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You can use Security Configuration Manager Powertoy for Windows
Mobile to digitally sign your development project's setup and
executable files with a development certificate. Doing so gives
your application the credentials that allow it to be deployed, and
to run on mobile devices that have enabled security features. You
can sign executable (.exe) files,
To sign a file with a Development Certificate
On Security Configuration Manager Powertoy for Windows Mobile’s menu bar, click File, click Sign File, and then click either With Normal Development Certificateor With Privileged Development Certificate.
When the Choose File to Signdialog box appears, navigate through the file system to the file that you want to sign, click it, and then click Open.
Security Configuration Manager Powertoy for Windows Mobile digitally signs the file and then overwrites the original copy with a new signed copy. In Windows Explorer, the properties of the file show that the file has been digitally signed.