RubyMine offers you to exclude directories from search, meaning faster search results and less "noise" in the list of result.

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Right-click a folder in your project tree and click "Mark Directory As" → "Excluded".

Do it for your your log, data, and other directories that you don't need to access during development and whose search results are irrelevant.
They won't be deleted but simply ignored when searching across a project's files.

Also see How to exclude single files