The Mutex is taken in the projectui which calls j2seproject.

It happens regularly adding library to the run classpath of a j2se project

There is not data loss I guess.

For me there was no data loss, but i can't speak for others.

This issue has already 20 duplicates 
see http://statistics.netbeans.org/exceptions/detail.do?id=144990

Build: NetBeans IDE Dev (Build 20081219090959)
VM: Java HotSpot(TM) Client VM, 11.0-b15, Java(TM) SE Runtime Environment, 1.6.0_10-b33
OS: Linux, 2.6.27-10-generic, i386

User Comments: 
trying to update library and run args for a (locally modified) project (http://hg.netbeans.org/nb-quality/file/e27f6fff8b6c/tools/nblocCounter/) in project properties

(and now loosing all unsaved changes since I'm not able to find any way to "close" build-impl was modified externaly dialog because this ex. is still poping up whatever I do ...)

Stacktrace: 
java.lang.IllegalStateException: Should not acquire Children.MUTEX while holding ProjectManager.mutex()
        at org.openide.nodes.Children$ProjectManagerDeadlockDetector.execute(Children.java:1799)
        at org.openide.util.Mutex.doWrapperAccess(Mutex.java:1320)
        at org.openide.util.Mutex.readAccess(Mutex.java:275)
        at org.openide.explorer.view.TreeView$ExplorerTree$GuardedActions.<init>(TreeView.java:2029)
        at org.openide.explorer.view.TreeView$ExplorerTree.paint(TreeView.java:1676)
        at javax.swing.JComponent.paintChildren(JComponent.java:864)

Created attachment 75202 [details]
stacktrace

*** This issue has been marked as a duplicate of 148066 ***

J2SEProjectProperties.showModifiedMessage is at fault. As I have said before, this dialog should be rewritten. It should
_not_ block project saving asking whether to regenerate build-impl.xml. This file should _always_ be regenerated; if it
was modified, save a backup copy and the notify the user of this fact later.

This is another issue. It can be changed but it does not fix problem introduced by fix of issue #148066: It effectively
blocks opening any modal dialog under PM.mutex(). Is it correct or not?

*** Issue 158771 has been marked as a duplicate of this issue. ***

IMHO the problem is in these lines:

        at org.netbeans.modules.project.uiapi.CustomizerDialog$OptionListener$1.run(CustomizerDialog.java:213)
        at org.openide.util.Mutex.writeAccess(Mutex.java:394)
        at org.netbeans.modules.project.uiapi.CustomizerDialog$OptionListener.actionPerformed(CustomizerDialog.java:211)

Holding the mutex and calling outside - whatever you do might eventually end up trying to acquire the other mutex...
Please check also the #158771.

Root cause is too restrictive check for 'possible' deadlock condition introduced by issue #148066 as I said above.
Current usage of ProjectManager.mutex().writeAccess() on pressing OK button is to make sure no one else is
writing/reading data at the same time. Every 3rd party customizear panel is expected to save its data and #148066 blocks
any modal dialog to be used under ProjectManager.mutex().writeAccess(). Sorry there is nothing we can do with it.
Jesse's suggestion is just workaround to this restriction but it does not solve root cause.

Issue 148066 does not check for deadlock conditions. It simply ensures correct lock ordering. Acquiring Children.MUTEX
while holding ProjectManager.mutex() is illegal. No code is allowed to do that, because other code is allowed to acquire
PM.mutex() while holding Children.MUTEX. So the check in issue 148066 is not too restrictive. It simply enforces an
invariant. Any code that leads to Children.MUTEX being acquired under PM.mutex() is breaking that invariant and needs to
be fixed.

As for this issue, you are right that customizer panels are expected to save the data in the AWT thread under
PM.mutex(). Issue 148066 does not prevent you from doing that. You simply need to make sure that you don't display
dialogs under PM.mutex(), since that causes redraws elsewhere and the redraws might acquire Children.MUTEX.

Ok. Then we will follow Jesse's suggestion: java/project code should not display any dialog 'synchronously'. It should
just save file and eventually make backup first if it was modified by user and show info dialog about it asynchronously
(using invokeLater).

If there will be need to display synchronous dialog it must be done in some PRE_OK action without PM.mutex. (But it
would require API change if I am not wrong.)

Build: NetBeans IDE Dev (Build 200903310200)
VM: Java HotSpot(TM) 64-Bit Server VM, 11.3-b02, Java(TM) SE Runtime Environment, 1.6.0_13-b03
OS: Linux, 2.6.27-11-generic, amd64

User Comments: 


Stacktrace: 
java.lang.IllegalStateException: Should not acquire Children.MUTEX while holding ProjectManager.mutex()
        at org.openide.nodes.Children$ProjectManagerDeadlockDetector.execute(Children.java:1805)
        at org.openide.util.Mutex.doWrapperAccess(Mutex.java:1320)
        at org.openide.util.Mutex.readAccess(Mutex.java:275)
        at org.openide.explorer.view.TreeView$ExplorerTree$GuardedActions.<init>(TreeView.java:2086)
        at org.openide.explorer.view.TreeView$ExplorerTree.processFocusEvent(TreeView.java:1847)
        at java.awt.Component.processEvent(Component.java:5972)

Created attachment 79142 [details]
stacktrace

Build: NetBeans IDE Dev (Build 200903250219)
VM: Java HotSpot(TM) Client VM, 1.5.0_16-133, Java(TM) 2 Runtime Environment, Standard Edition, 1.5.0_16-b06-284
OS: Mac OS X, 10.5.6, i386

User Comments: 
Changing from project platform.
This project was modified on an other machine with JDK 1.6 soylate, which is not installed on the current machine where JDK 1.6 from apple lies.
So I decided to move to JDK 1.6 and got this error

Stacktrace: 
java.lang.IllegalStateException: Should not acquire Children.MUTEX while holding ProjectManager.mutex()
        at org.openide.nodes.Children$ProjectManagerDeadlockDetector.execute(Children.java:1805)
        at org.openide.util.Mutex.doWrapperAccess(Mutex.java:1320)
        at org.openide.util.Mutex.readAccess(Mutex.java:275)
        at org.openide.explorer.view.TreeView$ExplorerTree$GuardedActions.<init>(TreeView.java:2086)
        at org.openide.explorer.view.TreeView$ExplorerTree.paint(TreeView.java:1794)
        at javax.swing.JComponent.paintChildren(JComponent.java:843)

Created attachment 79187 [details]
stacktrace

Build: NetBeans IDE Dev (Build 200903250219)
VM: Java HotSpot(TM) Client VM, 1.5.0_16-133, Java(TM) 2 Runtime Environment, Standard Edition, 1.5.0_16-b06-284
OS: Mac OS X, 10.5.6, i386

User Comments: 
Same as already described : moving to JDK 1.6 from appel
For information: project was created on an other machine. The 2 JDK were not on the same PC. This occured when movong the project from one machine to an other where change took place.


Stacktrace: 
java.lang.IllegalStateException: Should not acquire Children.MUTEX while holding ProjectManager.mutex()
        at org.openide.nodes.Children$ProjectManagerDeadlockDetector.execute(Children.java:1805)
        at org.openide.util.Mutex.doWrapperAccess(Mutex.java:1320)
        at org.openide.util.Mutex.readAccess(Mutex.java:275)
        at org.openide.explorer.view.TreeView$ExplorerTree$GuardedActions.<init>(TreeView.java:2086)
        at org.openide.explorer.view.TreeView$ExplorerTree.paint(TreeView.java:1794)
        at javax.swing.JComponent.paintChildren(JComponent.java:843)

Created attachment 79190 [details]
stacktrace

Fixed jet-main:c8a4967de00c

Integrated into 'main-golden', will be available in build *200904040200* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
Changeset: http://hg.netbeans.org/main-golden/rev/c8a4967de00c
User: Tomas Zezula <tzezula@netbeans.org>
Log: #150540:IllegalStateException: Should not acquire Children.MUTEX while holding ProjectManager.mutex()

*** Issue 162647 has been marked as a duplicate of this issue. ***

*** Issue 162674 has been marked as a duplicate of this issue. ***

Build: NetBeans IDE Dev (Build 200910310201)
VM: Java HotSpot(TM) Client VM, 14.2-b01, Java(TM) SE Runtime Environment, 1.6.0_16-b01
OS: Linux, 2.6.22-14-generic, i386

User Comments: 


Stacktrace: 
java.lang.IllegalStateException: Should not acquire Children.MUTEX while holding ProjectManager.mutex()
        at org.openide.nodes.Children$ProjectManagerDeadlockDetector.execute(Children.java:1809)
        at org.openide.util.Mutex.doWrapperAccess(Mutex.java:1320)
        at org.openide.util.Mutex.readAccess(Mutex.java:275)
        at org.openide.explorer.view.TreeView$ExplorerTree$GuardedActions.<init>(TreeView.java:2128)
        at org.openide.explorer.view.TreeView$ExplorerTree.paint(TreeView.java:1838)
        at javax.swing.JComponent.paintChildren(JComponent.java:864)

Created attachment 90427 [details]
stacktrace

Created attachment 95639 [details]
stacktrace

Created attachment 97588 [details]
stacktrace