Hi Tobias,
On Fri, 11 Apr 2014, Tobias Pietzsch wrote:
> What is the rationale behind putting jars in either fiji/jars/ or
> /fiji/plugins/?
ImageJ 1.x determines that a .jar file contains plugins by the telltale of
an underscore in its file name. If a plugins.config is found inside the
.jar file, it is then parsed, if there is no such file, all the contained
classes having an underscore in their name are considered to be plugins.
Now, this is slightly error prone: who is to say that completely
independent Java libraries do not have underscores in their file *and*
class names?
And that is exactly what happened: jai_codec.
ImageJ 1.x now has a work-around (which is not quite complete; it is
probably a matter of time until an edge case falls through the
work-around's cracks), but the safe way for Fiji was to put all the
libraries into jars/ and all the .jar files containing plugins into
plugins/.
Ciao,
Johannes
P.S.: Please feel more than free to take this information, put it into
your own words and enhance the FAQ on the Fiji Wiki. That way, the
documentation does not depend on yours truly only.