Updates to enable new pre-processor to use the FileTree to store
include-relationship information
Checkpoint: more work on the new Argument File index. File changes are
now tracked, unprocessed regions are collected, and some aspects of the
Index are implement (eg extracting a file from the containing root file)
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Merge pull request #179 from mballance-sf/master

Merge progress on new ArgFile index
Enable ArgFileIndex2 to be swapped in
Merge remote-tracking branch 'origin/master'