Is there a way to run Selenium WebDriver tests in a browser (or just run a test scenario manually in a browser), and get the code coverage of the web-app written in JavaScript? Are there any other code coverage tools except JSCover that can do such task?
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JSCover can when run in proxy mode (without HTTPS). A more robust approach would be to pre-instrument your JS before running your tests, which can be done by JSCOver and other tools (see answer to second question).
JSCover can also save data between pages using local-storage which can be useful for re-using existing selenium suites.
You'll need to add some code to the end of your tests to save the coverage data. To do that with JSCover, see http://tntim96.github.io/JSCover/manual/manual.xml#fileSystemSave.
There is also Istanbul and BlanketJS which may be able to be used with the pre-instrumentation approach.