Fixed broken behavior in the makeflow wrapper support:
Substitution of the nodeid into a wrapper command or file
is now done on the symbol %% instead of $RULE.

The dollar-syntax doesn't work, because dollar either indicates
macro-substitution that happens during parsing, or environment
variable substitution at runtime.  The substitution for the wrapper
happens in a third place (at command generation) and must simply
be represented by a different symbol.

This fixes the failing makeflow export tests.
Updated docs to describe the %% substitution
%% can now be escaped by %%%% if needed.
Note that a backslash escape won't work here
b/c that will conflict with shell backslashes.
Merge pull request #601 from dthain/master

Makeflow Wrapper: $RULE -> %%