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I discovered that I could recreate the behaviour manually if I deleted the TEMP index files. For about 1 minute I got 0 results, but then it fixed itself. Using the debugger, I discovered the ExamineIndexRebuilder class and the RebuildOnStartupHandler. As it turns out, these are the key classes that handle index initialisation. There were a few changes that I had to make in order to get my integration tests to work:
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