Most of the time, you'll be debugging in DevMode, against your Java code, 
within your Java IDE, using any Java debugger.

GWT 2.5 will generate SourceMaps so you can see your Java code in your 
browser's dev tools, set breakpoints in the Java code to pause the JS 
engine, etc. 
See https://plus.google.com/110412141990454266397/posts/iqXo5AyHkyd and 
http://www.2ality.com/2011/07/firefox-sourcemap.html

In the mean time, or in browsers where SourceMaps aren't supported, GWT 
generates symbolMaps that allow you to find where an obfuscated function 
name comes from in your Java code. It can also be used to automatically 
deobfuscate stack traces (so you can, for instance, send a client-side 
exception to the server for logging –using java.util.logging and the 
SimpleRemoteLogHandler or RequestFactoryLogHandler–, and have the 
stacktrace automatically deobfuscated in your logs). You can also use the 
StackTraceDeobfuscator "manually" on the server-side; or look-up in the 
symbolMaps by yourself (I regularly do it when I can't reproduce a bug in 
DevMode).
It's important to note that symbolMaps only map methods, whereas SourceMaps 
map down to the expression level.

So no, it's not a problem.

Also, if your application is "big enough", even if you use "plain 
JavaScript" instead of GWT, you'll want to use a "JS compiler" (such as the 
Closure Compiler) or "JS minifier"; so you'll have the same "issues". The 
Closure Compiler generates SourceMaps, but I don't think any compiler but 
GWT produces the equivalent of the symbolMaps and have the equivalent of 
the StackTraceDeobfuscator.

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