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Eclipse on Linux install

So once again, I have to install Eclipse on Linux.
Several options :
- JPackage : as I posted before, unless you share your install, there are no compelling reason to depend on JPackage.
- Download from Eclipse site. Generally, I download a tiny Eclipse : the "Portable runtime Binary" and then I select only the plugins I need.

Still, I always wonder what is the "good" way to install Java Apps on Linux. They don't fit the /etc, /usr /bin folders. The FHS (File Hierarchy Standard) doesn't seem to be followed very much.
For example, FreeNX from NoMachine is installed in /usr/NX, as if /usr was "\Program files" !

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