So I migrated my projects from a Debian 8 (Jessie) system to a Debian 9 (Stretch) system. The default NetBeans installed by apt-get install netbeans on Strech was 8.1, and it didn’t include PHP support, so I manually installed NetBeans 8.2.
When I opened my old projects I got an error about an invalid global PHP include path.
So initially I edited ~/.netbeans/8.2/build.properties to change the php.global.include.path settings (to remove /usr/share/php5, because in Stretch I’m running PHP 7.0). But that didn’t work. Each time I ran NetBeans the build.properties file was overwritten with the old php5 directory.
So then I found ~/.netbeans/8.2/config/Preferences/org/netbeans/modules/php/project/general.properties. In there I edited the phpGlobalIncludPath and removed the /usr/share/php5 directory.
Then when I reopened NetBeans all of my projects opened properly without an error! Everything is easy when you know how!