The war plugin provides a providedCompile configuration for dependencies.
The java plugin needs this also. There are some workarounds but they are incomplete or require third party libraries.
Justification: if building a jar file for a servlet filter, the servlet needs to have a providedCompile dependency on servlet-api. The servlet filter is a reusable class that is meant to be embedded in war files. Thus, the project is not a war project, just a jar, so using the war plugin is incorrect.
By extension, the eclipse and other ide plugins should recognize this configuration and perform the correct code/configuration code generation for java projects.