[ScanDependency] Fix a regression caused by rewrite in #76700
In the refactoring change #76700, it accidentally introduced a behavior
change that causes the generated PCM command-line to have useful
VFSOverlay files getting dropped. Clang module command-line and its
unused VFS pruning should be done by the clang dependency scanner
already so there is no need to touch that in the swift scanner. Since
the original logics is not used to handle clang module commands, it will
actually dropped the useful vfs overlay that is needed when none of the
dependencies uses it. Fix the regression by restoring the old behavior
and ignoring clang modules when pruning VFS overlay.
rdar://139233781
