I'm too frequently, during "normal" operation (dev workspace with like many yangtools and controller projects open in it) seeing this exception make the Error Log pop-up, when probably this should somehow be handled (ignored?) in the code:

java.io.FileNotFoundException: /org.opendaylight.yangide.org.opendaylight.yangide.yangparser/libs/jsr305-3.0.0.jar (No such file or directory)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:219)
at java.util.zip.ZipFile.<init>(ZipFile.java:149)
at java.util.jar.JarFile.<init>(JarFile.java:166)
at java.util.jar.JarFile.<init>(JarFile.java:130)
at org.opendaylight.yangide.core.model.YangProject.buildStructure(YangProject.java:90)
at org.opendaylight.yangide.core.model.YangElement.generateInfos(YangElement.java:232)
at org.opendaylight.yangide.core.model.YangElement.openWhenClosed(YangElement.java:276)
at org.opendaylight.yangide.core.model.YangElement.getElementInfo(YangElement.java:161)
at org.opendaylight.yangide.core.indexing.IndexAllProject.execute(IndexAllProject.java:108)
at org.opendaylight.yangide.core.indexing.JobManager.run(JobManager.java:414)
at java.lang.Thread.run(Thread.java:745)

also very similarly but not identical this one:

java.io.FileNotFoundException: /home/vorburger/.p2/pool/plugins/org.eclipse.m2e.maven.runtime_1.7.0.20160524-1811 (Is a directory)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(ZipFile.java:219)
at java.util.zip.ZipFile.<init>(ZipFile.java:149)
at java.util.jar.JarFile.<init>(JarFile.java:166)
at java.util.jar.JarFile.<init>(JarFile.java:130)
at org.opendaylight.yangide.core.model.YangProject.buildStructure(YangProject.java:90)
at org.opendaylight.yangide.core.model.YangElement.generateInfos(YangElement.java:232)
at org.opendaylight.yangide.core.model.YangElement.openWhenClosed(YangElement.java:276)
at org.opendaylight.yangide.core.model.YangElement.getElementInfo(YangElement.java:161)
at org.opendaylight.yangide.core.indexing.IndexAllProject.execute(IndexAllProject.java:108)
at org.opendaylight.yangide.core.indexing.JobManager.run(JobManager.java:414)
at java.lang.Thread.run(Thread.java:745)

It is possible that both are specific to *.yang files in Eclipse plugin projects only (note both errors are in yangide, and that's where I see it, not on real ODL projects with yang), which is admittedly not a typical use case, but it would still be nicer if we didn't throw this.