I wonder what's the relationship with web services here. Also the full stack trace is needed. Who knows where is this
exception coming from ?

Oops, I found the table http://statistics.netbeans.org/exceptions/detail.do?id=5068

There is a bunch of different reasons for the exception.
The last three come from Maven Web Services support.
Other come from web module. 

I'll fix the WS problem, then reassign to web project.

I found:
<br/><span style='text-weight:bold'>java.io.FileNotFoundException: /home/etjenkins/config/environment.xml (No such file
or directory)</span><br/> at java.io.FileInputStream.open(FileInputStream.java:0) at
java.io.FileInputStream.<init>(FileInputStream.java:106) at java.io.FileInputStream.<init>(FileInputStream.java:66) at
sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:70) at
sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:161) at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:653) at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1315) at
com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1252) at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEntityReference(XMLDocumentFragmentScannerImpl.java:1898)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:3024)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648) at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:807) at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737) at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:107) at
com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:225) at
com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:283) at
org.netbeans.modules.j2ee.dd.api.webservices.DDProvider.parseDD(DDProvider.java:305) at
org.netbeans.modules.j2ee.dd.api.webservices.DDProvider.parseDD(DDProvider.java:290) at
org.netbeans.modules.j2ee.dd.api.webservices.DDProvider.parseDD(DDProvider.java:285) at
org.netbeans.modules.j2ee.dd.api.webservices.DDProvider.getDDRoot(DDProvider.java:134) at
org.netbeans.modules.j2ee.dd.impl.webservices.annotation.WebservicesMetadataModelImpl.<init>(WebservicesMetadataModelImpl.java:76)
at
org.netbeans.modules.j2ee.dd.spi.webservices.WebservicesMetadataModelFactory.createMetadataModel(WebservicesMetadataModelFactory.java:57)
at org.netbeans.modules.maven.j2ee.web.WebModuleImpl.getWebservicesMetadataModel(WebModuleImpl.java:473) 

I fixed the last 3 cases:
See: http://statistics.netbeans.org/exceptions/detail.do?id=5068

Fix:
http://hg.netbeans.org/main?cmd=changeset;node=3199714b305f

Reassigning to web project to evaluate exceptions starting with:

java.io.FileNotFoundException: \common-ant.xml (The system cannot find the file specified) at 
...

This issue already has 20 duplicates 
see http://statistics.netbeans.org/exceptions/detail.do?id=5068

Lowering back to P3: it is the same exception but cause is different now.  Last couple of exceptions are about

  java.io.FileNotFoundException: /usr/local/java/build/app_build.xml (No such file or directory)

and it looks to me like glassfish problem in maven project? I cannot say positively where the problem lies. Milos please
have a look.

the glassfish plugin does not write a file named app_build.xml... last I checked (about 15 seconds ago).

I did not find a reference to an 'app_build' in the entire web-main repo...

David: what leads you to believe that this is a glassfish plugin problem?

Re. "David: what leads you to believe that this is a glassfish plugin problem" - given stacktrace. But as I said I was
not positive about it. I could not find anything about "app_build.xml". The only google search hit (obsolete now)
mentions Weblogic. I'm passing to Milos/Maven - have you ever heard about "app_build.xml" Milos?

the appl_build.xml file case is triggered from this stacktrace:
        at org.openide.xml.XMLUtil.parse(XMLUtil.java:348)
        at org.netbeans.modules.j2ee.sun.ide.j2ee.BuildExtension.abbreviateBuildXml(BuildExtension.java:126)
        at
org.netbeans.modules.j2ee.sun.ide.j2ee.ModuleConfigurationImpl$StaticBuildExtensionListener.rewriteBuildImpl(ModuleConfigurationImpl.java:356)
        at
org.netbeans.modules.j2ee.sun.ide.j2ee.ModuleConfigurationImpl$StaticBuildExtensionListener.access$100(ModuleConfigurationImpl.java:316)
        at
org.netbeans.modules.j2ee.sun.ide.j2ee.ModuleConfigurationImpl$StaticBuildExtensionListener$1.run(ModuleConfigurationImpl.java:412)


which seems like j2eeserver or glassfish packages, reassigning to vkraemer (please reassign appropriately if I got it wrong)

maven by itself is not using any build scripts whatsoever, so the usage of BuildExtensions and build scripts sounds wrong..

I will take a second look at this... I did not see the line

org.netbeans.modules.j2ee.sun.ide.j2ee.BuildExtension.abbreviateBuildXml(BuildExtension.java:126)

when I looked at the ST.

RE. "BuildExtension.abbreviateBuildXml" - that's why I originally passed it to GF but that method is pretty innocent -
it passes "build.xml". Could it be related that build script is customized and is importing "app_build.xml" which cannot
be found? There seems to be quite a lot of people having this problem though.

Integrated into 'main-golden', will be available in build *200907090200* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
Changeset: http://hg.netbeans.org/main-golden/rev/d40842fbb932
User: Vince Kraemer <vkraemer@netbeans.org>
Log: #161038: FileNotFoundException

in main

verified in NB 6.8 M1