Though I am not an OSX user I am a Mac-in-the know. Basically I get invited to their house parties and politely decline to run amok with Windows and Linux/Unix (who is OSX's older sister, it is all so very confusing). In any case, Mac adds extra files to everything. I know when a designer is using a mac vs a pc. I get extra files and directories in their attachments if there is a folder. As far as project files, there needs to be a way to set up netbeans to keep the files for project in a different location from your working on files. If not then shame on your IDE. Well, if nothing works, since Linux/Unix is close to my heart I can write a script for you to pull all files of a list of extensions out and copy them to a new directory with subfolders in tact. Here ya are:
This should work
find . -name '*.php' | xargs rsync -avuzb '{}' exportdirectory/
I do not have a machine to test it on right now and Cygwin, for all it's effort just fails sometimes. Let me know how it goes, otherwise use Unix wizardy :D Because yes, as we know OSX uses Unix command line. The crude script is mainly to give you an idea of a way you can do it. I am sure there is php, html, css, js, and other files and on rare occasion (god lets hope not) just knowing extensions isn't going to be enough.
Personally I use gvim and refuse to use project managers, I use gvim and command line and though I have used both, I am highly preferential to the current way I am doing everything. Hey, it's a choice though. No criticism here if you walk another journey.