There are multiple issues according to your logs
2013-12-25 20:32:56.168:WARN:oejw.WebAppContext:Failed startup of context o.m.j.p.JettyWebAppContext{/api,file:/home/scorpio/Downloads/swagger-core-swagger-project_2.9.1-1.3.0-RC1/samples/java-jaxrs/target/swagger-java-sample-app_2.9.1-1.3.0-RC1/},file:/home/scorpio/Downloads/swagger-core-swagger-project_2.9.1-1.3.0-RC1/samples/java-jaxrs/target/swagger-java-sample-app_2.9.1-1.3.0-RC1/
java.util.zip.ZipException: invalid entry size (expected 6164 but got 4968 bytes)
This simply means that th ZIP file is invalid/improper. Either it was not creates properly or an inturrupt occured during download. I would recommend deleting the file and re-creating/re-donwloading it
'/home/scorpio/.m2/repository/com/fasterxml/jackson/core/jackson-databind/2.1.5/jackson-databind-2.1.5.jar' in project 'swagger-java-sample-app_2.9.1' cannot be read or is not a valid ZIP file swagger-java-sample-app_2.9.1 Build path Build Path Problem
Delete this file and re-acquire it
maven-dependency-plugin (goals "copy-dependencies", "unpack") is not supported by m2e. pom.xml /swagger-java-sample-app_2.9.1 line 2 Maven Project Build Lifecycle Mapping Problem
Plugin execution not covered by lifecycle configuration: net.alchim31.maven:scala-maven-plugin:3.1.0:add-source (execution: default, phase: initialize) pom.xml /swagger-java-sample-app_2.9.1 line 2 Maven Project Build Lifecycle Mapping Problem
Plugin execution not covered by lifecycle configuration: net.alchim31.maven:scala-maven-plugin:3.1.0:testCompile (execution: default, phase: test-compile) pom.xml /swagger-java-sample-app_2.9.1 line 2 Maven Project Build Lifecycle Mapping Problem
All these errors points to one things, the limitation of the m2e eclipse plugin. There are certain plugin goals that are not covered by m2e plugin. THeres nothing much that you can do about it except make sure to verify that the wars are made properly with each build.