Are you deploying pure web applications?
If yes, then NetBeans does what is called as "directory deployment" of those applications in that your applications are kept at your workspace and the GlassFish server knows it only by location.
See:
https://glassfish.dev.java.net/javaee5/docs/AG/ablgw.html#ablie for some details.
In other words, it is perfectly OK to have private workspace that you let GlassFish know about.
This workspace where you application resides, does NOT have to be part of <domain-dir>/applications folder.
Writing the ANT task to touch the .reload file in your application's folder should be straightforward.
Hope that helps.
Regards,
Kedar
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