greg263 wrote:
...green button forces your dock out of sight, favourites disappear . The whole green button is a massive source of frustration for me as it removes things I need from my screen.
Clicking the green full-screen button expands Safari's window to full-screen mode to focus on the user content. You can also enter full-screen mode by pressing the Command-Control-F keys. The menu bar and Dock are automatically hidden by default. The menu bar is available and will reappear when the cursor is moved to the top of the screen, and the Dock will reappear when it is moved to the bottom.
Since the tab bar can't be hidden when a window has multiple tabs, take advantage of full-screen mode by opening content in its own window. By the same reasoning, hide the Favorites bar by pressing the Command-Shift-B keys, or selecting View > Hide Favorites Bar from Safari's menu bar. Use the same key combination or menu selection to show it again.
Be aware that if you hide Safari's toolbar prior to entering full-screen mode, selected by choosing View > Hide Toolbar from Safari's menu bar, it will remain unavailable until you exit to return to the standard view and select View > Show Toolbar.
If full-screen mode is inappropriate for your use case, don't use it. To maximize Safari's window to fill the visible content, click the green button while holding down the Option key. The green button will change its symbol from two opposing triangles, indicating full-screen mode is available, to a plus sign, indicating zoom mode is available. You can also zoom the window by double-clicking the window's title bar, or choosing Window > Zoom from Safari's menu bar. The keyboard shortcut is Command-Option-F.
Full-screen and zoom buttons:


While in standard view with the toolbar, Favorites bar, and Dock visible and available, you can hide them at any time with either a keyboard shortcut or by selecting the appropriate menu item. For instance, to hide or show the Dock press the Command-Option-D keys. The Dock can also be hidden by right-clicking or Option-clicking on the Dock separator and selecting "Turn Hiding On."

If you wish to change the green button's zoom behavior when holding down the Option key to click it, from the window expanding to fill the visible content to expanding to fill the usable dimensions of the Desktop (i.e. maximized), you can turn to third-party apps such as Spectacle, BetterTouchTool, or Moom. Moom has a visible control overlay that appears when hovering the cursor over the green button.
Maximize the window (Moom):

Return to previous window dimensions (Moom):

OS X Yosemite: Take apps full screen
OS X Yosemite: Window basics