Clean makeflow's local environment

This request is a step forward to fix issue #39.

Now every rule has its own variable scope, and scopes cascade. This is, the values for variables defined just before rule n, apply for rules n, n+1, etc., unless the variables are reassigned.

In this process, some bugs related to special variables, such for resources needed and exported variables, and when appending to variables were fixed. 

Variables with category scope were removed, as their are superseded by the new scopes, with resources variables from categories to nodes.

As a debug option, I added -Dfile, to see the output of the parsed dag together with the scope of the variables. To fix #39, we need to send the groupings of variables-files-command to wq, condor, etc. This request  makes this next step easier, as all this information is now contained in the respective task nodes.

As a final note, I think the functions dag_lookup_* need some re-factoring.

@dthain, @rampantmonkey