1. A computer program product comprising one or more physical computer storage media, excluding signals, having stored thereon computer-executable instructions that are structured such that, when executed by one or more processors of a signing authority computing system, cause the signing authority computing system to perform a method for signing a file, the method comprising: an act of accessing a file that includes a marker that is recognized by a signing authority, the marker comprising a predetermined data value recognized by the signing authority computing system as indicating a first execution transparent context that is ignored by a consumer of the file, the marker having been inserted into the file by an author or creator of the file within the first execution transparent context, the first execution transparent context being indicated within the file by prefix data prior to the marker and suffix data subsequent to the marker, the marker being usable by the signing authority computing system to identify the prefix data and the suffix data which were used to create the first execution transparent context within the file; an act of finding the marker within the file; based on finding the marker within the file, an act of identifying how execution transparent contexts are created within the file, including identifying the prefix data prior to the marker as beginning an execution transparent context and identifying the suffix data subsequent to the marker as ending an execution transparent context; and subsequent to identifying how execution transparent contexts are created within the file an act of modifying the file to include a signature placed within an execution transparent context by placing the signature between the prefix data and the suffix data of the first execution transparent context, or by placing the signature within a new second execution transparent context created within the file using the identified prefix data and suffix data.