I appears to be impossible to clean a web project without stopping GlassFish.

This problem persists since GlassFish V2. As suggested in issue 156019, I have used a workaround to copy library jars to the lib directory of the server.

However, this workaround causes classloader problems in some cases - it is quite dangerous.

Please refer to the attached project that I created with the following script:

- Start NetBeans with an empty userdir
- File|New Project|Java|Java Web|Samples|Java Web|Servlet Stateless (Java EE6)|Next|Finish
- Files Window|ServletStateless|New|Folder|lib
- Copy jasypt-1.5.jar, commons-codec-1.4.jar, commons-lang-2.4.jar into lib folder
- Project Window|ServletStateless|Properties|Run|Uncheck "Deploy on Save"
- Project Window|ServletStateless|Properties|Libraries|Add JAR/Folder|jasypt-1.5.jar, commons-codec-1.4.jar, commons-lang-2.4.jar
- Project Window|ServletStateless|Source Packages|servlet.stateless|StatelessSessionBean.java

Add one line and fix import:
    public String sayHello(String name) {
        BasicPasswordEncryptor passwordEncryptor = new BasicPasswordEncryptor();
        return "Hello, " + name + "!\n";
    }
- Project Window|ServletStateless|Run
- Try the app - should be ok
- Services Window|Servers|GlassFish Server 3.x|Applications|ServletStateless|Undeploy
- Project Window|ServletStateless|Clean and Build

init:
undeploy-clean:
Undeploying ...
deps-clean:
do-clean:
Deleting directory ...\ServletStateless\build
...\ServletStateless\nbproject\build-impl.xml:1047: Unable to delete file ...\ServletStateless\build\web\WEB-INF\lib\commons-codec-1.4.jar
BUILD FAILED (total time: 8 seconds)

The same happens if Clean and Build is executed without Undeploy.