If your “GWT Compile” process exports the “deploy” directory to the wrong place, you can correct this within the preferences file com.google.gdt.eclipse.core.prefs, which you can find within the “.settings” directory of you Eclipse project.
eclipse.preferences.version=1 jarsExcludedFromWebInfLib= lastWarOutDir=/path-to-your-project/src/main/webapp warSrcDir=src/main/webapp warSrcDirIsOutput=false
Change the “lastWarOutDir” to the correct path. It should contain the “WEB-INF” directory and GWT should create a “deploy” directory within it. Restart your IDE to load the new settings! You can check the results during “GWT Compile” with log level TRACE.