How to remove Quarantine from file permissions in OS X
First, use ls -l@ to see what extended attributes are attached to the file. Normally, a downloaded file will have xattrs named "com.apple.quarantine" and maybe "com.apple.metadata:kMDItemWhereFroms". To remove them, you can delete them individually with e.g. xattr -d com.apple.quarantine filename.pem, or clear all xattrs with xattr -c filename.pem