put back changes removed in sha: 1cb82084 and sha:76c21c6e

to check is the worst-case has been reached

- add sub_tree_size, parent, is_in_tree, is_out_tree
- fix height (was only working for out-trees)
- a predessors to Topology.t
- refactor a lot of strange things in the code
  - in the use of hashtbl in particular

Fixes #16

Indeed, the silent value was missing, which was blocking luciole