GWT 2.5.1 has finally fixed this problem. Release notes documenting this are here:
https://developers.google.com/web-toolkit/release-notes#Release_Notes_2_5_1
and they claim that:
"Applications created using DirectInstallLinker should work on a page where embedded scripts are not allowed (for example, the Chrome extension)"
This means that you can now use DirectInstallLinker to link your packaged Chrome application in a way that meets the new security requirements of the manifest version 2 for embedded scripts. That is, using DirectInstallLinker to associate your application with GWT 2.5.1, selected as your version of GWT, GWT will not place any script elements inside its generated Javascript and therefore a new version 2 requirement so that there are no inline scripts will be broken.
I found that SingleScriptLinker also works for my own application; however, issue 7685 warns of using SingleScriptLinker because "This generates the $ doc.write string, which is not allowed in packaged applications." I myself use DirectInstallLinker.
Here is the Javadoc for DirectInstallLinker:
http://google-web-toolkit.googlecode.com/svn/javadoc/2.5/com/google/gwt/core/linker/DirectInstallLinker.html
To use this linker, you can include the following in your * .gwt.xml file:
<define-linker name="dil" class="com.google.gwt.core.linker.DirectInstallLinker"/> <add-linker name="dil" />
(dil can be replaced with anything you choose if there are no dashes or other illegal characters).
You will need to select GWT 2.5.1 as your version of GWT. If you are using an older version of GWT in an older version of Eclipse, such as Ganymede (like me), you will need to upgrade to at least Helios and then import the project into a new Eclipse environment. The archive URLs for the Google Eclipse plugin that you can use for the last three versions of Eclipse can be found here:
https://developers.google.com/eclipse/docs/download
With the above you should set
"manifest_version": 2
in your manifest.json file and not experiencing errors due to the built-in JWB script generated by GWT. This should allow your Chrome web app to be acceptable for the Chrome Web Store (which now requires manifest version 2 for any new apps or app updates), unless there are other issues.