if you want the files interleaved in the same folder hierarchy (ie. not separated into engine and web-files as @shorbaji suggests) to my knowledge there is no way to do this. I doubt any folder based version control system will allow you to do that. You would have to use something like RCS :shudder:
If you are considering such a structure, ask your self: why? This is not a common structure (thus the lack of tool support), but your problem is common.
If you want to separate your files into two subdirectories as suggested, I recommend using a top level git repo to track all of it, and using git submodule for your engine:
projects
| engine # directory containing you engine code
| .git
| files...
| MyProject
| .git
| .gitmodules
| engine # a clone of your engine repository above
| ...
| the rest of your files ...
If you don't know how git submodule works, read the man pages.
