Productivity is all about tools. Having the right tools for the job always saves times; and the right tools for cross-platform (Windows-to-Linux) development are built on secure transfer technologies like SSH, SCP and SFTP.
If you develop on a Windows platform and deploy on a Linux platform (one of the industry's most widely used development scenarios), then you need a convenient, reliable, safe way to update files across the great divide. One popular tool for doing this is WinSCP, a dual-paned window that allows you to easily navigate the file hierarchy of your local Windows computer and your remote Linux computer at the same time.
The perfect complement to WinSCP is PuTTY, the terminal emulator that lets you use Windows to run a command shell on your Linux box, opening a direct channel to all the Linux command line tools.
If you use Eclipse as your development workbench, the functionality of WinSCP can largely be replaced with the Remote System Explorer (RSE) plugin. This plugin gives you the familiar hierarchical display of your Linux filesystem plus a limited set of context-menu operations for renaming, deleting, and setting permissions.
The best part of RSE though is the seamless way you can edit and save your code base: double-clicking a filename opens the remote file in your local workbench editor, while issuing the "save" command quietly transfers yours changes back to the Linux computer. It's seamless enough that you can almost forget that you're working on remotely hosted files. Plus, Eclipse is a whole workbench and has much more to offer than just RSE.