the plugin loading mechanism of Micro-Manager (and ImageJ) uses services
from the scijava class, that in turn uses annotations.
Those annotations should be in the jar file as a consequence of running
so called processors, which eclipse do not run by default.
That makes the jar files generated by eclipse "transparent" to the
If you want to know more, google is your friend with keywords eclipse,
The issue can be dealt with in a number of ways. Maven and Ant seem to
have building systems aware of processors.
If you, like me, do not use either, there is a Git repo:
https://github.com/scijava/eclipse-scijava-project that shows how to deal with this.
In short, you have to add a project builder with a specific
configuration that calls the scijava processor, and then export the jar,
making sure you select all output artifacts (to include the
META-INf/json/org.scijava.plugin.Plugin file which is key to all this.
The EclipseHelper.launch is attached for reference (which goes into the
project .externalToolBuilders folder)