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Netbeans and Eclipse doesn't show modal window and locks itself on MAC

I have downloaded Netbeans 8.1 on OSX and when I try to install Darcula theme it is not possible. I press install and the way IDE responds is like situation when user dialogue pops out which locks the application until user acts upon the dialogue. However this dialogue is not visible! The way I know it is there is because when I press ESC button, IDE is responsive back again.
The same happens when I go to preferences and click "Import" button. Application locks itself but I don't see any dialogue that I can do something about.
This happens also on Eclipse. As you can see in a picture below after I clicked "Add libraries", tab "Libraries" turned from blue to gray because some unvisible window has opened and rest of IDE is unresponsive until I press "ESC"(which usually closes the modal window).
EDIT:
I just found out that this happens when IDE is maximized. So I would like to know if I can fix it somehow that I don't have to un-maximize IDE everytime editor shows me some dialog.

For Eclipse this has been reported as bug 478975 but as yet there is no fix.

Disable showing of run window in IntelliJ

In IntelliJ every time I make a change in code and I run the app afterwards, "run window" is automatically popped up. Is there any way to disable this annoying behaviour or how to make it less distracting?

I finally could solve this one. At least it worked for me. At the bottom of "Run/Debug configurations" window and in "Before launch" part, uncheck "Activate tool window" check box.

There is currently no solution to do this permanently. However, there is a workaround to prevent it from popping up. Try this:
After the first time the window pops-up simply resize it all the way to the bottom (i.e. grab the TOP and drag down until the window disappears). This will prevent it from popping up again until you manually click one of the buttons to open any window in the same area (i.e. Run, TODO, Android, Terminal, Messages, (and Find Results) - or whatever you have in that same area if you've customized it).
To keep it from popping up, never click the hide button on any of these windows but rather use the same "drag from top to bottom" to hide them (the effect is the same).
This is annoying, to say the least, but once you get used to it it works fine and is much less annoying than dealing with that blasted Run popup window :)
NOTE
I should mention that this is completely safe to do as the windows are only hidden when you do this, and clicking the window's button at the bottom will show it in its original size - so nothing goes missing or breaks using this method :-)

These are called Tool Windows. Right-click the tool window, it pops up a menu, the last option of which is 'Hide'.
Alternatively,
You can install the plugin ToolWindow Manager to show/hide the Tool Window of your choice.

Either
1. Set the run window to be in either split and then shrink it down to be as small as possible.
2. Set the windows to be in floating mode and then shrink it down and move it somewhere less distracting.

disabling checkboxes in "Window | Background tasks solved my problem.

It is soooo annoying oO I just dragged the windows to an other screen and/or set their height to a minimum.. Not "best practise" but it is better than nothing -.-

In intellij go to main menu windows->active tool window->disable floating mode option there.
thanks

For those who are facing this issue with "Run" window they can follow below instruction
From dropdown select "Edit Configuration":
Open Logs tab:
Uncheck these 2 checkboxes:

I have found a solution!!!!
There old plugin for Intellij IDE called "Hide Tool Window Ex".
It hides any tool windows that being opened just after you click in editor again.
(plugin page)
visual example

Eclipse is running as applet not application. How do i go back?

I'm not exactly sure what i changed, but my project is running as an applet and not an application anymore so therefore its trash. How do i go back to application? You'd think there would be something on the internet for this..

when you right click to do "Run as ..." you should also see "Run Configurations" - click on this. On the left side you will see Applets, delete what is below this.

Java Perspective in Eclipse

Whenever I open Java perspective in Eclipse, it appears like the image.
Java EE perspective is totally fine.
Has anyone had the same problem and fixed it?

Try to reset your perspective. With the Java perspective already selected go to
Window > Reset Perspective...

Eclipse android project always lauching in debug

I feel silly asking this and even more silly to have this problem. I have a android project that has been executing fine until now.
but a couple of days ago, without me doing anything particular that I know of, my project has been always launching itself in debug no matter what I try (clicking on the debug or run gives me the same result). I try looking in the project settings and the build configuration but can't see anything justifying this.
so right now each time I launch the app I have to go to go to debug tab and click on disconnect...
Any ideas

Restart the device
I was experiencing the same problem where my app was always being run in debug mode. Restarting the device did the trick for me.

Have you checked your run configurations menu? You might have some extraneous configurations in there that Eclipse is defaulting to when you choose to launch the project.
Failing that, there is an option called "Launch in debug mode whenever the workspace contains breakpoints" in the Run/Debug -> Launching preference page. You might want to check to make sure that this option is not enabled.
As a last resort when facing these kinds of quirks I will sometimes create a new project and copy over my source files (provided the project is not very large). Closing and re-launching Eclipse sometimes works wonders for me as well.

As said above, the problem is with the device not eclipse.
Restarting the device will work, but also killing the application thread/process in the DDMS will do the same job.

On the emulator, go to App Drawer, launch application "Dev Tools". Inside there, pick "Development Settings". Make sure that the field "Debug App" has value "(none)".

Ok, I know I am a bit late with this one but I found a solution. It might be not acceptable for someone, but than again, it solved the problem.
I just reset my phone to factory settings. After that I was able to install the app without getting "waiting debugger to attach" message always.

I ran into the same problem these days, but none of the solutions above worked for me(except for factory reset, don't wanna do that for now).
As Kennifer stated, problem is with the device since this happens only on my Zync Z5 phone (I have several other devices with Android on which app start in Run mode, not Debug mode).
The only trick that worked for me was to delete the launch configuration every time wanted to run app after a debug, but it's annoying to do this every time I need a debug.

I'd tried everything on here and was surprised by the overwhelming acceptance of the top answer
Restart the device
then I realised, "this is a development phone, stop treating it like a business's server", and proceeded to restart.
Worth risking an answer to endorse this solution as a last resort.
My outcome- the app quickly, but quietly died. Result ! :(

My Eclipse version:
Luna.
My case:
The option Launch in debug mode when workspace contains breakpoints is Never, but eclipse launches in debug mode.
My Solution:
Go to Window->Preferences->Run/Debug->Launching.
Mark Prompt in option Launch in debug mode when workspace contains breakpoints.
Launch.
A dialog will popup: There are breakpoints enabled in the workspace. Would you rather launch in debug mode?
Check Remember my decision, then press No button,
and problem resolved.