This is a problem new to Yosemite. I have a folder called "com.acme.epub". The Finder sees this as an ePub file and won't let me access it as a folder. I can access it as a directory via the Terminal but if I do "open .", then it launches iBooks (which is not my default epub application). How do I get the Finder to see this folder as an actual folder/directory and not as an epub file? Note: Renaming the folder is not an option.

This same behavior occurs with folders that end with a ".key" string; it probably happens with certain other strings as well.

I am using OS X 10.10.3. This problem did not occur in 10.9 or 10.8.

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    This is happening most likely because a file in epub format on OS X is really a folder structure and is not just a monolithic file. I just tested this, and folders with .epub extensions become associated with iBooks.app; .key extensions with Keynote.app, .pages with Pages.app; .numbers with Numbers.app, etc. This is unexpected, and unfortunate, but there seems to be no remedy! I also tested changing the app in the Open with: dialog in Get-Info to /System/Library/CoreServices/Finder.app, but that gave me an 'unidentified developer' pop-up error message. Curiouser and curiouser. – IconDaemon Apr 15 '15 at 0:07
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    Thanks for confirming. I will file a bug report with Apple. – TddOrBust Apr 15 '15 at 0:15
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    It seems, over the years and decades Apple has learned from Microsoft. It always was a bad idea to guess the file type from the name. Instead, in years up to the first OS X, Apple kept the idea of Type and Creator, which worked. Obviously they have given up the idea for bad... – Martin Allert Apr 15 '15 at 7:31

You could look at using duti, a command line tool that lets you change the the file type association of an extension.

Along with duti, something like this could work:

com.apple.finder    .epub
com.apple.finder    .key
com.apple.finder    .numbers

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