No, the MPL has a per-file copyleft, so any file that does not include MPL material does not need the notice.
You quote:
You must duplicate the notice in Exhibit A in each file of the Source Code.
Where Source Code is the source form of Covered Code:
"Source Code" means the preferred form of the Covered Code for making modifications to it, including all modules it contains, plus any associated interface definition files, scripts used to control compilation and installation of an Executable...
So, if Source Code is the source form of Covered Code, what is Covered Code?
"Covered Code" means the Original Code or Modifications or the combination of the Original Code and Modifications, in each case including portions thereof.
So Covered Code (for which you must supply Appendix-A-annotated Source Code) is made of your Modifications on top of the Original Code. But Modifications are limited to files that contain some quantity of MPL-licensed Original Code or previous Covered Code (i.e., something previously published under the MPL before now):
When Covered Code is released as a series of files, a Modification is:
a. Any addition to or deletion from the contents of a file containing Original Code or previous Modifications.
b. Any new file that contains any part of the Original Code or previous Modifications.
So any file which contains on MPL-licensed material is not a Modification, and is therefore excluded from Covered Code. The set of files which must be annotated with Appendix A is limited to the source forms of file with Covered Code only.
