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You are correct that its not just compiled files that need to be copied. In fact, if you have just .js files then Chutzpah does no compiling but would still need to copy the files.
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The TestHarnessDirectory setting was created to help with RequireJS tests since the html test harness should be at the root of your testing directory. While you can override the paths in a require.js config section most people have the html file at the root. Chutzpah used to generate the html test harness file adjacent to the .js (or .ts/.coffee) test file. This worked well for normal tests but for requirejs that file needs to be loaded like a module so you need the HTML file at the root of your module folder structure. I hope that makes sense.
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Having a separate setting to determine if you should copy things to a new folder makes sense. But as you alluded to that name is not good since it is not just compiled files but all files that are part of the test reference graph. A better name might be something like "RunTestsInPlace" which defaults to true. But I am open to naming suggestions.
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One interesting catch is that Chutzpah can run tests in parallel. So if test1.js and test2.js are running in parallel and use the same chutzpah.json file then they will be trying to copy files at the same time to the same folder! This would require some synchronization code to make sure that errors dont occur.
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I think a warning makes sense. And in that case Chutzpah will still work but just not copy that file, it will just reference that file from its current location.
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Whether this is worthwhile depends on the person and their use case. I have received this request once or twice before but its not something everyone is demanding. I try to add new features mostly based on concrete use cases from users. What we can do is create a issue and see if people vote on it. That said if you are passionate about this feature and work out the kinks I would be fine including it in the product. If you move forward we can talk more about some of the tricky parts.
If you are interesting in contributing a different feature email me and we can talk about some of the main interesting things that I havent had time to work on.