Your question is a bit confusing and ambiguous. Of course a relative URI is necessarily relative to some base URI. So you can't deresolve an absolute (and hierarchical) URI except against some other absolute (and hierarchical) base URI.
You ask about "where the tool is executed" but it's not clear what you mean by that. Perhaps you mean the process's current working directory, i.e., System.getProperty("user.dir"). Of course you can create a file URI from this location and use that as a base URI against which to resolve. Failing that, you'll need to clarify what you mean by "where the tool is currently running" because I can't think of another interpretation of that.