How can a PHP developer troubleshoot and resolve file permission issues when accessing a Linux server from a Windows machine using tools like Putty?

File permission issues can be resolved by checking and adjusting the permissions of the files or directories in question. This can be done using the "chmod" command in the Linux terminal. A PHP developer can use Putty to access the Linux server and run the necessary commands to change the file permissions.

// Change file permissions using Putty
// Example: change file.php to have read, write, and execute permissions for the owner
ssh2_exec($connection, 'chmod 700 file.php');