GSC available): If GSC MCP is available and

site

param was provided: Use ToolSearch to find the GSC search analytics tool. Call it with:

• Site/property: {site}
• Filter: high impressions (e.g., > 1000), low CTR (e.g., < 0.05)
• Row limit: 20

This identifies pages/queries with visibility but poor click-through rate.

Store result as Wave3_GSC_Opportunities. If error or GSC unavailable: log

SKIPPED: GSC opportunities — {reason}

Tool call 3b — GSC Traffic Drops (only if GSC available): If GSC MCP is available and

site

param was provided: Call GSC search analytics comparing last 28 days vs previous 28 days:

• Site/property: {site}
• Date range: last 28 days vs prior 28 days
• Sort by: click decline

Store result as Wave3_GSC_Drops. If error or GSC unavailable: log

SKIPPED: GSC drops — {reason}

Tool call 3c — Top Pages (top 10): Call

mcp__claude_ai_ahrefs__site-explorer-top-pages

with:

• target

  : {domain}
• Limit to top 10

Returns: top organic pages by estimated traffic

Store result as Wave3_TopPages. If error: log

SKIPPED: site-explorer-top-pages — {reason}

Tool call 3d — Anchor Text: Call

mcp__claude_ai_ahrefs__site-explorer-anchors

with:

• target

  : {domain}

Returns: anchor text distribution with count and percentage

Store result as Wave3_Anchors. If error: log

SKIPPED: site-explorer-anchors — {reason}

Wave 3 Checkpoint Save: Use the Write tool to APPEND Wave 3 results to the checkpoint file:

## Wave 3 Results — Content and Technical Insights
**Completed:** {timestamp}
**Status:** All waves complete

### GSC Opportunities (high impressions, low CTR)
{Wave3_GSC_Opportunities data or "SKIPPED: not requested or GSC unavailable"}

### GSC Traffic Drops (last 28 days)
{Wave3_GSC_Drops data or "SKIPPED: not requested or GSC unavailable"}

### Top Pages (by organic traffic)
{Wave3_TopPages data or "SKIPPED: {reason}"}

### Anchor Text Distribution
{Wave3_Anchors data or "SKIPPED: {reason}"}

---

Tell the user: "Wave 3 complete (Content & Technical). All waves done. Generating final report..."

---

Step Final — Cross-MCP Synthesis and Final Report

Read back all stored wave data. Generate the comprehensive audit report below. Print the full report to the terminal.

CRITICAL monetary conversion: All Ahrefs fields ending in

_cost

,

_value

, or

cpc

are in CENTS. Divide by 100 before display. Format as USD with commas. Example:

traffic_cost = 125000

→ display as

$1,250

CTR conversion: GSC CTR values are decimals. Multiply by 100 for display. Example:

ctr = 0.0523

→ display as

5.23%

---

# Site Audit Pro: {domain}
**Date:** {current date}
**Waves completed:** 3 of 3
**Data sources:** Ahrefs{, Google Search Console (via {site})}
**Checkpoint file:** {absolute path to checkpoint file}

---

## Executive Summary

{AI-generated 3–5 sentence analysis of the domain's overall SEO health based
on all collected data. Synthesize DR, traffic, keyword position, content gaps,
and GSC performance into a coherent narrative. Be specific — use actual numbers
from the data.}

---

## Domain Authority Profile

| Metric | Value |
|--------|-------|
| Domain Rating | {domain_rating}/100 |
| Ahrefs Rank | #{ahrefs_rank} |
| Total Backlinks | {backlinks} |
| Referring Domains | {referring_domains} |
| Organic Keywords | {organic_keywords} |
| Est. Monthly Traffic | {organic_traffic} visits |
| Traffic Value | ${traffic_cost / 100}/mo |

{If any metrics were SKIPPED, note which ones and why.}

---

## Backlink Health

### Top Backlinks (up to 20)
{Table with source URL, anchor text, DR, link type from Wave1_Backlinks}
{Or: "Data unavailable — site-explorer-all-backlinks was skipped ({reason})"}

### Broken Backlinks (Reclamation Opportunities)
{List of backlinks pointing to broken pages, with source domain and target URL}
{Or: "Data unavailable — site-explorer-broken-backlinks was skipped ({reason})"}
{If broken links exist: "**Action:** Redirect or restore these {N} broken pages to reclaim link equity."}

---

## Keyword Portfolio

### Top Organic Keywords (by traffic)
{Table: keyword | position | volume | est. traffic from Wave2_Keywords}
{Or: "Data unavailable — site-explorer-organic-keywords was skipped ({reason})"}

### Organic Competitors
{Table: competitor domain | overlap score | common keywords | their organic traffic}
{Or: "Data unavailable — site-explorer-organic-competitors was skipped ({reason})"}

---

## Content Gaps

Keywords top competitors rank for that {domain} does not currently rank for:

{Table or list from Wave2_ContentGap}
{Or: "Data unavailable — keywords-explorer-matching-terms was skipped ({reason})"}

{If data available: Highlight top 5 highest-value gap keywords with estimated volume.}

---

## GSC Performance

{ONLY include this section if Wave2_GSC or Wave3_GSC_Opportunities or Wave3_GSC_Drops has data.
If no GSC data was collected, replace this entire section with:
"*GSC data not included — either no `site` parameter was provided or GSC MCP was unavailable.*"}

### Top Queries (by clicks)
{Table: query | clicks | impressions | CTR (×100%) | avg position from Wave2_GSC}

### Click-Through Opportunities
{Queries/pages with high impressions but low CTR from Wave3_GSC_Opportunities}
{Include suggested action: "Improve title/meta description for better CTR"}

### Traffic Drops (last 28 days)
{Pages or queries showing declining clicks from Wave3_GSC_Drops}

---

## Top Pages Analysis

{Table: page URL | est. organic traffic | top keyword from Wave3_TopPages}
{Or: "Data unavailable — site-explorer-top-pages was skipped ({reason})"}

{If data available: Note which pages drive disproportionate traffic and any concentration risk.}

---

## Anchor Text Profile

{Summary of anchor text distribution: branded vs. exact-match vs. generic vs. naked URLs}
{Raw data from Wave3_Anchors}
{Thresholds: branded >40% = healthy; exact-match >10% = over-optimized risk; generic >30% = low-quality signal}
{Or: "Data unavailable — site-explorer-anchors was skipped ({reason})"}

---

## Cross-MCP Insights

{ONLY include this section when BOTH Ahrefs AND GSC data are present in the report.
If only one data source was available, omit this section entirely.}

{Generate 3–5 specific insights that REQUIRE both data sources to identify. Examples:}

- "You rank #{GSC_position} for '{GSC_keyword}' per GSC but Ahrefs shows {N} competitors
  with DR {X}+ points higher — this is a priority opportunity where improving content
  quality could yield significant ranking gains"
- "GSC shows traffic declining for {page} but Ahrefs shows {N} new backlinks this month
  — possible algorithm volatility, not link loss. Monitor for 2 more weeks before acting."
- "Top organic keyword per GSC has {clicks} clicks but Ahrefs estimates {traffic} monthly
  traffic for this keyword — gap suggests click-through rate optimization opportunity"
- "Content gap keyword '{keyword}' (competitor ranks #{position}) correlates with GSC
  impressions for related term '{related}' — you have some visibility; targeted content
  could convert impressions to rankings"

{Each insight should be actionable and specific to the actual data collected.}

---

## Skipped Data Sources

{If ALL tools completed successfully: "None — all data sources returned successfully."}

{If any tools were skipped:}

| Tool | Reason Skipped |
|------|---------------|
| {tool-name} | {error reason — rate limit / error / not requested} |

*Skipped tools mean those report sections are incomplete. Re-run the audit when
API limits reset, or use individual `/seo ahrefs {command}` commands for specific data.*

---

## Prioritized Recommendations

Based on all available data, here are the top action items:

**Critical (address immediately):**
1. {Recommendation based on actual findings}

**High Priority (this week):**
2. {Recommendation}
3. {Recommendation}

**Medium Priority (this month):**
4. {Recommendation}
5. {Recommendation}

**Monitoring:**
- {Ongoing items to watch}

---

*Full data checkpoint saved to: {absolute path to checkpoint file}*
*Re-run this audit monthly to track progress.*

---

Output Format

The full report is printed to the terminal. The checkpoint file remains on disk at the path shown in the report header. Unlike

seo-report

, this command does NOT save the final report to a file — the checkpoint file is the on-disk artifact.

---

Error — Ahrefs MCP Not Available

If the Ahrefs MCP check fails, display this message and stop:

## Ahrefs MCP Not Available

The `/seo site-audit-pro` command requires the Ahrefs MCP, which is not
currently connected.

**What you can do:**
- Use `/seo audit <url>` for a full static SEO analysis without live Ahrefs data
- Use `/seo ahrefs overview <domain>` once Ahrefs is connected for a quick domain check

**To connect Ahrefs MCP:**
- Ensure the Ahrefs MCP is registered at user scope in ~/.claude/mcp.json
- Verify with: cat ~/.claude/mcp.json | grep -i ahrefs
- Ahrefs MCP must be registered at user scope (not project scope) to work in subagents

Error — GSC Unavailable (Non-Fatal)

If GSC MCP is unavailable but

site

param was provided:

**Note:** GSC MCP is not available. The audit will proceed using Ahrefs data only.
GSC-dependent sections (GSC Performance, Traffic Drops, CTR Opportunities) will
show "Data unavailable — GSC not connected." The Cross-MCP Insights section will
be omitted. All Ahrefs waves will run normally.

Continue execution — this is NOT a stop condition.