Shallow manifest support

[GatorQue]

The default behaviour of repo manifest is to save a comprehensive version of the currently loaded manifest file. This means that all referenced manifest files (e.g. <include> elements, local_manifest file adjustments, etc.) to be saved into a single manifest file output. This feature would allow for creating a shallow copy of the manifest file by only copying the contents of the manifest file into the new file (probably while also fixing the revisions to either a branch or commit hash at the same time). This has the advantage of preserving other elements in the file (e.g. <include>, <default>, and other elements).

[GatorQue]

@smipi1 ,
Please review my changes in the feature branch associated with this issue. The purpose of the changes is to preserve the original XML file as correctly as possible so we can later add tagging and branching to the repo manifest command (for use by the repo flow commands). I'm pretty happy with the changes but would like you to experiment with them before I deliver them to develop. Here is the commit hash: 48ce38e