I was momentarily assigned to a secret project, as in DOD clearance type of work.

While there I was told that the tools being used on the project were classified as secret.  This is interesting.  If notepad.exe is a tool on a secret project, the the name of the tool itself is a secret and falls under the classification of DOD secret and you are in violation if you devulged such information to anyone out of the project.

So, assume you are working on a secret project, using tools x, y an z for the typical contract of 6-12 months.  On your resume you can not state what tools you were working with during that time.

Further lets assume at the end of that period you are looking for another project.  The current environment in the industry is have you had recent (read yesterday) experience using tools x, y and z.  You can not tell anyone that you have.  Therefore you will probably not be hired or even approached about the position as you do not meet the requirements for the position.