[git] IDEA-103375 Fix understanding Git submodule roots

Git submodule repository is located not in submodule/.git, but
in supermodule/modules/.git.
At the same time submodule/.git is a file which contains the path to
the real repository location.
We already detect this, but we didn't use refresh to search for the
root as a VirtualFile, and in most cases it was not in the VFS yet.
IDEA-98701 Maven multimodule project fails to resolve system scoped dependencies
IDEA-103628 The 'Replace in Path' functionality is completely broken [rev=nik]
(cherry picked from commit 446096e)
OC-6986 Dictionary: The word mashalling is not included
(cherry picked from commit 846f6b9)
more on IDEA-96340 Replace in Path (with a grouping RegEx) makes a mess (depending on input)