I upgraded my STS from 3.6.1 to 3.9.15 and since then I've started getting this error. The archive C:/Program File(x86)/sts-bundle3.6.1/sts3.6.1.RELEASE/plugins/org.apache.axis_1.4.0.v201005080400/lib/axis.jar which is referenced by the classpath does not exist.
I don't even have sts in this location and I am not sure why STS is throwing this error? I don't see any error in the build path of the project by going through Project's build path -> configure build path.
It looks like the JAR file that you mentioned is directly referenced on the classpath of one of your projects. Maybe you used some Eclipse-specific tooling for generating web services in the past? That might be the root cause of this library being added to your projects.
This JAR file is not part of the default distribution of STS3 anymore. If your project still needs that JAR file on the classpath, I would recommend to add it as a dependency to your build configuration (e.g. the Maven pom.xml file in case you use Maven) and remove it as a direct entry from the classpath.