If you write enterprise-size software in Java, you ran sooner or later into a dilemma regarding tools.
On one hand you know that using IDEs like Eclipse drives efficiency and adds support for streamlined workflows. IDEs provide handy features like call hierarchy and integrated debugging.
On the other hand IDEs tend to introduce questionable artefacts into the overall build infrastructure, and sometimes lead decisions for questions regarding architecture.
If you e.g. use maven as your dependency and build infrastructure then those IDEs have to completely understand your maven declarations to know about the classpath, output folders, compiler level etc. You tend to avoid maven features that your favorite IDE does not understand.
If you always follow standard solutions and best practises, there might be no big issue between IDE and maven build. But sooner or later there will appear challenges for the IDE such as cross compiling, multi-projects, generated code.
In such situations it is recommended to take a step back and analyze the overall requirements for architecture and build infrastructure. Why do we have this generated code, where is it used, what does the generation depend on, when should it executed? As a result, you should have created a reasonable model of all build steps and an acyclic module dependency model. Often the root of all evil lies in unmanaged architecture and build infrastructure. Fix this and go ahead.
Step number two should reflect the findings from step one into the actual dependency declarations and build infrastructure. A valid result of this step is a working command line build.
And then it is the last step that the IDE is tweaked to support the desired architecture. Sometimes, during this step, build infrastructure needs to be extended or even changed a little bit, but never should the changes go so far as to change the desired architecture. If the IDE is not able to cover the target architecture then you should propable rethink if this IDE is a good choice or if your requirements are too ambitious.