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I'm using Projectile to index a Rails 4 project. When I use M-x projectile-find-file to locate files using their file name, some files simply don't appear.

For example, I have a file located in app/controllers/api/v1/test_controller.rb, but typing M-x projectile-find-file entertest_controllerenter returns no results.

Is there a way to re-index the project, or figure out what's filtering out certain files?

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The quick answer is to invalidate the projectile cache. When using projectile-find-file if you use C-u to send the universal argument before running the function, it will invalidate the cache before searching it. To match your example;

C-u M-x projectile-find-file

There are a number of other functions in projectile that use the prefix argument, check for any that call projectile-maybe-invalidate-cache if the universal argument is present.

More generally though, projectile provides projectile-invalidate-cache which is by default bound to C-c p i.

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