1. A computer program product for operating an application controller on an endpoint in an enterprise network, the computer program product embodied in a non-transitory computer readable medium that, when executing on one or more computers, performs the steps of: a. in response to a selection of a file, retrieving a reputation of the file stored in metadata for the file, wherein the reputation includes at least one access and security parameter for the file and wherein the reputation is remotely stored in a database independent of the application controller and accessible by the application controller, the access and security parameter corresponding to the file being a secure encrypted file or an insecure unencrypted file; b. in response to the access and security parameter, selecting a software application from at least two software applications in an application environment on the endpoint to open the file based on a security configuration of each of the at least two software applications and a corresponding determination of whether the file is a secure encrypted file or an insecure unencrypted file, wherein one of the at least two software applications is a first software application configured to access secure encrypted files and another one of the at least two software applications is a second software application not configured to access secure encrypted files, and wherein the application controller can control access to encrypted files on the endpoint; and c. launching the selected software application to open the file and access the file in accordance with the security configuration for the selected software application.