[clang] Processing real directories added as virtual ones (#91645)

The `FileManager` might create a virtual directory that can be used
later as a search path. This is the case when we use remapping, as
demonstrated in the suggested LIT test.

We might encounter a 'false cache miss' and add the same directory
twice into `FileManager::SeenDirEntries` if the added record is a real
directory that is present on a disk:
- Once as a virtual directory 
- And once as a real one

This isn't a problem if the added directories have the same name, as in
this case, we will get a cache hit. However, it could lead to
compilation errors if the directory names are different but point to the
same folder. For example, one might use an absolute name and another a
relative one. For instance, the **implicit-module-remap.cpp** LIT test
will fail with the following message:
```
/.../implicit-module-remap.cpp.tmp/test.cpp:1:2: fatal error: module 'a' 
was built in directory '/.../implicit-module-remap.cpp.tmp' but now 
resides in directory '.'
    1 | #include "a.h"
      |  ^
1 error generated.
```

The suggested fix checks if the added virtual directory is present on
the disk and handles it as a real one if that is the case.