[clang][deps] Stop using `ClangTool` for virtual files

This patch changes how the dependency scanner creates the fake input file when scanning dependencies of a single module (introduced in D109485). The scanner now has its own `InMemoryFilesystem` which sits under the minimizing FS (when that's requested). This makes it possible to drop the duplicate work in `DependencyScanningActions::runInvocation` that sets up the main file ID. Besides that, this patch makes it possible to land D108979, where we drop `ClangTool` entirely.

Depends on D109485.

Reviewed By: dexonsmith

Differential Revision: https://reviews.llvm.org/D109498