Fix missing files in MSI

[speth]

Changes proposed in this pull request

• Fix builds of the MSI installer so they actually contain the data files, samples, and Matlab toolbox

If applicable, fill in the issue number this pull request is fixing

Fixes problems introduced by some changes that were incorrectly modifying "prefix" and ignoring the stage directory when the stage directory was being specified internally by the SCons msi target rather than directly as a command line option.

Checklist

• The pull request includes a clear description of this code change
• Commit messages have short titles and reference relevant issues
• Build passes (scons build & scons test) and unit tests address code coverage
• Style & formatting of contributed code follows contributing guidelines
• The pull request is ready for review