Merge pull request #176 from mballance-sf/master

Windows bug fixes, support for -F switch
Update for 1.1.6
Refactor indexes to remove dependency on AbstractSVDBIndex
Correct a thread deadlock related to indexing and other threads
Update for 1.1.7
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)