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Shell Aliases

Atomic runs bash in non-interactive mode (bash -c), which doesn’t expand aliases by default. To enable your shell aliases, add to ~/.atomic/agent/settings.json (legacy ~/.pi/agent/settings.json is also read): 
{
  "shellCommandPrefix": "shopt -s expand_aliases\neval \"$(grep '^alias ' ~/.zshrc)\""
}
Adjust the path (~/.zshrc, ~/.bashrc, etc.) to match your shell config.