The system is heavily modified by third-party software. Each such configuration is unique and unpredictable. I can only guess which of the many modifications may be contributing to the problem. As a start toward solving it, I suggest the following steps.
A
If you haven't already done so, disconnect the external display and see whether there's an improvement.
B
Some of your user files (not system files) have incorrect permissions or are locked. This procedure will unlock those files and reset their ownership, permissions, and access controls to the default. If you've intentionally set special values for those attributes, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it, but you do need to follow the instructions below.
Back up all data before proceeding.
Step 1
If you have more than one user, and the one in question is not an administrator, then go to Step 2.
Enter the following command in the Terminal window in the same way as before (triple-click, copy, and paste):
sudo find ~ $TMPDIR.. -exec chflags -h nouchg,nouappnd,noschg,nosappnd {} + -exec chown -h $UID {} + -exec chmod +rw {} + -exec chmod -h -N {} + -type d -exec chmod -h +x {} + 2>&-
You'll be prompted for your login password, which won't be displayed when you type it. Type carefully and then press return. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command may take several minutes to run, depending on how many files you have. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.
Step 2 (optional)
Take this step only if you have trouble with Step 1, if you prefer not to take it, or if it doesn't solve the problem.
Start up in Recovery mode. When the OS X Utilities screen appears, select
Utilities ▹ Terminal
from the menu bar. A Terminal window will open. In that window, type this:
resetp
Press the tab key. The partial command you typed will automatically be completed to this:
resetpassword
Press return. A Reset Password window will open. You’re not going to reset a password.
Select your startup volume ("Macintosh HD," unless you gave it a different name) if not already selected.
Select your username from the menu labeled Select the user account if not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select
▹ Restart
from the menu bar.
C
Back up all data.
Run the following command in the same way as before. It moves to the Trash "semaphore" files that have not been cleaned up by the system and may be interfering with normal operation. The files are empty; they contain no data. There will be no output this time.
find L*/{Con*/*/Data/L*/,}Pref* -type f -size 0c -name *.plist.??????? -exec mv {} .Trash/ \; 2>&-
Log out or restart the computer and empty the Trash.
D
Storing many files on the Desktop may slow down the Finder, especially if the files have custom icons. Move most or all of the files to another subfolder of your home folder.
E
Back up all data before proceeding.
Launch the Font Book application and validate all fonts. You must select the fonts in order to validate them. See the built-in help and this support article for instructions. If Font Book finds any issues, resolve them.
Start up in safe mode to rebuild the font caches. Restart as usual and test.
Note: If FileVault is enabled in OS X 10.9 or earlier, or if a firmware password is set, or if the startup volume is a software RAID, you can’t start in safe mode. In that case, ask for instructions.
If you still have problems, then from the Font Book menu bar, select
File ▹ Restore Standard Fonts...
You'll be prompted to confirm, and then to enter your administrator login password.
Also note that if you deactivate or remove any built-in fonts, for instance by using a third-party font manager, the system may become unstable.
F
"CleanMyMac" is a scam and a common cause of instability and poor performance. Depending on what version you have, the developer's instructions may not completely remove it. Follow those instructions, then do as below.
Back up all data before proceeding.
Triple-click anywhere in the line below on this page to select it:
/Library/LaunchDaemons/com.macpaw.CleanMyMac2.Agent.plist
Right-click or control-click the highlighted line and select
Services ▹ Reveal in Finder (or just Reveal)
from the contextual menu.* A folder may open with an item selected. If it does, move the selected item to the Trash. You may be prompted for your administrator login password.
Repeat with this line:
/Library/PrivilegedHelperTools/com.macpaw.CleanMyMac2.Agent
Restart the computer and empty the Trash.
You may also have to remove these items in the same way:
~/Library/LaunchAgents/com.macpaw.CleanMyMac.helperTool.plist
~/Library/LaunchAgents/com.macpaw.CleanMyMac.volumeWatcher.plist
Never again install "CleanMyMac" or anything like it.
*If you don't see the contextual menu item, copy the selected text to the Clipboard by pressing the key combination command-C. In the Finder, select
Go ▹ Go to Folder...
from the menu bar and paste into the box that opens by pressing command-V. You won't see what you pasted because a line break is included. Press return.
G
Remove "LiteIcon." Never install any third-party software that modifies the user interface. That's the surest way there is to end up with an unstable system.
Any third-party software that doesn't install from the App Store or by drag-and-drop into the Applications folder, and uninstall by drag-and-drop to the Trash, is a system modification.
Whenever you remove system modifications, they must be removed completely, and the only way to do that is to use the uninstallation tool, if any, provided by the developers, or to follow their instructions. If the software has been incompletely removed, you may have to re-download or even reinstall it in order to finish the job.
I never install system modifications myself, and except as stated in this comment, I don't know how to uninstall them. You'll have to do your own research to find that information.
Here are some general guidelines to get you started. Suppose you want to remove something called “BrickMyMac” (a hypothetical example.) First, consult the product's Help menu, if there is one, for instructions. Finding none there, look on the developer's website, say www.brickmymac.com. (That may not be the actual name of the site; if necessary, search the Web for the product name.) If you don’t find anything on the website or in your search, contact the developer. While you're waiting for a response, download BrickMyMac.dmg and open it. There may be an application in there such as “Uninstall BrickMyMac.” If not, open “BrickMyMac.pkg” and look for an Uninstall button. The uninstaller might also be accessed by clicking the Customize button, if there is one.
Back up all data before making any changes.
You will generally have to restart the computer in order to complete an uninstallation. Until you do that, there may be no effect, or unpredictable effects.
If you can’t remove software in any other way, you’ll have to erase and install OS X. Never install any third-party software unless you're sure you know how to uninstall it; otherwise you may create problems that are very hard to solve.
Trying to remove complex system modifications by hunting for files by name often will not work and may make the problem worse. The same goes for "utilities" such as "AppCleaner" and the like that purport to remove software.
H
"CleanMyMac" and "LiteIcon" may have damaged the system after reinstallation. If you still have the problem, reinstall again after removing them.
I
"Soundflower" is obsolete and should be either updated or removed.
J
If a graphics tablet (Wacom or similar) is connected, or has been connected in the past, there will be a preference pane named Ink in System Preferences. Open it and disable the feature.
K
This procedure will erase all your settings in the Network preference pane. Back up all data before you begin, and recreate the settings afterwards.
Triple-click the line below on this page to select it:
/Library/Preferences/SystemConfiguration
Right-click or control-click the highlighted line and select
Services ▹ Reveal
from the contextual menu.* A folder should open with an item named "SystemConfiguration" selected. Move the selected item to the Trash. You may be prompted for your administrator password.
Restart the computer and empty the Trash.
*If you don't see the contextual menu item, copy the selected text to the Clipboard by pressing the key combination command-C. In the Finder, select
Go ▹ Go to Folder...
from the menu bar and paste into the box that opens by pressing command-V. You won't see what you pasted because a line break is included. Press return.
