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How to correctly debug a GWT application with Jetty Runner in IntelliJ IDEA

I'm trying to migrate some legacy GWT applications from eclipse to IntelliJ. Oh man, what a nightmare. I've come very near to a dead end with my research. I'm at the point where there is simply no related page or documentation that I have not seen, not to mention the information on this topic is very, very sparse.
My setup is as follows:
IntelliJ IDE
GWT 2.9 plugin
Jetty Runner that is using Jetty v11.0.7
Here are my GWT and Jetty debug configuration settings:
When I navigate to the jetty server URL I always get "Error 404 Not Found" message.
Now, when I navigate to the "Debug" directory that is specified in the GWT configuration I do see that there is no RSS.html which is a problem but even the "blank.html" is not able to be navigated to. One potential issue is maybe I am somehow not compiling the debuggable version of the GWT application correctly?
My other guess is that I have to somehow point to an actual .war file. I do have an ant build script that works just fine and generates a .war that works correctly in production. Below is a screenshot of the generated war file as well as the directory used to build the war archive.
In summation, how do you correctly debug a GWT application in IntelliJ using the GWT configuration with a Jetty Runner server?
I can promptly provide any additional info that I may have left out.
EDIT
I would like to add that this How to get GWT Super Dev Mode to work with IntelliJ question is very similar to what I am asking here and it was never edited with the correct answer, also since this was posted super dev mode was added. It would be great to get a clear solution documented for myself and others. To reiterate the answer needs to achieve these three things,
Use a Jetty Runner configuration (to enable use of different Jetty versions as there can be a cascade of conflicts depending on your codebase)
Use a GWT configuration to run a code server with the Jetty Runner instance so debugging is possible.
Use IntelliJ IDEA

MyEclipse 2016 Debugger Using Wrong Version of Code

I just updated to MyEclipse 2016, and I am having some issues getting my code to debug.
I wrote some changes in a java file and am trying to debug them on my websphere application server, but I noticed the debugger wasn't following the code at all. After a little investigation it turns out that I'm on V5 of the code, but the debugger is running V4 of the code.
I've tried going into the menu at
Run -> Debug Configurations... -> (Select My Server) -> Source
and changing the sources listed in here to just the workspace projects, but the debugger still goes through the old version of the code.
I'm at a loss and don't know what to do to get the debugger to pick up the right code. Does anybody have any suggestions I could try to get my debugger to pick up the new version of my code?
Edit: Forgot to include, Project --> Build Automatically is checked in the menus, and I have tried manually cleaning this a few times myself as well.

From your last comment, this means that the V4 code is actually executing on the server. The debugger is not executing anything; it is the server that is executing the code. So you have the wrong version deployed, somehow. Try a clean on the server, to remove any deployments and then re-deploy your project.

Given what everybody had said I checked into the deployment to the server. Looks like I had a WAR deployed to my server, when there is actually an EAR I can deploy to the server which includes the WAR I had deployed. Apparently doing just the WAR broke things, but deploying the EAR seemed to fix it all. Thank you all for the input though, definitely helped me get to the root of the issue!

Update startup.bat tomcat7

I'm working on tomcat7 project on Eclipse (only the manager part). I get the project here. This is the first time I'm working on this kind of project, and when I turn on the server and look at my page, nothing has changed (It was only a test changing some string in java/org/catalina/manager/LocalStrings_fr.properties).
I guess the startup.bat is not updated or something like that. Nothing about it on Google (else the build of the project with Linux command line, but I'm working on Windows).
Does anyone knows what have to be done?
Edit: It seems that my question is not easyly understandable, so I put some pictures to explain:
I work on Tomcat7 in my workspace:
I try to change the file (just to test, I need to work on servlets too).
When I change the language file as:
htmlManagerServlet.title=Gestionnaire d''applications WEB Tomcat TEST
instead of
htmlManagerServlet.title=Gestionnaire d''applications WEB Tomcat
I get nothing after re-run the server:
I hope it's more easy to understand.
Thanks

Spring MVC App runs in Eclipse but not Intellij - 404 Not Found

I've written a Spring MVC app that is functional on an app server. I'm attempting to switch development of this app from Eclipse and to Intellij. I am very new to the IDE so I'm not sure where I have gone wrong here.
When I run this application on the server in Eclipse it goes to localhost just fine and works as expected. I created a run configuration in IntelliJ, the app compiles and the server log says it was deployed successfully.
However in the browser it gives the standard HTTP Status 404 - Resource Not Available.
I really don't think it's the servlet or web.xml because those are working just fine in Eclipse. I've also created a brand new app in Intellij to test it and it works fine. So it must be something specific to IntelliJ that I have misconfigured or not setup at all...any ideas? Let me know if you need to see specific screens or anything.

So after toying with this, making it worse a few times, and then getting it back to the original 404 I found the difference.
Eclipse has an internal tomcat server it runs projects on, Intellij runs its projects on the default tomcat server installed on your computer. Intellij exports the project you are running to the server in the web apps folder as the name of your project.
So after I found that, in my tomcat run configuration in Intellij I had to specifiy the application context. Edit Configurations -> Deployment tab -> Application context, and set it to /YourProjectName. My guess is that this tells tomcat where to find your project within the web apps folder.
I hope this can help anyone else who is a relative beginner to tomcat/java EE and intellij like I am.

There is a plugin in intellij called "Smart Tomcat", it allows running spring or web app with much fewer configurations.

Why Intellij deletes obsolete files when trying to run DevMode?

I'm currently working on a GWT project in my company. Although DevMode works perfectly fine in eclipse, I still want to use Intellij Ultimate Edition for development.
But after all setups were done (Facet, Run/Debug configuration) I'm getting this weird processing window saying "Deleting Obsolete Files..." when I run the program and after that all my pre-deployed resource files in the war directory were gone (recursively...).
BTW, I use a script to deploy all my stuff. And the only argument I set for DevMode is:
-war /absolute/path/before/war/folder/war
Does anyone know the reason why Intellij is deleting my files?

After sending a request to Intellij support team, they gave me the following answer:
Adding the following two lines to the IDEA_HOME/bin/idea.properties file:
idea.gwt.clear.unit.cache.before.run=false
idea.gwt.clean.files.created.by.dev.mode=false
Which makes sense, because the only thing I need is to prevent Intellij from deleting my local cached files. Problem solved.

I switched to IntelliJ from Eclipse and never had a problem with GWT debugging in IntelliJ. It is most likely deployment-related.
First, I use Tomcat on the client side just like I'd use it in production. No built-in Jetty. Specify -noserver in Dev Mode Parameters. And make sure to start you server (in Debug mode since you are likely to debug it as well).
Other than that you may be doing custom build/deployment which is causing it. I do everything by the book. IntelliJ is Maven-centric, so it needs to be a textbook Web App module. Unlike Eclipse you don't need to specify where you war directory is. It is "webapp" per Maven convention. I suggest recreating the module from scratch.