Remove assumption of uniqueness of nodes w.r.t. state and mode

This is a cross-cutting change that provides a more general representation
of strategies.  It should also make debugging easier because the output
routines previously made that assumption.  A new function, anode_index(),
provides generation of node indices using anode_t pointers.

Finally, grjit and sim_rhc() have been marked in the corresponding
documentation with warnings that they were not thoroughly checked as
part of this change, and so should be used with caution.
add_metric_sysgoal: Post-patching pruning that preserves initial nodes
TRIV: Improve code comments and verbose logging messages
DOC: Split help string to conform to max length; add missing args
Delete unused original_num_ variables in main() of gr1c
Change "Building...transition BDD..." messages to be verbose > 1

...so, requiring -vv rather than merely -v switch at command-line.
DOC TRIV
Preserve initiality of Entry and Exit nodes in rm_sysgoal()
DOC: rm_sysgoal() details and caveats
EXAMPLE: hotswapping examples do not need separate directory

...instead, it is possible to perform demonstrations using existing
example spc files.  Descriptions to this end will be added to the
examples/README.txt at the next commit.
DOC: Brief example of add_metric_sysgoal() and reorganization of README
Check for clandestine variables in formula from command-line

...e.g., as being passed to grpatch via the -f switch.
DOC: READMEs now use Markdown formatting

...instead of reStructuredText.