Remove the Boot Camp partition only with Boot Camp Assistant, not with Disk Utility.
Install or Reinstall OS X from Scratch
Fix MacBook folder with question mark issue – reset the default startup disk. Difficulty level. Update your software. The first step to optimizing the inside of your Mac is to update your software. On a MacBook, all of the space on the single hard drive is assigned to one partition called MacBook Pro/Air # where the number represents the year it was distributed (e.g., MacBook Pro 13). Open your hard drive by double-clicking the MacBook Pro/Air # drive icon on your desktop (Figure 1). MacBook Pro with HDD – Drive Genius. Since you need a third-party tool to defragment a MacBook Pro, we decided to highlight Drive Genius, a well-reputed computer cleaning tool with an efficient defragging feature. Before running the defragmentation, you should make sure to create a backup of your files.
Be sure you backup your files to an external drive or second internal drive because the following procedure will remove everything from the hard drive.
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
Erase the hard drive:
1. Select Disk Utility from the main menu and click on the Continue button.
2. After DU loads select your startup volume (usually Macintosh HD) from the
left side list. Click on the Erase tab in the DU main window.
3. Set the format type to Mac OS Extended (Journaled.) Optionally, click on
the Security button and set the Zero Data option to one-pass. Click on
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the Erase button and wait until the process has completed.
4. Quit DU and return to the main menu.
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Reinstall OS X: Select Reinstall OS X and click on the Install button.
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Note: You will need an active Internet connection. I suggest using Ethernet if possible
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because it is three times faster than wireless.