When troubleshooting .bashrc loading issues in Cygwin, it's crucial to understand how bash processes startup files. Unlike standard Linux environments, Cygwin has some unique behaviors:

# The correct loading order in Cygwin:
1. /etc/profile
2. ~/.bash_profile
3. ~/.bashrc (only if invoked by .bash_profile)

These are the most frequent causes I've encountered in Cygwin environments:

• Missing .bash_profile: Cygwin often doesn't create this by default
• Incorrect file permissions: Cygwin respects Windows permissions differently
• Path case sensitivity: Windows filesystem can cause issues with ~/.bashrc vs ~/.BASHRC

Here's how to properly set up your environment, including the SSH alias you mentioned:

# First, ensure .bash_profile exists and sources .bashrc
if [ ! -f ~/.bash_profile ]; then
    echo "if [ -f ~/.bashrc ]; then" >> ~/.bash_profile
    echo "    . ~/.bashrc" >> ~/.bash_profile
    echo "fi" >> ~/.bash_profile
fi

# Then verify your .bashrc content
cat > ~/.bashrc << 'EOF'
# SSH alias example with proper quoting
alias name@server="ssh server sname"

# Debug output (remove after testing)
echo "DEBUG: .bashrc successfully loaded"
EOF

If the basic solution doesn't work, try these diagnostic steps:

# Check which files are being sourced
echo "Testing bash startup sequence..."
env -i bash --noprofile --norc -l -x

# Verify file permissions
ls -la ~/ | grep -E 'bashrc|bash_profile'

# Alternative loading method
exec bash --login

Pay special attention to these Cygwin quirks:

• Path conversions between Windows and Unix formats
• Line ending differences (CRLF vs LF)
• Antivirus software interference with profile loading

For your specific SSH alias case, consider this more robust version:

# Improved SSH alias with error handling
alias name@server="ssh -t server 'sname || echo \"Command failed with status $?\"'"

# Alternative using a function for more complex logic
name@server() {
    local status
    ssh -t server "sname"
    status=$?
    [ $status -ne 0 ] && echo "SSH command failed (status: $status)" >&2
    return $status
}

After making changes, verify everything works:

# Start a fresh Cygwin session
exit
# Reopen terminal

# Check if alias exists
type name@server

# Test the alias
name@server

When working with Cygwin on Windows, you might encounter situations where your carefully crafted .bashrc aliases don't execute as expected:

# Example problematic .bashrc content
alias name@server="ssh server sname"
echo "bashrc read"  # Debug statement

Cygwin has specific rules about which startup files it reads:

• ~/.bash_profile: Executed for login shells
• ~/.bashrc: Executed for non-login interactive shells
• ~/.profile: Alternative for login shells

Cygwin often starts as a login shell by default, which means it reads .bash_profile but not .bashrc. Here's how to verify:

# Check if current shell is login shell
echo $0
# If it starts with '-', it's a login shell

Option 1: Source .bashrc from .bash_profile

# Add to ~/.bash_profile
if [ -f ~/.bashrc ]; then
    . ~/.bashrc
fi

Option 2: Force non-login shell behavior

# Modify Cygwin shortcut to use:
bash --norc
# Or alternatively:
bash --rcfile ~/.bashrc

Option 3: Proper Alias Implementation

# Consider this more robust alias format:
alias sshserver='ssh -t server "sname"'
# The -t flag forces pseudo-terminal allocation

Add these debug statements to identify the issue:

# In .bash_profile
echo "bash_profile executed" >> ~/bash_debug.log

# In .bashrc 
echo "bashrc executed at $(date)" >> ~/bash_debug.log

For complex environments, consider this hybrid approach:

# ~/.bash_profile
case $- in
    *i*) . ~/.bashrc ;;
esac

# ~/.bashrc
export PATH="/usr/local/bin:$PATH"
alias ll='ls -alF'

Watch for these common Cygwin pitfalls:

• File permissions (run chmod +x ~/.bashrc)
• Line endings (use dos2unix if edited in Windows)
• Antivirus interference with config files