[versions.mk] Make path to SUBMODULES.json based on srcdir (#3314)

[versions.mk] Make path to SUBMODULES.json based on srcdir (#3314)

Since acceptance-tests/Makefile (and llvm/Makefile) include scripts/submodules/versions.mk which evals versions.py which looks
for a SUBMODULES.json file in the current working directory we got confusing error messages if the build directory is not the src dir:

```
Traceback (most recent call last):
  File "../../mono/scripts/submodules/versions.py", line 22, in <module>
    submodules = json.load(open(CONFIG_FILE))
IOError: [Errno 2] No such file or directory: 'SUBMODULES.json'
```

Instead we now pass the path to SUBMODULES.json as a variable to versions.py and set it based on $(top_srcdir) so it works
even for out-of-tree builds.