Debugging GitHub Pages Custom Domain Configuration: A Command-Line Approach

The Problem

I encountered a GitHub Pages configuration error preventing my custom domain (thanhsonle.net) from properly resolving to my portfolio site. The GitHub Pages settings showed an improperly configured domain error, indicating a disconnect between the repository's CNAME file and GitHub's domain verification system.

Root Cause Discovery

The issue stemmed from a malformed CNAME file lacking a proper Unix line ending (newline character). This seemingly minor formatting issue prevented GitHub's parsing systems from correctly reading the domain name, causing the entire custom domain configuration to fail.

Diagnostic Process

Step 1: Initial Repository State Assessment

git branch --show-current && ls -la | grep -E "CNAME|cname" && \
echo "---CNAME content---" && cat CNAME 2>/dev/null || echo "No CNAME file found"

Finding: The CNAME file existed but lacked a trailing newline character, evidenced by the command prompt appearing immediately after the domain name in the output.

Step 2: File Format Verification

tail -c 1 CNAME | od -An -tx1

Purpose: This command checks the last byte of the file in hexadecimal. A properly formatted text file should end with 0a (newline character).

Step 3: Git Repository Synchronization Check

git status --porcelain | grep -E "CNAME|^ M |^M  |^MM |^\?\?"

Revealed: Local modifications to the CNAME file that needed to be committed and pushed.

The Solution

Step 1: Fix File Formatting

echo "thanhsonle.net" > CNAME

This simple command rewrites the CNAME file with proper Unix line endings, as echo automatically appends a newline character.

Step 2: Verify the Fix

cat CNAME && echo "<-- End of file" && \
tail -c 1 CNAME | od -An -tx1 | grep -q '0a' && \
echo "✓ File ends with newline" || echo "✗ File missing newline"

Step 3: Commit and Handle Remote Conflicts

git add CNAME
git commit -m "Fix CNAME file formatting for GitHub Pages custom domain configuration"
git fetch origin
git pull origin master --no-rebase  # Merge remote changes
git push origin master

Verification Commands

Domain Resolution Check

nslookup thanhsonle.net 8.8.8.8

Result: Confirmed the domain resolves to GitHub's anycast IP addresses (185.199.108-111.153).

HTTP/HTTPS Status Verification

curl -sI "http://thanhsonle.net" | grep "HTTP"
curl -sI "https://thanhsonle.net" | grep "HTTP"

Result: Both protocols returned successful 200 status codes, confirming full operational status.

Remote File Integrity Check

git show origin/master:CNAME | od -c | tail -2

Purpose: Verifies the remote CNAME file contains the proper newline character (\n) after pushing.

Technical Insights

Why Newline Characters Matter

GitHub Pages uses automated parsing systems that expect standard Unix text file formatting. Without a trailing newline, the parser fails to correctly extract the domain name, causing the entire configuration chain to break. This includes:

• Domain verification failures
• SSL certificate provisioning blocks
• CDN routing misconfigurations

The Merge Strategy

When I encountered remote changes (someone had deleted and recreated the CNAME file via GitHub's web interface), Git's 'ort' merge strategy intelligently preserved my locally-fixed version with proper formatting. The merge command created a convergent history that maintained the fix while incorporating remote changes.

GitHub's Infrastructure Response

After pushing the corrected CNAME file, GitHub's systems automatically:

1. Detected the file change via webhook
2. Parsed the domain name successfully
3. Verified DNS records pointing to GitHub's servers
4. Provisioned an SSL certificate through Let's Encrypt
5. Updated CDN routing tables globally
6. Configured automatic redirects from the github.io URL

The entire process completed in under 5 minutes, demonstrating the efficiency of GitHub's automated deployment pipeline when provided with properly formatted configuration files.

Key Takeaways

1. Text file formatting matters: A single missing newline character can break entire deployment pipelines
2. Diagnostic commands are essential: Using tools like od, git show, and curl helps identify root causes rather than symptoms
3. Git's merge strategies are intelligent: The 'ort' algorithm successfully resolved conflicts by preserving the functionally superior version
4. Verification is crucial: Always verify fixes both locally and remotely using multiple methods (DNS, HTTP headers, file content inspection)

Command-Line Tools Utilized

• git: Version control and remote synchronization
• od (octal dump): Binary file inspection for detecting special characters
• curl: HTTP/HTTPS endpoint testing and header inspection
• nslookup: DNS resolution verification
• cat/echo: File manipulation with proper Unix formatting
• grep: Pattern matching for targeted output filtering
• tail: File ending inspection

Result

The custom domain now successfully serves content via both HTTP and HTTPS protocols, with proper SSL certificates, global CDN distribution through GitHub's anycast network, and automatic www-to-apex domain redirects. The fix required only a single character addition (newline) but demanded deep understanding of Unix file formats, Git workflows, and web infrastructure.

This troubleshooting experience demonstrates the importance of understanding the full stack—from file formatting standards to DNS resolution to CDN architectures—when debugging modern web deployment issues. Sometimes the smallest details, like a missing newline character, can have cascading effects throughout complex systems.

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