If Visual Assist finds a .git subdirectory in a parent directory of the current solution, Visual Assist assumes the current solution is one module of a set maintained by a single git repo. Hence, Open File in Solution (OFIS) searches all files under that parent directory when include-all-files-in-solution-directories is enabled in the context menu of the OFIS dialog.
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Prevent Visual Assist from expanding the set of searched files, i.e. retaining the solution directory as the root of OFIS searches, by modifying the registry:
HKCU\Software\Whole Tomato\Visual Assist X\<IDE spec>\UseGitRootForAugmentSolution = 00
Set to 01 to restore default behavior.