Tool window closes on re-index

Hi all, I'm writing a plugin with a tool window. The plugin peridically changes some files on the file system behind the scenes. It seems like the file changes cause intellij to re-index the project, which causes the tool window to close. I would like the tool window to stay open, is there something like toolWindow.neverClose that I can call?
Thanks

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I've noticed that most tool windows I have also display this behavior (closing on re-indexing), but the project tool window doesn't. Can I mimic this behavior somehow?

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Probably Your ToolWindowFactory class needs to implement com.intellij.openapi.project.DumbAware (see documentation of this interface for details).

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