I have an eclipse plug-in working fine within eclipse environment.
I wanted to export it into a jar file, so I chose Export > Deployable plug-ins and fragments.

I could get a jar file, but an error was reported.

Opening the log file, it reports that I have 1242 problems (191 errors, 1051 warnings). This is some copy from the error log.
2. ERROR in /Users/LSclipse/src/lsclipse/LSDiffRunner.java (at line 61)
import edu.washington.cs.induction.OnePipeLineScript;
^^^
The import edu cannot be resolved
----------
3. ERROR in /Users/LSclipse/src/lsclipse/LSDiffRunner.java (at line 261)
OnePipeLineScript.getMatchingForRefFinder(projName, proj1, proj1Loc
^^^^^^^^^^^^^^^^^
OnePipeLineScript cannot be resolved
Why I got errors? I had 2049 warnings, but no error when I compile the plugin in eclipse IDE.
The main project references two other projects, and references many external libraries. I attach the package view and Java build path.

There were multiple issues involved for this problem. However, the core issue was that the project apimatching and originanalysis were not eclipse plugins but just java projects. As a result, those two projects were not included in the final jar file to break the build.
I solved this issue by symbolic link the src directory into the main eclipse plugin project.
ln -s /workspace/seal/edu.ucsc.originanalysis/src /LSclipse/originanalysis
ln -s /workspace/seal/edu.ucsc.apimatching/src /LSclipse/apimatching
From the Java Build Path/Source tab, I added those two included projects as source. Eclipse Java Missing required source folder: 'src'
Now I have eclipse plugin jar file without error.

Then click F-5 to refresh the project explorer and check they are java src directory.
Select the included projects in Build tab.

Updating bin.include and source.. in build.properties tab is important. One should understand that in bin.include the ordering is also critical. lib/cdtparser.jar and lib/cdtcore.jar should be placed prior to the user of them - origin analysis/.

I also had to copy some jar files in those projects file into the main project, and select them in Binary Build tab.

And add tim in Runtime/Classpath tab.

I have lots of "Must Override a Superclass Method" errors. With the hint from this post - 'Must Override a Superclass Method' Errors after importing a project into Eclipse , I removed the J2SE-1.5 to resolve this issue.

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